=>> Building biology/vt build started at Sat May 3 13:03:55 BST 2025 port directory: /usr/ports/biology/vt package name: vt-0.57721_3 building for: FreeBSD pkg-builder.dan.net.uk 14.2-RELEASE FreeBSD 14.2-RELEASE amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 541 Dec 29 14:16 /usr/ports/biology/vt/Makefile Ports top last git commit: 5529c5919b Ports top unclean checkout: yes Port dir last git commit: 1a35b19e6d Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1402000 Jail OSVERSION: 1402000 Job Id: 01 ---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/01/.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-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=/usr/local/bin/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=/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 --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=/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 " 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=14.2 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 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 ===> vt-0.57721_3 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 ===> 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-0.23.1... [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 ===> 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-3.0.16,1.pkg [pkg-builder.dan.net.uk] Installing openssl-3.0.16,1... [pkg-builder.dan.net.uk] Extracting openssl-3.0.16,1: .......... done ===> vt-0.57721_3 depends on file: /usr/local/lib/libcrypto.so.12 - found ===> Returning to build of vt-0.57721_3 ===> vt-0.57721_3 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. ===> vt-0.57721_3 depends on file: /usr/local/bin/ccache - 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-1.21.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] | `-- 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 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 ===> 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. -- ===> NOTICE: The libsvm 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 ===> 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; /usr/local/bin/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; /usr/local/bin/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 bcf_genotyping_buffered_reader.cpp:2110:18: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 2110 | float pG[no_genotypes]; | ^~~~~~~~~~~~ bcf_genotyping_buffered_reader.cpp:2110:18: note: read of non-const variable 'no_genotypes' is not allowed in a constant expression bcf_genotyping_buffered_reader.cpp:2108:17: note: declared here 2108 | int32_t no_genotypes = (no_alleles * (no_alleles+1)) >> 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 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] 128 | bcf_hdr_write(file, hdr); | ^~~~~~~~~~~~~ ~~~~~~~~~ bcf_ordered_writer.cpp:167:43: warning: format specifies type 'int' but the argument has type 'hts_pos_t' (aka 'long') [-Wformat] 161 | fprintf(stderr, "[%s:%d %s] Might not be sorted for window size %d at current record %s:%d < %d (%d [last record] - %d), please increase window size to at least %d.\n", | ~~ | %ld 162 | __FILE__, 163 | __LINE__, 164 | __FUNCTION__, 165 | window, 166 | bcf_get_chrom(hdr, v), 167 | bcf_get_pos1(v), | ^~~~~~~~~~~~~~~ ./hts_utils.h:464:25: note: expanded from macro 'bcf_get_pos1' 464 | #define bcf_get_pos1(v) ((v)->pos+1) | ^~~~~~~~~~~~ bcf_ordered_writer.cpp:169:43: warning: format specifies type 'int' but the argument has type 'hts_pos_t' (aka 'long') [-Wformat] 161 | fprintf(stderr, "[%s:%d %s] Might not be sorted for window size %d at current record %s:%d < %d (%d [last record] - %d), please increase window size to at least %d.