=>> Building biology/plink build started at Fri Apr 5 04:26:28 BST 2024 port directory: /usr/ports/biology/plink package name: plink-1.90.b6.17_3 building for: FreeBSD pkg-builder.dan.net.uk 13.2-RELEASE-p10 FreeBSD 13.2-RELEASE-p10 amd64 maintained by: mzaki@e-mail.ne.jp Makefile datestamp: -rw-r--r-- 1 root wheel 1385 Jan 3 00:12 /usr/ports/biology/plink/Makefile Ports top last git commit: c2c35d895e Ports top unclean checkout: yes Port dir last git commit: bbab7f59e9 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.99.20240122_1 Host OSVERSION: 1400097 Jail OSVERSION: 1302001 Job Id: 18 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1302001 UNAME_v=FreeBSD 13.2-RELEASE-p10 UNAME_r=13.2-RELEASE-p10 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.99.20240122_1 MASTERMNT=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/18/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=13-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.99.20240122_1 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for plink-1.90.b6.17_3: EXAMPLES=on: Build and/or install examples ====> BLAS/LAPACK implementation: you have to select exactly one of them NETLIB=off: Netlib's reference OPENBLAS=on: OpenBLAS BLAS implementation ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- mzaki@e-mail.ne.jp --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake F77="gfortran13" F90="gfortran13" FC="gfortran13" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc13" F90FLAGS="-O -Wl,-rpath=/usr/local/lib/gcc13" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc13" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/plink/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/plink/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/plink/work/.cache HOME=/wrkdirs/usr/ports/biology/plink/work TMPDIR="/tmp" PATH=/ccache/libexec/ccache:/wrkdirs/usr/ports/biology/plink/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/plink/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCACHE_DIR="/root/.ccache" --End CONFIGURE_ENV-- --MAKE_ENV-- F77="gfortran13" F90="gfortran13" FC="gfortran13" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc13" F90FLAGS="-O -Wl,-rpath=/usr/local/lib/gcc13" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc13" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/plink/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/plink/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/plink/work/.cache HOME=/wrkdirs/usr/ports/biology/plink/work TMPDIR="/tmp" PATH=/ccache/libexec/ccache:/wrkdirs/usr/ports/biology/plink/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/plink/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 ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -lthr -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -L/usr/local/lib -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing " CCACHE_DIR="/root/.ccache" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- PORTEXAMPLES="" OSREL=13.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/plink" EXAMPLESDIR="share/examples/plink" DATADIR="share/plink" WWWDIR="www/plink" ETCDIR="etc/plink" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/plink DOCSDIR=/usr/local/share/doc/plink EXAMPLESDIR=/usr/local/share/examples/plink WWWDIR=/usr/local/www/plink ETCDIR=/usr/local/etc/plink --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### CCACHE_CPP2=1 WITH_SSP_PORTS=yes WITH_SSP=yes #WITH_LTO=yes DISABLE_LICENSES=yes LICENSES_ACCEPTED=AGPLv3 APACHE10 APACHE11 APACHE20 ART10 ARTPERL10 ART20 BSD BSD2CLAUSE BSD3CLAUSE BSD4CLAUSE BSL CC0-1.0 CDDL ClArtistic EPL GFDL GMGPL GPLv1 GPLv2 GPLv3 GPLv3RLE ISCL LGPL20 LGPL21 LGPL3 LPPL10 LPPL11 LPPL12 LPPL13 LPPL13a LPPL13b LPPL13c MIT MPL OpenSSL OFL10 OFL11 OWL PostgreSQL PHP202 PHP30 PHP301 PSFL RUBY ZLIB ZPL21 SVM-Light EULA ALASIR Microsoft-exFAT SIMIAN UDEVGAME unknown MTA COMMERCIAL teamspeak NO_LICENSES_DIALOGS=yes #### #### NO_IGNORE=yes DEFAULT_VERSIONS+=ssl=openssl mysql=8.0 imagemagick=7 samba=4.13 java=18 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache NO_CCACHE_DEPEND=1 