=>> Building biology/vt build started at Fri Mar 29 11:53:26 GMT 2024 port directory: /usr/ports/biology/vt package name: vt-0.57721_3 building for: FreeBSD pkg-builder.dan.net.uk 13.2-RELEASE-p10 FreeBSD 13.2-RELEASE-p10 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 541 Mar 8 2023 /usr/ports/biology/vt/Makefile Ports top last git commit: c2c35d895e Ports top unclean checkout: yes Port dir last git commit: c014f9c79a Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.99.20240122_1 Host OSVERSION: 1400097 Jail OSVERSION: 1302001 Job Id: 03 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1302001 UNAME_v=FreeBSD 13.2-RELEASE-p10 UNAME_r=13.2-RELEASE-p10 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.99.20240122_1 MASTERMNT=/usr/local/poudriere/data/.m/13-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/13-amd64-default-dan/03/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=13-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.99.20240122_1 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-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/vt/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/vt/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/vt/work/.cache HOME=/wrkdirs/usr/ports/biology/vt/work TMPDIR="/tmp" PATH=/ccache/libexec/ccache:/wrkdirs/usr/ports/biology/vt/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/vt/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCACHE_DIR="/root/.ccache" --End CONFIGURE_ENV-- --MAKE_ENV-- OPENSSLBASE=/usr/local OPENSSLDIR=/usr/local/openssl OPENSSLINC=/usr/local/include OPENSSLLIB=/usr/local/lib OPENSSLRPATH=/usr/local/lib XDG_DATA_HOME=/wrkdirs/usr/ports/biology/vt/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/vt/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/vt/work/.cache HOME=/wrkdirs/usr/ports/biology/vt/work TMPDIR="/tmp" PATH=/ccache/libexec/ccache:/wrkdirs/usr/ports/biology/vt/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/vt/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -Wl,-rpath,/usr/local/lib -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CCACHE_DIR="/root/.ccache" 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-- OSREL=13.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/vt" EXAMPLESDIR="share/examples/vt" DATADIR="share/vt" WWWDIR="www/vt" ETCDIR="etc/vt" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/vt DOCSDIR=/usr/local/share/doc/vt EXAMPLESDIR=/usr/local/share/examples/vt WWWDIR=/usr/local/www/vt ETCDIR=/usr/local/etc/vt --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### CCACHE_CPP2=1 WITH_SSP_PORTS=yes WITH_SSP=yes #WITH_LTO=yes DISABLE_LICENSES=yes LICENSES_ACCEPTED=AGPLv3 APACHE10 APACHE11 APACHE20 ART10 ARTPERL10 ART20 BSD BSD2CLAUSE BSD3CLAUSE BSD4CLAUSE BSL CC0-1.0 CDDL ClArtistic EPL GFDL GMGPL GPLv1 GPLv2 GPLv3 GPLv3RLE ISCL LGPL20 LGPL21 LGPL3 LPPL10 LPPL11 LPPL12 LPPL13 LPPL13a LPPL13b LPPL13c MIT MPL OpenSSL OFL10 OFL11 OWL PostgreSQL PHP202 PHP30 PHP301 PSFL RUBY ZLIB ZPL21 SVM-Light EULA ALASIR Microsoft-exFAT SIMIAN UDEVGAME unknown MTA COMMERCIAL teamspeak NO_LICENSES_DIALOGS=yes #### #### NO_IGNORE=yes DEFAULT_VERSIONS+=ssl=openssl mysql=8.0 imagemagick=7 samba=4.13 java=18 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache NO_CCACHE_DEPEND=1 CCACHE_WRAPPER_PATH= /ccache/libexec/ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> vt-0.57721_3 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.9_1.pkg [pkg-builder.dan.net.uk] Installing pkg-1.20.9_1... [pkg-builder.dan.net.uk] Extracting pkg-1.20.9_1: .......... done ===> vt-0.57721_3 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of vt-0.57721_3 =========================================================================== =================================================== ===== 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 vt-0.57721_3 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by vt-0.57721_3 for building => SHA256 Checksum OK for atks-vt-0.57721_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 vt-0.57721_3 for building ===> Extracting for vt-0.57721_3 => SHA256 Checksum OK for atks-vt-0.57721_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 vt-0.57721_3 ===> Applying FreeBSD patches for vt-0.57721_3 from /usr/ports/biology/vt/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> vt-0.57721_3 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-0.22.3_1... [pkg-builder.dan.net.uk] | `-- Installing indexinfo-0.3.1... [pkg-builder.dan.net.uk] | `-- Extracting indexinfo-0.3.1: . done [pkg-builder.dan.net.uk] `-- Extracting gettext-runtime-0.22.3_1: .......... done [pkg-builder.dan.net.uk] Extracting gmake-4.4.1: .......... done ===> vt-0.57721_3 depends on package: gmake>=4.4.1 - found ===> Returning to build of vt-0.57721_3 ===> vt-0.57721_3 depends on file: /usr/local/lib/libcrypto.so.12 - not found ===> Installing existing package /packages/All/openssl-3.0.13_1,1.pkg [pkg-builder.dan.net.uk] Installing openssl-3.0.13_1,1... [pkg-builder.dan.net.uk] Extracting openssl-3.0.13_1,1: .......... done ===> vt-0.57721_3 depends on file: /usr/local/lib/libcrypto.so.12 - found ===> Returning to build of vt-0.57721_3 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> vt-0.57721_3 depends on shared library: libhts.so - not found ===> Installing existing