\n", | ~~ | %ld 162 | __FILE__, 163 | __LINE__, 164 | __FUNCTION__, 165 | window, 166 | bcf_get_chrom(hdr, v), 167 | bcf_get_pos1(v), 168 | cutoff_pos1, 169 | bcf_get_pos1(buffer.front()), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./hts_utils.h:464:25: note: expanded from macro 'bcf_get_pos1' 464 | #define bcf_get_pos1(v) ((v)->pos+1) | ^~~~~~~~~~~~ bcf_ordered_writer.cpp:171:43: warning: format specifies type 'int' but the argument has type 'hts_pos_t' (aka 'long') [-Wformat] 161 | fprintf(stderr, "[%s:%d %s] Might not be sorted for window size %d at current record %s:%d < %d (%d [last record] - %d), please increase window size to at least %d.\n", | ~~ | %ld 162 | __FILE__, 163 | __LINE__, 164 | __FUNCTION__, 165 | window, 166 | bcf_get_chrom(hdr, v), 167 | bcf_get_pos1(v), 168 | cutoff_pos1, 169 | bcf_get_pos1(buffer.front()), 170 | window, 171 | bcf_get_pos1(buffer.front())-bcf_get_pos1(v)+1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./hts_utils.h:464:25: note: expanded from macro 'bcf_get_pos1' 464 | #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] 194 | 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] 244 | 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] 260 | 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 compute_features.cpp:217:23: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 217 | int32_t g[ploidy]; | ^~~~~~ compute_features.cpp:217:23: note: read of non-const variable 'ploidy' is not allowed in a constant expression compute_features.cpp:193:21: note: declared here 193 | int32_t ploidy = bcf_get_genotypes(odr->hdr, v, >s, &n_gts); | ^ compute_features.cpp:219:24: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 219 | int32_t AC[no_alleles]; | ^~~~~~~~~~ compute_features.cpp:219:24: note: read of non-const variable 'no_alleles' is not allowed in a constant expression compute_features.cpp:202:21: note: declared here 202 | int32_t no_alleles = bcf_get_n_allele(v); | ^ compute_features.cpp:220:22: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 220 | float AF[no_alleles]; | ^~~~~~~~~~ compute_features.cpp:220:22: note: read of non-const variable 'no_alleles' is not allowed in a constant expression compute_features.cpp:202:21: note: declared here 202 | int32_t no_alleles = bcf_get_n_allele(v); | ^ compute_features.cpp:225:24: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 225 | int32_t GC[no_genotypes]; | ^~~~~~~~~~~~ compute_features.cpp:225:24: note: read of non-const variable 'no_genotypes' is not allowed in a constant expression compute_features.cpp:224:21: note: declared here 224 | int32_t no_genotypes = bcf_an2gn(no_alleles); | ^ compute_features.cpp:227:22: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 227 | float GF[no_genotypes]; | ^~~~~~~~~~~~ compute_features.cpp:227:22: note: read of non-const variable 'no_genotypes' is not allowed in a constant expression compute_features.cpp:224:21: note: declared here 224 | int32_t no_genotypes = bcf_an2gn(no_alleles); | ^ compute_features.cpp:247:30: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 247 | float MLE_HWE_AF[no_alleles]; | ^~~~~~~~~~ compute_features.cpp:247:30: note: read of non-const variable 'no_alleles' is not allowed in a constant expression compute_features.cpp:202:21: note: declared here 202 | int32_t no_alleles = bcf_get_n_allele(v); | ^ compute_features.cpp:248:30: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 248 | float MLE_HWE_GF[no_genotypes]; | ^~~~~~~~~~~~ compute_features.cpp:248:30: note: read of non-const variable 'no_genotypes' is not allowed in a constant expression compute_features.cpp:224:21: note: declared here 224 | int32_t no_genotypes = bcf_an2gn(no_alleles); | ^ compute_features.cpp:258:26: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 258 | float MLE_AF[no_alleles]; | ^~~~~~~~~~ compute_features.cpp:258:26: note: read of non-const variable 'no_alleles' is not allowed in a constant expression compute_features.cpp:202:21: note: declared here 202 | int32_t no_alleles = bcf_get_n_allele(v); | ^ compute_features.cpp:259:26: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 259 | float MLE_GF[no_genotypes]; | ^~~~~~~~~~~~ compute_features.cpp:259:26: note: read of non-const variable 'no_genotypes' is not allowed in a constant expression compute_features.cpp:224:21: note: declared here 224 | int32_t no_genotypes = bcf_an2gn(no_alleles); | ^ 9 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 compute_features2.o -c compute_features2.cpp compute_features2.cpp:219:23: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 219 | int32_t g[ploidy]; | ^~~~~~ compute_features2.cpp:219:23: note: read of non-const variable 'ploidy' is not allowed in a constant expression compute_features2.cpp:195:21: note: declared here 195 | int32_t ploidy = bcf_get_genotypes(odr->hdr, v, >s, &n_gts); | ^ compute_features2.cpp:221:24: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 221 | int32_t AC[no_alleles]; | ^~~~~~~~~~ compute_features2.cpp:221:24: note: read of non-const variable 'no_alleles' is not allowed in a constant expression compute_features2.cpp:204:21: note: declared here 204 | int32_t no_alleles = bcf_get_n_allele(v); | ^ compute_features2.cpp:222:22: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 222 | float AF[no_alleles]; | ^~~~~~~~~~ compute_features2.cpp:222:22: note: read of non-const variable 'no_alleles' is not allowed in a constant expression compute_features2.cpp:204:21: note: declared here 204 | int32_t no_alleles = bcf_get_n_allele(v); | ^ compute_features2.cpp:227:24: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 227 | int32_t GC[no_genotypes]; | ^~~~~~~~~~~~ compute_features2.cpp:227:24: note: read of non-const variable 'no_genotypes' is not allowed in a constant expression compute_features2.cpp:226:21: note: declared here 226 | int32_t no_genotypes = bcf_an2gn(no_alleles); | ^ compute_features2.cpp:229:22: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 229 | float GF[no_genotypes]; | ^~~~~~~~~~~~ compute_features2.cpp:229:22: note: read of non-const variable 'no_genotypes' is not allowed in a constant expression compute_features2.cpp:226:21: note: declared here 226 | int32_t no_genotypes = bcf_an2gn(no_alleles); | ^ compute_features2.cpp:249:30: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 249 | float MLE_HWE_AF[no_alleles]; | ^~~~~~~~~~ compute_features2.cpp:249:30: note: read of non-const variable 'no_alleles' is not allowed in a constant expression compute_features2.cpp:204:21: note: declared here 204 | int32_t no_alleles = bcf_get_n_allele(v); | ^ compute_features2.cpp:250:30: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 250 | float MLE_HWE_GF[no_genotypes]; | ^~~~~~~~~~~~ compute_features2.cpp:250:30: note: read of non-const variable 'no_genotypes' is not allowed in a constant expression compute_features2.cpp:226:21: note: declared here 226 | int32_t no_genotypes = bcf_an2gn(no_alleles); | ^ compute_features2.cpp:260:26: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 260 | float MLE_AF[no_alleles]; | ^~~~~~~~~~ compute_features2.cpp:260:26: note: read of non-const variable 'no_alleles' is not allowed in a constant expression compute_features2.cpp:204:21: note: declared here 204 | int32_t no_alleles = bcf_get_n_allele(v); | ^ compute_features2.cpp:261:26: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 261 | float MLE_GF[no_genotypes]; | ^~~~~~~~~~~~ compute_features2.cpp:261:26: note: read of non-const variable 'no_genotypes' is not allowed in a constant expression compute_features2.cpp:226:21: note: declared here 226 | int32_t no_genotypes = bcf_an2gn(no_alleles); | ^ 9 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 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 consolidate.cpp:497:23: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 497 | char alts[no_alleles]; | ^~~~~~~~~~ consolidate.cpp:497:23: note: read of non-const variable 