------------------------------------------------------------------------------- -- Phase: Environment ------------------------------------------------------------------------------- NO_DEPENDS=1 UNAME_r=5.9 UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=unknown UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 LANG=C HOME=/root USER=root TERM=dumb SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: showconfig ------------------------------------------------------------------------------- ===> The following configuration options are available for plink-1.90.b6.17_1: 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 SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ENV ------------------------------------------------------------------------------- MAKE=gmake F77="gfortran8" FC="gfortran8" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc8" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc8" XDG_DATA_HOME=/construction/biology/plink XDG_CONFIG_HOME=/construction/biology/plink HOME=/construction/biology/plink TMPDIR="/tmp" PATH=/construction/biology/plink/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ARGS ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ENV ------------------------------------------------------------------------------- F77="gfortran8" FC="gfortran8" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc8" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc8" XDG_DATA_HOME=/construction/biology/plink XDG_CONFIG_HOME=/construction/biology/plink HOME=/construction/biology/plink TMPDIR="/tmp" PATH=/construction/biology/plink/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc80 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 NOPROFILE=1 CC="cc" CFLAGS="-pipe -DDYNAMIC_ZLIB -I/usr/local/include -Wno-stringop-truncation -Wno-stringop-overflow -O2 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -pthread -Wl,-rpath=/usr/local/lib/gcc8 -L/usr/local/lib/gcc8 -B/usr/local/bin -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS=" -pipe -DDYNAMIC_ZLIB -I/usr/local/include -Wno-stringop-truncation -Wno-stringop-overflow -O2 -fno-strict-aliasing " MANPREFIX="/usr/local" 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" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ARGS ------------------------------------------------------------------------------- ZLIB=-lz BLASFLAGS="-lopenblas -lopenblas" DESTDIR=/construction/biology/plink/stage SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: PLIST_SUB ------------------------------------------------------------------------------- PORTEXAMPLES="" OSREL=5.9 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/plink" EXAMPLESDIR="share/examples/plink" DATADIR="share/plink" WWWDIR="www/plink" ETCDIR="etc/plink" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: 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 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: /etc/make.conf ------------------------------------------------------------------------------- DPORTS_BUILDER=yes DISABLE_LICENSES=yes DEFAULT_VERSIONS=ssl=openssl FORCE_PACKAGE=yes DEVELOPER=yes USE_PACKAGE_DEPENDS_ONLY=yes PORTSDIR=/xports PORT_DBDIR=/options PKG_DBDIR=/var/db/pkg PKG_CACHEDIR=/var/cache/pkg PKG_SUFX=.txz DEVELOPER=1 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500908 OSVERSION=9999999 OSREL=5.9 _OSRELEASE=5.9-SYNTH DISTDIR=/distfiles WRKDIRPREFIX=/construction BATCH=yes PACKAGE_BUILDING=yes PKG_CREATE_VERBOSE=yes MAKE_JOBS_NUMBER=10 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gettext-runtime-0.21.txz Installing /packages/All/gmake-4.3_2.txz Installing /packages/All/gmp-6.2.1.txz Installing /packages/All/mpfr-4.1.0.txz Installing /packages/All/mpc-1.1.0_2.txz UNFLAVORED devel/binutils -> use devel/binutils@native Installing /packages/All/binutils-2.33.1_4,1.txz Installing /packages/All/gcc8-8.4.0.txz ===== Message from gcc8-8.4.0: -- 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/gcc8 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. Installing /packages/All/openblas-0.3.12,1.txz UNFLAVORED devel/binutils -> use devel/binutils@native SUCCEEDED 00:00:13 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> plink-1.90.b6.17_1 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> plink-1.90.b6.17_1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by plink-1.90.b6.17_1 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> plink-1.90.b6.17_1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by plink-1.90.b6.17_1 for building => SHA256 Checksum OK for chrchang-plink-ng-v1.90b6.17-79b2df8c_GH0.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> plink-1.90.b6.17_1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by plink-1.90.b6.17_1 for building ===> Extracting for plink-1.90.b6.17_1 ===> plink-1.90.b6.17_1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by plink-1.90.b6.17_1 for building => SHA256 Checksum OK for chrchang-plink-ng-v1.90b6.17-79b2df8c_GH0.tar.gz. Extracted Memory Use: 14.32M SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for plink-1.90.b6.17_1 ===> Applying ports patches for plink-1.90.b6.17_1 from /xports/biology/plink/files SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> plink-1.90.b6.17_1 depends on package: gmake>=4.3 - found ===> plink-1.90.b6.17_1 depends on executable: gfortran8 - found ===> plink-1.90.b6.17_1 depends on file: /usr/local/bin/as - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> plink-1.90.b6.17_1 depends on shared library: libopenblas.so - found (/usr/local/lib/libopenblas.so) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> plink-1.90.b6.17_1 depends on package: gmake>=4.3 - found ===> plink-1.90.b6.17_1 depends on executable: gfortran8 - found ===> plink-1.90.b6.17_1 depends on file: /usr/local/bin/as - found ===> plink-1.90.b6.17_1 depends on shared library: libopenblas.so - found (/usr/local/lib/libopenblas.so) ===> Configuring for plink-1.90.b6.17_1 SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for plink-1.90.b6.17_1 gmake[2]: Entering directory '/construction/biology/plink/plink-ng-79b2df8c/1.9' c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -Wno-stringop-truncation -Wno-stringop-overflow -O2 -fno-strict-aliasing plink.c -o plink.