package /packages/All/htslib-1.17_1.pkg [pkg-builder.dan.net.uk] Installing htslib-1.17_1... [pkg-builder.dan.net.uk] `-- Installing curl-8.6.0... [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 libidn2-2.3.7... [pkg-builder.dan.net.uk] | | `-- Installing libunistring-1.2... [pkg-builder.dan.net.uk] | | `-- Extracting libunistring-1.2: .......... done [pkg-builder.dan.net.uk] | `-- Extracting libidn2-2.3.7: .......... done [pkg-builder.dan.net.uk] | `-- Installing libnghttp2-1.60.0... [pkg-builder.dan.net.uk] | `-- Extracting libnghttp2-1.60.0: ....... done [pkg-builder.dan.net.uk] | `-- Installing librtmp-2.4.20190330_1... [pkg-builder.dan.net.uk] | `-- Extracting librtmp-2.4.20190330_1: ......... done [pkg-builder.dan.net.uk] | `-- Installing libssh2-1.11.0_1,3... [pkg-builder.dan.net.uk] | `-- Extracting libssh2-1.11.0_1,3: .......... done [pkg-builder.dan.net.uk] | `-- Installing zstd-1.5.5_1... [pkg-builder.dan.net.uk] | | `-- Installing liblz4-1.9.4_1,1... [pkg-builder.dan.net.uk] | | `-- Extracting liblz4-1.9.4_1,1: .......... done [pkg-builder.dan.net.uk] | `-- Extracting zstd-1.5.5_1: .......... done [pkg-builder.dan.net.uk] `-- Extracting curl-8.6.0: .......... done [pkg-builder.dan.net.uk] `-- Installing libdeflate-1.19... [pkg-builder.dan.net.uk] `-- Extracting libdeflate-1.19: .......... done [pkg-builder.dan.net.uk] Extracting htslib-1.17_1: .......... done ===> vt-0.57721_3 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> Returning to build of vt-0.57721_3 ===> vt-0.57721_3 depends on shared library: libsvm.so - not found ===> Installing existing package /packages/All/libsvm-3.24.pkg [pkg-builder.dan.net.uk] Installing libsvm-3.24... [pkg-builder.dan.net.uk] Extracting libsvm-3.24: .......... done ===== Message from libsvm-3.24: -- Some useful tools are installed to /usr/local/share/libsvm. Most of them are written in Python, please install lang/python before trying them. ===> vt-0.57721_3 depends on shared library: libsvm.so - found (/usr/local/lib/libsvm.so) ===> Returning to build of vt-0.57721_3 ===> vt-0.57721_3 depends on shared library: libdeflate.so - found (/usr/local/lib/libdeflate.so) ===> vt-0.57721_3 depends on shared library: libcurl.so - found (/usr/local/lib/libcurl.so) =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for vt-0.57721_3 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for vt-0.57721_3 cd lib/Rmath; gmake libRmath.a || exit 1; gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/vt/work/vt-0.57721/lib/Rmath' cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c bd0.c -o bd0.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c dnbeta.c -o dnbeta.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c i1mach.c -o i1mach.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c pnbinom.c -o pnbinom.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qlnorm.c -o qlnorm.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c rgeom.c -o rgeom.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c bessel_i.c -o bessel_i.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c dnbinom.c -o dnbinom.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c imax2.c -o imax2.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c pnchisq.c -o pnchisq.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qlogis.c -o qlogis.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c rhyper.c -o rhyper.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c bessel_j.c -o bessel_j.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c dnchisq.c -o dnchisq.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c imin2.c -o imin2.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c pnf.c -o pnf.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qnbeta.c -o qnbeta.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c rlnorm.c -o rlnorm.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c bessel_k.c -o bessel_k.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c dnf.c -o dnf.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c lbeta.c -o lbeta.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c pnorm.c -o pnorm.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qnbinom.c -o qnbinom.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c rlogis.c -o rlogis.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c bessel_y.c -o bessel_y.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c dnorm.c -o dnorm.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c lgamma.c -o lgamma.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c pnt.c -o pnt.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qnchisq.c -o qnchisq.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c rmultinom.c -o rmultinom.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c beta.c -o beta.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c dnt.c -o dnt.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c lgammacor.c -o lgammacor.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c polygamma.c -o polygamma.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qnf.c -o qnf.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c rnbinom.c -o rnbinom.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c chebyshev.c -o chebyshev.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c dpois.c -o dpois.