'no_alleles' is not allowed in a constant expression consolidate.cpp:494:21: note: declared here 494 | int32_t no_alleles = vs.size(); | ^ consolidate.cpp:734:27: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 734 | char alts[no_alleles]; | ^~~~~~~~~~ consolidate.cpp:734:27: note: read of non-const variable 'no_alleles' is not allowed in a constant expression consolidate.cpp:731:25: note: declared here 731 | int32_t no_alleles = vs.size(); | ^ 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 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 estimate.cpp:391:31: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 391 | int32_t g[ploidy]; | ^~~~~~ estimate.cpp:391:31: note: read of non-const variable 'ploidy' is not allowed in a constant expression estimate.cpp:344:21: note: declared here 344 | int32_t ploidy = bcf_get_genotypes(odr->hdr, v, >s, &n_gts); | ^ estimate.cpp:393:32: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 393 | int32_t AC[no_alleles]; | ^~~~~~~~~~ estimate.cpp:393:32: note: read of non-const variable 'no_alleles' is not allowed in a constant expression estimate.cpp:358:21: note: declared here 358 | int32_t no_alleles = bcf_get_n_allele(v); | ^ estimate.cpp:394:30: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 394 | float AF[no_alleles]; | ^~~~~~~~~~ estimate.cpp:394:30: note: read of non-const variable 'no_alleles' is not allowed in a constant expression estimate.cpp:358:21: note: declared here 358 | int32_t no_alleles = bcf_get_n_allele(v); | ^ estimate.cpp:399:32: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 399 | int32_t GC[no_genotypes]; | ^~~~~~~~~~~~ estimate.cpp:399:32: note: read of non-const variable 'no_genotypes' is not allowed in a constant expression estimate.cpp:381:21: note: declared here 381 | int32_t no_genotypes = bcf_an2gn(no_alleles); | ^ estimate.cpp:401:30: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 401 | float GF[no_genotypes]; | ^~~~~~~~~~~~ estimate.cpp:401:30: note: read of non-const variable 'no_genotypes' is not allowed in a constant expression estimate.cpp:381:21: note: declared here 381 | int32_t no_genotypes = bcf_an2gn(no_alleles); | ^ estimate.cpp:423:30: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 423 | float MLE_HWE_AF[no_alleles]; | ^~~~~~~~~~ estimate.cpp:423:30: note: read of non-const variable 'no_alleles' is not allowed in a constant expression estimate.cpp:358:21: note: declared here 358 | int32_t no_alleles = bcf_get_n_allele(v); | ^ estimate.cpp:424:30: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 424 | float MLE_HWE_GF[no_genotypes]; | ^~~~~~~~~~~~ estimate.cpp:424:30: note: read of non-const variable 'no_genotypes' is not allowed in a constant expression estimate.cpp:381:21: note: declared here 381 | int32_t no_genotypes = bcf_an2gn(no_alleles); | ^ estimate.cpp:444:26: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 444 | float MLE_AF[no_alleles]; | ^~~~~~~~~~ estimate.cpp:444:26: note: read of non-const variable 'no_alleles' is not allowed in a constant expression estimate.cpp:358:21: note: declared here 358 | int32_t no_alleles = bcf_get_n_allele(v); | ^ estimate.cpp:445:26: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 445 | float MLE_GF[no_genotypes]; | ^~~~~~~~~~~~ estimate.cpp:445:26: note: read of non-const variable 'no_genotypes' is not allowed in a constant expression estimate.cpp:381:21: note: declared here 381 | int32_t no_genotypes = bcf_an2gn(no_alleles); | ^ 9 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 estimator.o -c estimator.cpp estimator.cpp:120:26: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 120 | int32_t gt_indiv[ploidy]; | ^~~~~~ estimator.cpp:120:26: note: function parameter 'ploidy' with unknown value cannot be used in a constant expression estimator.cpp:41:70: note: declared here 41 | void Estimator::compute_af(int32_t *gts, int32_t no_samples, int32_t