CCACHE_WRAPPER_PATH= /ccache/libexec/ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> plink-1.90.b6.17_3 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.9_1.pkg [pkg-builder.dan.net.uk] Installing pkg-1.20.9_1... [pkg-builder.dan.net.uk] Extracting pkg-1.20.9_1: .......... done ===> plink-1.90.b6.17_3 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of plink-1.90.b6.17_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 plink-1.90.b6.17_3 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by plink-1.90.b6.17_3 for building => SHA256 Checksum OK for chrchang-plink-ng-v1.90b6.17-79b2df8c_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 plink-1.90.b6.17_3 for building ===> Extracting for plink-1.90.b6.17_3 => SHA256 Checksum OK for chrchang-plink-ng-v1.90b6.17-79b2df8c_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 plink-1.90.b6.17_3 ===> Applying FreeBSD patches for plink-1.90.b6.17_3 from /usr/ports/biology/plink/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> plink-1.90.b6.17_3 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [pkg-builder.dan.net.uk] Installing gmake-4.4.1... [pkg-builder.dan.net.uk] `-- Installing gettext-runtime-0.22.3_1... [pkg-builder.dan.net.uk] | `-- Installing indexinfo-0.3.1... [pkg-builder.dan.net.uk] | `-- Extracting indexinfo-0.3.1: . done [pkg-builder.dan.net.uk] `-- Extracting gettext-runtime-0.22.3_1: .......... done [pkg-builder.dan.net.uk] Extracting gmake-4.4.1: .......... done ===> plink-1.90.b6.17_3 depends on package: gmake>=4.4.1 - found ===> Returning to build of plink-1.90.b6.17_3 ===> plink-1.90.b6.17_3 depends on executable: gfortran13 - not found ===> Installing existing package /packages/All/gcc13-13.2.0_4.pkg [pkg-builder.dan.net.uk] Installing gcc13-13.2.0_4... [pkg-builder.dan.net.uk] `-- Installing binutils-2.40_5,1... [pkg-builder.dan.net.uk] | `-- Installing zstd-1.5.5_1... [pkg-builder.dan.net.uk] | | `-- Installing liblz4-1.9.4_1,1... [pkg-builder.dan.net.uk] | | `-- Extracting liblz4-1.9.4_1,1: .......... done [pkg-builder.dan.net.uk] | `-- Extracting zstd-1.5.5_1: .......... done [pkg-builder.dan.net.uk] `-- Extracting binutils-2.40_5,1: .......... done [pkg-builder.dan.net.uk] `-- Installing gmp-6.3.0... [pkg-builder.dan.net.uk] `-- Extracting gmp-6.3.0: .......... done [pkg-builder.dan.net.uk] `-- Installing mpc-1.3.1_1... [pkg-builder.dan.net.uk] | `-- Installing mpfr-4.2.1,1... [pkg-builder.dan.net.uk] | `-- Extracting mpfr-4.2.1,1: .......... done [pkg-builder.dan.net.uk] `-- Extracting mpc-1.3.1_1: ...... done [pkg-builder.dan.net.uk] Extracting gcc13-13.2.0_4: .......... done create symlink for gcc13 create symlink for gcc13 (world) create symlink for g++13 create symlink for g++13 (world) create symlink for cpp13 create symlink for cpp13 (world) ===== Message from gcc13-13.2.0_4: -- To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc13 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> plink-1.90.b6.17_3 depends on executable: gfortran13 - found ===> Returning to build of plink-1.90.b6.17_3 ===> plink-1.90.b6.17_3 depends on file: /usr/local/bin/as - found =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> plink-1.90.b6.17_3 depends on shared library: libopenblas.so - not found ===> Installing existing package /packages/All/openblas-0.3.25,2.pkg [pkg-builder.dan.net.uk] Installing openblas-0.3.25,2... [pkg-builder.dan.net.uk] Extracting openblas-0.3.25,2: .......... done ===> plink-1.90.b6.17_3 depends on shared library: libopenblas.so - found (/usr/local/lib/libopenblas.so) ===> Returning to build of plink-1.90.b6.17_3 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for plink-1.90.b6.17_3 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for plink-1.90.b6.17_3 c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing plink.c -o plink.o c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing plink_assoc.c -o plink_assoc.o c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing plink_calc.c -o plink_calc.o c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing plink_cluster.c -o plink_cluster.o