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c log1p.c -o log1p.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c ppois.c -o ppois.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qnorm.c -o qnorm.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c rnchisq.c -o rnchisq.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c choose.c -o choose.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c dt.c -o dt.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c mlutils.c -o mlutils.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c pt.c -o pt.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qnt.c -o qnt.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c rnorm.c -o rnorm.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c d1mach.c -o d1mach.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c dunif.c -o dunif.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c pbeta.c -o pbeta.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c ptukey.c -o ptukey.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qpois.c -o qpois.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c rpois.c -o rpois.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c dbeta.c -o dbeta.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c dweibull.c -o dweibull.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c pbinom.c -o pbinom.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c punif.c -o punif.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qt.c -o qt.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c rt.c -o rt.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c dbinom.c -o dbinom.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c expm1.c -o expm1.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c pcauchy.c -o pcauchy.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c pweibull.c -o pweibull.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qtukey.c -o qtukey.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c runif.c -o runif.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c dcauchy.c -o dcauchy.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c fmax2.c -o fmax2.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c pchisq.c -o pchisq.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qbeta.c -o qbeta.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qunif.c -o qunif.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c rweibull.c -o rweibull.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c dchisq.c -o dchisq.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c fmin2.c -o fmin2.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c pexp.c -o pexp.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qbinom.c -o qbinom.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qweibull.c -o qweibull.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c dexp.c -o dexp.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c fprec.c -o fprec.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c pf.c -o pf.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qcauchy.c -o qcauchy.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c rbeta.c -o rbeta.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c sign.c -o sign.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c df.c -o df.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c fround.c -o fround.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c pgamma.c -o pgamma.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qchisq.c -o qchisq.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c rbinom.c -o rbinom.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c signrank.c -o signrank.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c dgamma.c -o dgamma.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c fsign.c -o fsign.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c pgeom.c -o pgeom.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qexp.c -o qexp.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c rcauchy.c -o rcauchy.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c dgeom.c -o dgeom.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c ftrunc.c -o ftrunc.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c phyper.c -o phyper.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qf.c -o qf.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c rchisq.c -o rchisq.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c stirlerr.c -o stirlerr.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c dhyper.c -o dhyper.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c gamma.c -o gamma.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c plnorm.c -o plnorm.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qgamma.c -o qgamma.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c rexp.c -o rexp.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c toms708.c -o toms708.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c dlnorm.c -o dlnorm.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c gamma_cody.c -o gamma_cody.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c plogis.c -o plogis.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qgeom.c -o qgeom.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c rf.c -o rf.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c wilcox.c -o wilcox.