ploidy, | ^ estimator.cpp:193:22: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 193 | int32_t imap[no_samples]; | ^~~~~~~~~~ estimator.cpp:193:22: note: function parameter 'no_samples' with unknown value cannot be used in a constant expression estimator.cpp:179:57: note: declared here 179 | void Estimator::compute_gl_af_hwe(int32_t *pls, int32_t no_samples, int32_t ploidy, | ^ estimator.cpp:261:22: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 261 | int32_t imap[no_samples]; | ^~~~~~~~~~ estimator.cpp:261:22: note: function parameter 'no_samples' with unknown value cannot be used in a constant expression estimator.cpp:179:57: note: declared here 179 | void Estimator::compute_gl_af_hwe(int32_t *pls, int32_t no_samples, int32_t ploidy, | ^ estimator.cpp:274:18: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 274 | float af[no_alleles]; | ^~~~~~~~~~ estimator.cpp:274:18: note: function parameter 'no_alleles' with unknown value cannot be used in a constant expression estimator.cpp:180:25: note: declared here 180 | int32_t no_alleles, float *MLE_HWE_AF, float *MLE_HWE_GF, int32_t& n, | ^ estimator.cpp:280:18: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 280 | float gf[no_genotypes]; | ^~~~~~~~~~~~ estimator.cpp:280:18: note: read of non-const variable 'no_genotypes' is not allowed in a constant expression estimator.cpp:262:17: note: declared here 262 | int32_t no_genotypes = bcf_an2gn(no_alleles); | ^ estimator.cpp:281:24: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 281 | float gf_indiv[no_genotypes]; | ^~~~~~~~~~~~ estimator.cpp:281:24: note: read of non-const variable 'no_genotypes' is not allowed in a constant expression estimator.cpp:262:17: note: declared here 262 | int32_t no_genotypes = bcf_an2gn(no_alleles); | ^ estimator.cpp:369:22: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 369 | int32_t imap[nsamples]; | ^~~~~~~~ estimator.cpp:369:22: note: function parameter 'nsamples' with unknown value cannot be used in a constant expression estimator.cpp:360:53: note: declared here 360 | void Estimator::compute_gl_af(int32_t *pls, int32_t nsamples, int32_t ploidy, | ^ estimator.cpp:439:22: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 439 | int32_t imap[nsamples]; | ^~~~~~~~ estimator.cpp:439:22: note: function parameter 'nsamples' with unknown value cannot be used in a constant expression estimator.cpp:360:53: note: declared here 360 | void Estimator::compute_gl_af(int32_t *pls, int32_t nsamples, int32_t ploidy, | ^ estimator.cpp:452:18: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 452 | float gf[no_genotypes]; | ^~~~~~~~~~~~ estimator.cpp:452:18: note: read of non-const variable 'no_genotypes' is not allowed in a constant expression estimator.cpp:440:17: note: declared here 440 | int32_t no_genotypes = bcf_an2gn(n_allele); | ^ estimator.cpp:453:24: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 453 | float gf_indiv[no_genotypes]; | ^~~~~~~~~~~~ estimator.cpp:453:24: note: read of non-const variable 'no_genotypes' is not allowed in a constant expression estimator.cpp:440:17: note: declared here 440 | int32_t no_genotypes = bcf_an2gn(n_allele); | ^ estimator.cpp:667:22: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 667 | float HWE_GF[no_genotypes]; | ^~~~~~~~~~~~ estimator.cpp:667:22: note: read of non-const variable 'no_genotypes' is not allowed in a constant expression estimator.cpp:665:17: note: declared here 665 | int32_t no_genotypes = bcf_an2gn(no_alleles); | ^ 11 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 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] 153 | 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] 428 | if ( h->dirty ) bcf_hdr_sync(h); | ^~~~~~~~~~~~ ~ hts_utils.cpp:443:13: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 443 | int len[m]; | ^ hts_utils.cpp:443:13: note: read of non-const variable 'm' is