c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing plink_cnv.c -o plink_cnv.o c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing plink_common.c -o plink_common.o c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing plink_data.c -o plink_data.o c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing plink_dosage.c -o plink_dosage.o c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing plink_family.c -o plink_family.o c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing plink_filter.c -o plink_filter.o c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing plink_glm.c -o plink_glm.o c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing plink_help.c -o plink_help.o c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing plink_homozyg.c -o plink_homozyg.o c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing plink_lasso.c -o plink_lasso.o c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing plink_ld.c -o plink_ld.o c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing plink_matrix.c -o plink_matrix.o c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing plink_misc.c -o plink_misc.o c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing plink_perm.c -o plink_perm.o c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing plink_rserve.c -o plink_rserve.o c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing plink_set.c -o plink_set.o c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing plink_stats.c -o plink_stats.o c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing SFMT.c -o SFMT.o c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing dcdflib.c -o dcdflib.o c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing pigz.c -o pigz.o c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing yarn.c -o yarn.o c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++ -x c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing Rconnection.cc -o Rconnection.o c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing hfile.c -o hfile.o c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing bgzf.c -o bgzf.o c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++ plink.o plink_assoc.o plink_calc.o plink_cluster.o plink_cnv.o plink_common.o plink_data.o plink_dosage.o plink_family.o plink_filter.o plink_glm.o plink_help.o plink_homozyg.o plink_lasso.o plink_ld.o plink_matrix.o plink_misc.o plink_perm.o plink_rserve.o plink_set.o plink_stats.o SFMT.o dcdflib.o pigz.o yarn.o Rconnection.o hfile.o bgzf.o -lopenblas -lopenblas -lthr -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -L/usr/local/lib -fstack-protector-strong -L. -lz -o plink (cd /wrkdirs/usr/ports/biology/plink/work/plink-ng-79b2df8c/1.9; cc -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing prettify.c -o prettify) =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> plink-1.90.b6.17_3 depends on executable: gfortran13 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for plink-1.90.b6.17_3 ===> Generating temporary packing list install -d /wrkdirs/usr/ports/biology/plink/work/stage/usr/local/bin install -c plink /wrkdirs/usr/ports/biology/plink/work/stage/usr/local/bin strip /wrkdirs/usr/ports/biology/plink/work/stage/usr/local/bin/plink install -s -m 555 /wrkdirs/usr/ports/biology/plink/work/plink-ng-79b2df8c/1.9/prettify /wrkdirs/usr/ports/biology/plink/work/stage/usr/local/bin install -m 0644 /wrkdirs/usr/ports/biology/plink/work/plink-ng-79b2df8c/1.9/toy.map /wrkdirs/usr/ports/biology/plink/work/plink-ng-79b2df8c/1.9/toy.ped /wrkdirs/usr/ports/biology/plink/work/stage/usr/local/share/examples/plink ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2024-04-05T03:26:28+0000' 'PKG_NOTE_ports_top_git_hash=c2c35d895e' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=bbab7f59e9' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.99.20240122_1' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for plink-1.90.b6.17_3 ===> Building plink-1.90.b6.17_3 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for plink-1.90.b6.17_3 build of biology/plink | plink-1.90.b6.17_3 ended at Fri Apr 5 04:28:56 BST 2024 build time: 00:02:31