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c dlogis.c -o dlogis.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c gammalims.c -o gammalims.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c pnbeta.c -o pnbeta.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qhyper.c -o qhyper.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c rgamma.c -o rgamma.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c sunif.c -o sunif.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c sexp.c -o sexp.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c snorm.c -o snorm.o rm -rf libRmath.a ar -rc libRmath.a bd0.o dnbeta.o i1mach.o pnbinom.o qlnorm.o rgeom.o bessel_i.o dnbinom.o imax2.o pnchisq.o qlogis.o rhyper.o bessel_j.o dnchisq.o imin2.o pnf.o qnbeta.o rlnorm.o bessel_k.o dnf.o lbeta.o pnorm.o qnbinom.o rlogis.o bessel_y.o dnorm.o lgamma.o pnt.o qnchisq.o rmultinom.o beta.o dnt.o lgammacor.o polygamma.o qnf.o rnbinom.o chebyshev.o dpois.o log1p.o ppois.o qnorm.o rnchisq.o choose.o dt.o mlutils.o pt.o qnt.o rnorm.o d1mach.o dunif.o pbeta.o ptukey.o qpois.o rpois.o dbeta.o dweibull.o pbinom.o punif.o qt.o rt.o dbinom.o expm1.o pcauchy.o pweibull.o qtukey.o runif.o dcauchy.o fmax2.o pchisq.o qbeta.o qunif.o rweibull.o dchisq.o fmin2.o pexp.o qbinom.o qweibull.o dexp.o fprec.o pf.o qcauchy.o rbeta.o sign.o df.o fround.o pgamma.o qchisq.o rbinom.o signrank.o dgamma.o fsign.o pgeom.o qexp.o rcauchy.o dgeom.o ftrunc.o phyper.o qf.o rchisq.o stirlerr.o dhyper.o gamma.o plnorm.o qgamma.o rexp.o toms708.o dlnorm.o gamma_cody.o plogis.o qgeom.o rf.o wilcox.o dlogis.o gammalims.o pnbeta.o qhyper.o rgamma.o sunif.o sexp.o snorm.o gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/vt/work/vt-0.57721/lib/Rmath' cd lib/pcre2; gmake libpcre2.a || exit 1; gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/vt/work/vt-0.57721/lib/pcre2' cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_auto_possess.o -c pcre2_auto_possess.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_chartables.o -c pcre2_chartables.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_compile.o -c pcre2_compile.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_config.o -c pcre2_config.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_context.o -c pcre2_context.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_dfa_match.o -c pcre2_dfa_match.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_error.o -c pcre2_error.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_jit_compile.o -c pcre2_jit_compile.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_maketables.o -c pcre2_maketables.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_match.o -c pcre2_match.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_match_data.o -c pcre2_match_data.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_newline.o -c pcre2_newline.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_ord2utf.o -c pcre2_ord2utf.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_pattern_info.o -c pcre2_pattern_info.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_string_utils.o -c pcre2_string_utils.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_study.o -c pcre2_study.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_substitute.o -c pcre2_substitute.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_substring.o -c pcre2_substring.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_tables.o -c pcre2_tables.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_ucd.o -c pcre2_ucd.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_valid_utf.o -c pcre2_valid_utf.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_xclass.o -c pcre2_xclass.c ar -rc libpcre2.a pcre2_auto_possess.o pcre2_chartables.o pcre2_compile.o pcre2_config.o pcre2_context.o pcre2_dfa_match.o pcre2_error.o pcre2_jit_compile.o pcre2_maketables.o pcre2_match.o pcre2_match_data.o pcre2_newline.o pcre2_ord2utf.o pcre2_pattern_info.o pcre2_string_utils.o pcre2_study.o pcre2_substitute.o pcre2_substring.o pcre2_tables.o pcre2_ucd.o pcre2_valid_utf.o pcre2_xclass.o ranlib libpcre2.a gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/vt/work/vt-0.57721/lib/pcre2' c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o ahmm.o -c ahmm.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o align.o -c align.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o allele.o -c allele.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o annotate_1000g.o -c annotate_1000g.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o annotate_dbsnp_rsid.o -c annotate_dbsnp_rsid.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o annotate_indels.o -c annotate_indels.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o annotate_indels2.o -c annotate_indels2.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o annotate_regions.o -c annotate_regions.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o annotate_variants.o -c annotate_variants.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o annotate_vntrs.o -c annotate_vntrs.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o augmented_bam_record.o -c augmented_bam_record.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o bcf_genotyping_buffered_reader.o -c bcf_genotyping_buffered_reader.