not allowed in a constant expression hts_utils.cpp:441:14: note: declared here 441 | int tid, m = kh_size(d); | ^ 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 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 'hts_pos_t' (aka 'long') [-Wformat] 278 | 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' 464 | #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] 215 | 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] 456 | 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] 34 | 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] 52 | 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 paste.cpp:166:20: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 166 | bcf1_t* vs[nfiles]; | ^~~~~~ paste.cpp:166:20: note: read of non-const variable 'nfiles' is not allowed in a constant expression paste.cpp:137:17: note: declared here 137 | int32_t nfiles = odrs.size(); | ^ paste.cpp:194:37: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 194 | int32_t nval_per_sample[vs[0]->n_fmt]; | ^~~~~~~~~~~~ paste.cpp:194:37: note: read of non-constexpr variable 'vs' is not allowed in a constant expression paste.cpp:166:17: note: declared here 166 | bcf1_t* vs[nfiles]; | ^ paste.cpp:195:26: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 195 | int32_t size[vs[0]->n_fmt]; | ^~~~~~~~~~~~ paste.cpp:195:26: note: read of non-constexpr variable 'vs' is not allowed in a constant expression paste.cpp:166:17: note: declared here 166 | bcf1_t* vs[nfiles]; | ^ 3 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 paste_and_compute_features_sequential.o -c paste_and_compute_features_sequential.cpp paste_and_compute_features_sequential.cpp:589:33: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 589 | const char* tmp_d_alleles[vn_alleles[k]]; | ^~~~~~~~~~~~~ paste_and_compute_features_sequential.cpp:589:44: note: read of non-const variable 'k' is not allowed in a constant expression 589 | const char* tmp_d_alleles[vn_alleles[k]]; | ^ paste_and_compute_features_sequential.cpp:582:16: note: declared here 582 | for(size_t k=0; k < v_rids.size(); ++k) { | ^ paste_and_compute_features_sequential.cpp:595:23: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 595 | int tmp_filts[v_filts[k].size()]; | ^~~~~~~~~~~~~~~~~ paste_and_compute_features_sequential.cpp:595:31: note: read of non-const variable 'k' is not allowed in a constant expression 595 | int tmp_filts[v_filts[k].size()]; | ^ paste_and_compute_features_sequential.cpp:582:16: note: declared here 582 | for(size_t k=0; k < v_rids.size(); ++k) { | ^ paste_and_compute_features_sequential.cpp:605:24: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 605 | float MLE_HWE_AF[vn_alleles[k]]; | ^~~~~~~~~~~~~ paste_and_compute_features_sequential.cpp:605:35: note: read of non-const variable 'k' is not allowed in a constant expression 605 | float MLE_HWE_AF[vn_alleles[k]]; | ^ paste_and_compute_features_sequential.cpp:582:16: note: declared here 582 | for(size_t k=0; k < v_rids.size(); ++k) { | ^ paste_and_compute_features_sequential.cpp:606:24: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 606 | float MLE_HWE_GF[vn_genos[k]]; | ^~~~~~~~~~~ paste_and_compute_features_sequential.cpp:606:33: note: read of non-const variable 'k' is not allowed in a constant expression 606 | float MLE_HWE_GF[vn_genos[k]]; | ^ paste_and_compute_features_sequential.cpp:582:16: note: declared here 582 | for(size_t k=0; k < v_rids.size(); ++k) { | ^ paste_and_compute_features_sequential.cpp:617:19: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 617 | int32_t acs[vn_alleles[k]]; | ^~~~~~~~~~~~~ paste_and_compute_features_sequential.cpp:617:30: note: read of non-const variable 'k' is not allowed in a constant expression 617 | int32_t acs[vn_alleles[k]]; | ^ paste_and_compute_features_sequential.cpp:582:16: note: declared here 582 | for(size_t k=0; k < v_rids.size(); ++k) { | ^ paste_and_compute_features_sequential.cpp:618:19: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 618 | int32_t gcs[vn_genos[k]]; | ^~~~~~~~~~~ paste_and_compute_features_sequential.cpp:618:28: note: read of non-const variable 'k' is not allowed in a constant expression 618 | int32_t gcs[vn_genos[k]]; | ^ paste_and_compute_features_sequential.cpp:582:16: note: declared here 582 | for(size_t k=0; k < v_rids.size(); ++k) { | ^ paste_and_compute_features_sequential.cpp:619:17: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 619 | float afs[vn_alleles[k]]; | ^~~~~~~~~~~~~ paste_and_compute_features_sequential.cpp:619:28: note: read of non-const variable 'k' is not allowed in a constant expression 619 | float afs[vn_alleles[k]]; | ^ paste_and_compute_features_sequential.cpp:582:16: note: declared here 582 | for(size_t k=0; k < v_rids.size(); ++k) { | ^ paste_and_compute_features_sequential.cpp:685:20: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 685 | float MLE_AF[vn_alleles[k]]; | ^~~~~~~~~~~~~ paste_and_compute_features_sequential.cpp:685:31: note: read of non-const variable 'k' is not allowed in a constant expression 685 | float MLE_AF[vn_alleles[k]]; | ^ paste_and_compute_features_sequential.cpp:582:16: note: declared here 582 | for(size_t k=0; k < v_rids.size(); ++k) { | ^ paste_and_compute_features_sequential.cpp:686:20: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 686 | float MLE_GF[vn_genos[k]]; | ^~~~~~~~~~~ paste_and_compute_features_sequential.cpp:686:29: note: read of non-const variable 'k' is not allowed in a constant expression 686 | float MLE_GF[vn_genos[k]]; | ^ paste_and_compute_features_sequential.cpp:582:16: note: declared here 582 | for(size_t k=0; k < v_rids.size(); ++k) { | ^ 9 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 paste_genotypes.o -c paste_genotypes.cpp paste_genotypes.cpp:617:33: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 617 | const char* tmp_d_alleles[vn_alleles[k]]; | ^~~~~~~~~~~~~ paste_genotypes.cpp:617:44: note: read of non-const variable 'k' is not allowed in a constant expression 617 | const char* tmp_d_alleles[vn_alleles[k]]; | ^ paste_genotypes.cpp:609:16: note: declared here 609 | for(size_t k=0; k < v_rids.size(); ++k) { | ^ paste_genotypes.cpp:623:23: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 623 | int tmp_filts[v_filts[k].size()]; | ^~~~~~~~~~~~~~~~~ paste_genotypes.cpp:623:31: note: read of non-const variable 'k' is not allowed in a constant expression 623 | int tmp_filts[v_filts[k].size()]; | ^ paste_genotypes.cpp:609:16: note: declared here 609 | for(size_t k=0; k < v_rids.size(); ++k) { | ^ paste_genotypes.cpp:633:24: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 633 | float MLE_HWE_AF[vn_alleles[k]]; | ^~~~~~~~~~~~~ paste_genotypes.cpp:633:35: note: read of non-const variable 'k' is not allowed in a constant expression 633 | float MLE_HWE_AF[vn_alleles[k]]; | ^ paste_genotypes.cpp:609:16: note: declared here 609 | for(size_t k=0; k < v_rids.size(); ++k) { | ^ paste_genotypes.cpp:634:24: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 634 | float MLE_HWE_GF[vn_genos[k]]; | ^~~~~~~~~~~ paste_genotypes.cpp:634:33: note: read of non-const variable 'k' is not allowed in a constant expression 634 | float MLE_HWE_GF[vn_genos[k]]; | ^ paste_genotypes.cpp:609:16: note: declared here 609 | for(size_t k=0; k < v_rids.size(); ++k) { | ^ paste_genotypes.cpp:645:19: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 645 | int32_t acs[vn_alleles[k]]; | ^~~~~~~~~~~~~ paste_genotypes.cpp:645:30: note: read of non-const variable 'k' is not allowed in a constant expression 645 | int32_t acs[vn_alleles[k]]; | ^ paste_genotypes.cpp:609:16: note: declared here 609 | for(size_t k=0; k < v_rids.size(); ++k) { | ^ paste_genotypes.cpp:646:19: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 646 | int32_t gcs[vn_genos[k]]; | ^~~~~~~~~~~ paste_genotypes.cpp:646:28: note: read of non-const variable 'k' is not allowed in a constant expression 646 | int32_t gcs[vn_genos[k]]; | ^ paste_genotypes.cpp:609:16: note: declared here 609 | for(size_t k=0; k < v_rids.size(); ++k) { | ^ paste_genotypes.cpp:647:17: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 647 | float afs[vn_alleles[k]]; | ^~~~~~~~~~~~~ paste_genotypes.cpp:647:28: note: read of non-const variable 'k' is not allowed in a constant expression 647 | float afs[vn_alleles[k]]; | ^ paste_genotypes.cpp:609:16: note: declared here 609 | for(size_t k=0; k < v_rids.size(); ++k) { | ^ paste_genotypes.cpp:713:20: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 713 | float MLE_AF[vn_alleles[k]]; | ^~~~~~~~~~~~~ paste_genotypes.cpp:713:31: note: read of non-const variable 'k' is not allowed in a constant expression 713 | float MLE_AF[vn_alleles[k]]; | ^ paste_genotypes.cpp:609:16: note: declared here 609 | for(size_t k=0; k < v_rids.size(); ++k) { | ^ paste_genotypes.cpp:714:20: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 714 | float MLE_GF[vn_genos[k]]; | ^~~~~~~~~~~ paste_genotypes.cpp:714:29: note: read of non-const variable 'k' is not allowed in a constant expression 714 | float MLE_GF[vn_genos[k]]; | ^ paste_genotypes.cpp:609:16: note: declared here 609 | for(size_t k=0; k < v_rids.size(); ++k) { | ^ 9 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 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 profile_chm1.cpp:295:31: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 295 | int32_t na12878_index[no_overlap_files]; | ^~~~~~~~~~~~~~~~ profile_chm1.cpp:295:31: note: read of non-const variable 'no_overlap_files' is not allowed in a constant expression profile_chm1.cpp:285:17: note: declared here 285 | int32_t no_overlap_files = input_vcf_files.size(); | ^ 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_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] 191 | 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 profile_na12878.cpp:380:31: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 380 | int32_t na12878_index[no_overlap_files]; | ^~~~~~~~~~~~~~~~ profile_na12878.cpp:380:31: note: read of non-const variable 'no_overlap_files' is not allowed in a constant expression profile_na12878.cpp:369:17: note: declared here 369 | int32_t no_overlap_files = input_vcf_files.size(); | ^ 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_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 sort.cpp:213:28: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 213 | bcf1_t *buffer[buffer_size]; | ^~~~~~~~~~~ sort.cpp:213:28: note: read of non-const variable 'buffer_size' is not allowed in a constant expression sort.cpp:211:20: note: declared here 211 | size_t buffer_size = 1000000; | ^ 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 subset.o -c subset.cpp subset.cpp:188:23: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 188 | int32_t g[ploidy]; | ^~~~~~ subset.cpp:188:23: note: read of non-const variable 'ploidy' is not allowed in a constant expression subset.cpp:185:21: note: declared here 185 | int32_t ploidy = bcf_get_genotypes(odw->hdr, v, >s, &n)/no_subset_samples; | ^ subset.cpp:190:24: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 190 | int32_t AC[n_allele]; | ^~~~~~~~ subset.cpp:190:24: note: read of non-const variable 'n_allele' is not allowed in a constant expression subset.cpp:186:21: note: declared here 186 | int32_t n_allele = bcf_get_n_allele(v); | ^ 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 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=2025-05-03T12:03:55+0000' 'PKG_NOTE_ports_top_git_hash=5529c5919b' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=1a35b19e6d' '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 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 Sat May 3 13:11:01 BST 2025 build time: 00:07:07