=>> Building biology/plink build started at Tue Dec 16 10:38:33 EST 2025 port directory: /usr/ports/biology/plink package name: plink-1.90.b6.17_5 building for: FreeBSD pkg.DaveG.ca 14.3-RELEASE-p1 FreeBSD 14.3-RELEASE-p1 1403000 amd64 maintained by: mzaki@e-mail.ne.jp Makefile datestamp: -rw-r--r-- 1 root wheel 1429 Aug 17 06:16 /usr/ports/biology/plink/Makefile Ports top last git commit: 10f7dee57a4c Ports top unclean checkout: no Port dir last git commit: 88aa90559b22 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1403000 Job Id: 09 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1403000 UNAME_v=FreeBSD 14.3-RELEASE-p1 1403000 UNAME_r=14.3-RELEASE-p1 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/freebsd_14_3_x64-HEAD-ALL/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/freebsd_14_3_x64-HEAD-ALL/09/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_14_3_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_14_3_x64-HEAD-ALL/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for plink-1.90.b6.17_5: 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=/usr/local/bin/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=/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 --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=/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 " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -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-- PORTEXAMPLES="" OSREL=14.3 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--- DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited pipebuf (-y) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> plink-1.90.b6.17_5 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.4.2_1.pkg [pkg.DaveG.ca] Installing pkg-2.4.2_1... [pkg.DaveG.ca] Extracting pkg-2.4.2_1: .......... done ===> plink-1.90.b6.17_5 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of plink-1.90.b6.17_5 =========================================================================== =================================================== ===== 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_5 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by plink-1.90.b6.17_5 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_5 for building ===> Extracting for plink-1.90.b6.17_5 => 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_5 ===> Applying FreeBSD patches for plink-1.90.b6.17_5 from /usr/ports/biology/plink/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> plink-1.90.b6.17_5 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [pkg.DaveG.ca] Installing gmake-4.4.1... [pkg.DaveG.ca] `-- Installing gettext-runtime-0.23.1... [pkg.DaveG.ca] | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] `-- Extracting gettext-runtime-0.23.1: .......... done [pkg.DaveG.ca] Extracting gmake-4.4.1: .......... done ===> plink-1.90.b6.17_5 depends on package: gmake>=4.4.1 - found ===> Returning to build of plink-1.90.b6.17_5 ===> plink-1.90.b6.17_5 depends on executable: gfortran13 - not found ===> Installing existing package /packages/All/gcc13-13.3.0_3.pkg [pkg.DaveG.ca] Installing gcc13-13.3.0_3... [pkg.DaveG.ca] `-- Installing binutils-2.44,1... [pkg.DaveG.ca] | `-- Installing zstd-1.5.7_1... [pkg.DaveG.ca] | `-- Extracting zstd-1.5.7_1: .......... done [pkg.DaveG.ca] `-- Extracting binutils-2.44,1: .......... done [pkg.DaveG.ca] `-- Installing gmp-6.3.0... [pkg.DaveG.ca] `-- Extracting gmp-6.3.0: .......... done [pkg.DaveG.ca] `-- Installing mpc-1.3.1_1... [pkg.DaveG.ca] | `-- Installing mpfr-4.2.2,1... [pkg.DaveG.ca] | `-- Extracting mpfr-4.2.2,1: .......... done [pkg.DaveG.ca] `-- Extracting mpc-1.3.1_1: ...... done [pkg.DaveG.ca] Extracting gcc13-13.3.0_3: .......... done ===== Message from gcc13-13.3.0_3: -- 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_5 depends on executable: gfortran13 - found ===> Returning to build of plink-1.90.b6.17_5 ===> plink-1.90.b6.17_5 depends on file: /usr/local/bin/as - found ===> plink-1.90.b6.17_5 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg.DaveG.ca] Installing ccache-3.7.12_8... [pkg.DaveG.ca] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for 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) 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. ===> plink-1.90.b6.17_5 depends on file: /usr/local/bin/ccache - found ===> Returning to build of plink-1.90.b6.17_5 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> plink-1.90.b6.17_5 depends on shared library: libopenblas.so - not found ===> Installing existing package /packages/All/openblas-0.3.30,2.pkg [pkg.DaveG.ca] Installing openblas-0.3.30,2... [pkg.DaveG.ca] Extracting openblas-0.3.30,2: .......... done ===> plink-1.90.b6.17_5 depends on shared library: libopenblas.so - found (/usr/local/lib/libopenblas.so) ===> Returning to build of plink-1.90.b6.17_5 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for plink-1.90.b6.17_5 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for plink-1.90.b6.17_5 c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing plink.c -o plink.o c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing plink_assoc.c -o plink_assoc.o c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing plink_calc.c -o plink_calc.o c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing plink_cluster.c -o plink_cluster.o c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing plink_cnv.c -o plink_cnv.o c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing plink_common.c -o plink_common.o c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing plink_data.c -o plink_data.o c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing plink_dosage.c -o plink_dosage.o c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing plink_family.c -o plink_family.o c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing plink_filter.c -o plink_filter.o c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing plink_glm.c -o plink_glm.o c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing plink_help.c -o plink_help.o c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing plink_homozyg.c -o plink_homozyg.o c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing plink_lasso.c -o plink_lasso.o c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing plink_ld.c -o plink_ld.o c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing plink_matrix.c -o plink_matrix.o c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing plink_misc.c -o plink_misc.o c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing plink_perm.c -o plink_perm.o c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing plink_rserve.c -o plink_rserve.o c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing plink_set.c -o plink_set.o c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing plink_stats.c -o plink_stats.o c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing SFMT.c -o SFMT.o c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing dcdflib.c -o dcdflib.o c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing pigz.c -o pigz.o c++ -c -O2 -pipe -DDYNAMIC_ZLIB -I/usr/local/include -fstack-protector-strong -fno-strict-aliasing yarn.c -o yarn.o 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++ -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++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] hfile.c:120:37: warning: implicit truncation from 'int' to a one-bit wide bit-field changes value from 1 to -1 [-Wsingle-bit-bitfield-constant-conversion] 120 | else if (n == 0) fp->at_eof = 1; | ^ ~ hfile.c:160:37: warning: implicit truncation from 'int' to a one-bit wide bit-field changes value from 1 to -1 [-Wsingle-bit-bitfield-constant-conversion] 160 | else if (n == 0) fp->at_eof = 1; | ^ ~ 2 warnings generated. c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] bgzf.c:160:21: warning: implicit truncation from 'int' to a one-bit wide bit-field changes value from 1 to -1 [-Wsingle-bit-bitfield-constant-conversion] 160 | fp->is_gzip = 1; | ^ ~ bgzf.c:502:21: warning: implicit truncation from 'int' to a one-bit wide bit-field changes value from 1 to -1 [-Wsingle-bit-bitfield-constant-conversion] 502 | fp->is_gzip = 1; | ^ ~ 2 warnings generated. c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 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 -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_5 depends on executable: gfortran13 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for plink-1.90.b6.17_5 ===> 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=2025-12-16T15:38:33+0000' 'PKG_NOTE_ports_top_git_hash=10f7dee57a4c' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=88aa90559b22' '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 plink-1.90.b6.17_5 ===> Building plink-1.90.b6.17_5 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for plink-1.90.b6.17_5 build of biology/plink | plink-1.90.b6.17_5 ended at Tue Dec 16 10:38:59 EST 2025 build time: 00:00:28