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o bcf_single_genotyping_buffered_reader.o -c bcf_single_genotyping_buffered_reader.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o bam_ordered_reader.o -c bam_ordered_reader.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o bcf_ordered_reader.o -c bcf_ordered_reader.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o bcf_ordered_writer.o -c bcf_ordered_writer.cpp bcf_ordered_writer.cpp:128:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] bcf_hdr_write(file, hdr); ^~~~~~~~~~~~~ ~~~~~~~~~ bcf_ordered_writer.cpp:167:43: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] bcf_get_pos1(v), ^~~~~~~~~~~~~~~ ./hts_utils.h:464:25: note: expanded from macro 'bcf_get_pos1' #define bcf_get_pos1(v) ((v)->pos+1) ^~~~~~~~~~~~ bcf_ordered_writer.cpp:169:43: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] bcf_get_pos1(buffer.front()), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./hts_utils.h:464:25: note: expanded from macro 'bcf_get_pos1' #define bcf_get_pos1(v) ((v)->pos+1) ^~~~~~~~~~~~ bcf_ordered_writer.cpp:171:43: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] bcf_get_pos1(buffer.front())-bcf_get_pos1(v)+1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./hts_utils.h:464:25: note: expanded from macro 'bcf_get_pos1' #define bcf_get_pos1(v) ((v)->pos+1) ^ bcf_ordered_writer.cpp:194:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] bcf_write(file, hdr, v); ^~~~~~~~~ ~~~~~~~~~~~~ bcf_ordered_writer.cpp:244:13: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] bcf_write(file, hdr, buffer.back()); ^~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~ bcf_ordered_writer.cpp:260:21: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] bcf_write(file, hdr, buffer.back()); ^~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~ 7 warnings generated. c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o bcf_synced_reader.o -c bcf_synced_reader.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o bed.o -c bed.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o candidate_motif_picker.o -c candidate_motif_picker.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o candidate_region_extractor.o -c candidate_region_extractor.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o cat.o -c cat.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o chmm.o -c chmm.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o complex_genotyping_record.o -c complex_genotyping_record.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o compute_concordance.o -c compute_concordance.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o compute_features.o -c compute_features.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o compute_features2.o -c compute_features2.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o compute_rl_dist.o -c compute_rl_dist.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o config.o -c config.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o consolidate_multiallelics.o -c consolidate_multiallelics.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o consolidate_vntrs.o -c consolidate_vntrs.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o consolidate.o -c consolidate.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o construct_probes.o -c construct_probes.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o decompose.o -c decompose.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o decompose2.o -c decompose2.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o decompose_blocksub.o -c decompose_blocksub.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o discover.o -c discover.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o duplicate.o -c duplicate.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o estimate.o -c estimate.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o estimator.o -c estimator.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o extract_vntrs.o -c extract_vntrs.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o filter.o -c filter.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o filter_overlap.o -c filter_overlap.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o flank_detector.o -c flank_detector.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o fuzzy_aligner.o -c fuzzy_aligner.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o fuzzy_partition.o -c fuzzy_partition.cpp fuzzy_partition.cpp:153:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] bcf_hdr_sync(odr->hdr); ^~~~~~~~~~~~ ~~~~~~~~ 1 warning generated. c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o gencode.o -c gencode.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o genome_interval.o -c genome_interval.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o genotype.o -c genotype.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o genotyping_record.o -c genotyping_record.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o ghmm.o -c ghmm.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o hts_utils.o -c hts_utils.cpp hts_utils.cpp:428:21: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] if ( h->dirty ) bcf_hdr_sync(h); ^~~~~~~~~~~~ ~ 1 warning generated. c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o hfilter.o -c hfilter.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o indel_annotator.o -c indel_annotator.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o indel_genotyping_record.o -c indel_genotyping_record.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o index.o -c index.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o info2tab.o -c info2tab.cpp info2tab.cpp:278:57: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] fprintf(out, "%s\t%d", bcf_get_chrom(h, v), bcf_get_pos1(v)); ~~ ^~~~~~~~~~~~~~~ %ld ./hts_utils.h:464:25: note: expanded from macro 'bcf_get_pos1' #define bcf_get_pos1(v) ((v)->pos+1) ^~~~~~~~~~~~ 1 warning generated. c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o interval_tree.o -c interval_tree.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o interval.o -c interval.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o lfhmm.o -c lfhmm.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o lhmm.o -c lhmm.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o lhmm1.o -c lhmm1.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o liftover.o -c liftover.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o log_tool.o -c log_tool.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o merge.o -c merge.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o merge_candidate_variants.o -c merge_candidate_variants.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o merge_genotypes.o -c merge_genotypes.cpp merge_genotypes.cpp:215:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] bcf_hdr_sync(odw->hdr); ^~~~~~~~~~~~ ~~~~~~~~ 1 warning generated. c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o milk_filter.o -c milk_filter.cpp milk_filter.cpp:456:96: warning: format specifies type 'int' but the argument has type 'hts_pos_t' (aka 'long') [-Wformat] fprintf(stderr,"Processing %d variants at %s:%d\n", nread + 1, bcf_seqname(odw->hdr,nv), nv->pos); ~~ ^~~~~~~ %ld 1 warning generated. c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o motif_tree.o -c motif_tree.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o motif_map.o -c motif_map.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o multi_partition.o -c multi_partition.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o multiallelics_consolidator.o -c multiallelics_consolidator.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o needle.o -c needle.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o normalize.o -c normalize.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o nuclear_pedigree.o -c nuclear_pedigree.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o ordered_bcf_overlap_matcher.o -c ordered_bcf_overlap_matcher.cpp ordered_bcf_overlap_matcher.cpp:34:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] bcf_hdr_sync(odr->hdr); ^~~~~~~~~~~~ ~~~~~~~~ ordered_bcf_overlap_matcher.cpp:52:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] bcf_hdr_sync(odr->hdr); ^~~~~~~~~~~~ ~~~~~~~~ 2 warnings generated. c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o ordered_region_overlap_matcher.o -c ordered_region_overlap_matcher.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o partition.o -c partition.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o paste.o -c paste.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o paste_and_compute_features_sequential.o -c paste_and_compute_features_sequential.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o paste_genotypes.o -c paste_genotypes.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o pedigree.o -c pedigree.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o peek.o -c peek.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o pileup.o -c pileup.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o pregex.o -c pregex.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o profile_afs.o -c profile_afs.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o profile_chm1.o -c profile_chm1.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o profile_chrom.o -c profile_chrom.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o profile_fic_hwe.o -c profile_fic_hwe.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o profile_hwe.o -c profile_hwe.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o profile_indels.o -c profile_indels.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o profile_len.o -c profile_len.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o profile_mendelian.o -c profile_mendelian.cpp profile_mendelian.cpp:191:13: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] bcf_hdr_sync(odw->hdr); ^~~~~~~~~~~~ ~~~~~~~~ 1 warning generated. c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o profile_na12878.o -c profile_na12878.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o profile_snps.o -c profile_snps.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o profile_vntrs.o -c profile_vntrs.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o program.o -c program.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o read_filter.o -c read_filter.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o reference_sequence.o -c reference_sequence.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o rfhmm.o -c rfhmm.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o rfhmm_x.o -c rfhmm_x.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o rminfo.o -c rminfo.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o seq.o -c seq.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o set_ref.o -c set_ref.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o snp_genotyping_record.o -c snp_genotyping_record.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o sort.o -c sort.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o subset.o -c subset.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o sv_tree.o -c sv_tree.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o svm_train.o -c svm_train.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o svm_predict.o -c svm_predict.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o tbx_ordered_reader.o -c tbx_ordered_reader.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o test.o -c test.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o trio.o -c trio.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o union_variants.o -c union_variants.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o uniq.o -c uniq.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o utils.o -c utils.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o validate.o -c validate.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o variant.o -c variant.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o variant_manip.o -c variant_manip.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o variant_filter.o -c variant_filter.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o view.o -c view.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o vntr.o -c vntr.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o vntr_annotator.o -c vntr_annotator.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o vntr_consolidator.o -c vntr_consolidator.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o vntr_extractor.o -c vntr_extractor.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o vntr_genotyping_record.o -c vntr_genotyping_record.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o vntr_tree.o -c vntr_tree.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o vntrize.o -c vntrize.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o wdp_ahmm.o -c wdp_ahmm.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o main.o -c main.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o vt ahmm.o align.o allele.o annotate_1000g.o annotate_dbsnp_rsid.o annotate_indels.o annotate_indels2.o annotate_regions.o annotate_variants.o annotate_vntrs.o augmented_bam_record.o bcf_genotyping_buffered_reader.o bcf_single_genotyping_buffered_reader.o bam_ordered_reader.o bcf_ordered_reader.o bcf_ordered_writer.o bcf_synced_reader.o bed.o candidate_motif_picker.o candidate_region_extractor.o cat.o chmm.o complex_genotyping_record.o compute_concordance.o compute_features.o compute_features2.o compute_rl_dist.o config.o consolidate_multiallelics.o consolidate_vntrs.o consolidate.o construct_probes.o decompose.o decompose2.o decompose_blocksub.o discover.o duplicate.o estimate.o estimator.o extract_vntrs.o filter.o filter_overlap.o flank_detector.o fuzzy_aligner.o fuzzy_partition.o gencode.o genome_interval.o genotype.o genotyping_record.o ghmm.o hts_utils.o hfilter.o indel_annotator.o indel_genotyping_record.o index.o info2tab.o interval_tree.o interval.o lfhmm.o lhmm.o lhmm1.o liftover.o log_tool.o merge.o merge_candidate_variants.o merge_genotypes.o milk_filter.o motif_tree.o motif_map.o multi_partition.o multiallelics_consolidator.o needle.o normalize.o nuclear_pedigree.o ordered_bcf_overlap_matcher.o ordered_region_overlap_matcher.o partition.o paste.o paste_and_compute_features_sequential.o paste_genotypes.o pedigree.o peek.o pileup.o pregex.o profile_afs.o profile_chm1.o profile_chrom.o profile_fic_hwe.o profile_hwe.o profile_indels.o profile_len.o profile_mendelian.o profile_na12878.o profile_snps.o profile_vntrs.o program.o read_filter.o reference_sequence.o rfhmm.o rfhmm_x.o rminfo.o seq.o set_ref.o snp_genotyping_record.o sort.o subset.o sv_tree.o svm_train.o svm_predict.o tbx_ordered_reader.o test.o trio.o union_variants.o uniq.o utils.o validate.o variant.o variant_manip.o variant_filter.o view.o vntr.o vntr_annotator.o vntr_consolidator.o vntr_extractor.o vntr_genotyping_record.o vntr_tree.o vntrize.o wdp_ahmm.o main.o -L/usr/local/lib -lhts lib/Rmath/libRmath.a lib/pcre2/libpcre2.a -ldeflate -lz -lpthread -lbz2 -llzma -lcurl -lcrypto =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> vt-0.57721_3 depends on file: /usr/local/lib/libcrypto.so.12 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for vt-0.57721_3 ===> Generating temporary packing list install -s -m 555 /wrkdirs/usr/ports/biology/vt/work/vt-0.57721/vt /wrkdirs/usr/ports/biology/vt/work/stage/usr/local/bin ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2024-03-29T11:53:26+0000' 'PKG_NOTE_ports_top_git_hash=c2c35d895e' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=c014f9c79a' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.99.20240122_1' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for vt-0.57721_3 ===> Building vt-0.57721_3 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for vt-0.57721_3 build of biology/vt | vt-0.57721_3 ended at Fri Mar 29 12:05:43 GMT 2024 build time: 00:12:17