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -Wno-stringop-truncation -Wno-stringop-overflow -O2 -fno-strict-aliasing plink_assoc.c -o plink_assoc.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -Wno-stringop-truncation -Wno-stringop-overflow -O2 -fno-strict-aliasing plink_calc.c -o plink_calc.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -Wno-stringop-truncation -Wno-stringop-overflow -O2 -fno-strict-aliasing plink_cluster.c -o plink_cluster.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -Wno-stringop-truncation -Wno-stringop-overflow -O2 -fno-strict-aliasing plink_cnv.c -o plink_cnv.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -Wno-stringop-truncation -Wno-stringop-overflow -O2 -fno-strict-aliasing plink_common.c -o plink_common.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -Wno-stringop-truncation -Wno-stringop-overflow -O2 -fno-strict-aliasing plink_data.c -o plink_data.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -Wno-stringop-truncation -Wno-stringop-overflow -O2 -fno-strict-aliasing plink_dosage.c -o plink_dosage.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -Wno-stringop-truncation -Wno-stringop-overflow -O2 -fno-strict-aliasing plink_family.c -o plink_family.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -Wno-stringop-truncation -Wno-stringop-overflow -O2 -fno-strict-aliasing plink_filter.c -o plink_filter.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -Wno-stringop-truncation -Wno-stringop-overflow -O2 -fno-strict-aliasing plink_glm.c -o plink_glm.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -Wno-stringop-truncation -Wno-stringop-overflow -O2 -fno-strict-aliasing plink_help.c -o plink_help.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -Wno-stringop-truncation -Wno-stringop-overflow -O2 -fno-strict-aliasing plink_homozyg.c -o plink_homozyg.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -Wno-stringop-truncation -Wno-stringop-overflow -O2 -fno-strict-aliasing plink_lasso.c -o plink_lasso.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -Wno-stringop-truncation -Wno-stringop-overflow -O2 -fno-strict-aliasing plink_ld.c -o plink_ld.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -Wno-stringop-truncation -Wno-stringop-overflow -O2 -fno-strict-aliasing plink_matrix.c -o plink_matrix.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -Wno-stringop-truncation -Wno-stringop-overflow -O2 -fno-strict-aliasing plink_misc.c -o plink_misc.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -Wno-stringop-truncation -Wno-stringop-overflow -O2 -fno-strict-aliasing plink_perm.c -o plink_perm.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -Wno-stringop-truncation -Wno-stringop-overflow -O2 -fno-strict-aliasing plink_rserve.c -o plink_rserve.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -Wno-stringop-truncation -Wno-stringop-overflow -O2 -fno-strict-aliasing plink_set.c -o plink_set.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -Wno-stringop-truncation -Wno-stringop-overflow -O2 -fno-strict-aliasing plink_stats.c -o plink_stats.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -Wno-stringop-truncation -Wno-stringop-overflow -O2 -fno-strict-aliasing SFMT.c -o SFMT.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -Wno-stringop-truncation -Wno-stringop-overflow -O2 -fno-strict-aliasing dcdflib.c -o dcdflib.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -Wno-stringop-truncation -Wno-stringop-overflow -O2 -fno-strict-aliasing pigz.c -o pigz.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -Wno-stringop-truncation -Wno-stringop-overflow -O2 -fno-strict-aliasing yarn.c -o yarn.o c++ -x c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -Wno-stringop-truncation -Wno-stringop-overflow -O2 -fno-strict-aliasing Rconnection.cc -o Rconnection.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -Wno-stringop-truncation -Wno-stringop-overflow -O2 -fno-strict-aliasing hfile.c -o hfile.o c++ -c -pipe -DDYNAMIC_ZLIB -I/usr/local/include -Wno-stringop-truncation -Wno-stringop-overflow -O2 -fno-strict-aliasing bgzf.c -o bgzf.o 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 -pthread -Wl,-rpath=/usr/local/lib/gcc8 -L/usr/local/lib/gcc8 -B/usr/local/bin -L/usr/local/lib -L. -lz -o plink gmake[2]: Leaving directory '/construction/biology/plink/plink-ng-79b2df8c/1.9' (cd /construction/biology/plink/plink-ng-79b2df8c/1.9; cc -pipe -DDYNAMIC_ZLIB -I/usr/local/include -Wno-stringop-truncation -Wno-stringop-overflow -O2 -fno-strict-aliasing prettify.c -o prettify) SUCCEEDED 00:00:27 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- ===> plink-1.90.b6.17_1 depends on executable: gfortran8 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for plink-1.90.b6.17_1 ===> plink-1.90.b6.17_1 depends on executable: gfortran8 - found ===> Generating temporary packing list gmake[2]: Entering directory '/construction/biology/plink/plink-ng-79b2df8c/1.9' install -d /construction/biology/plink/stage/usr/local/bin install -c plink /construction/biology/plink/stage/usr/local/bin strip /construction/biology/plink/stage/usr/local/bin/plink gmake[2]: Leaving directory '/construction/biology/plink/plink-ng-79b2df8c/1.9' install -s -m 555 /construction/biology/plink/plink-ng-79b2df8c/1.9/prettify /construction/biology/plink/stage/usr/local/bin install -m 0644 /construction/biology/plink/plink-ng-79b2df8c/1.9/toy.map /construction/biology/plink/plink-ng-79b2df8c/1.9/toy.ped /construction/biology/plink/stage/usr/local/share/examples/plink ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for plink-1.90.b6.17_1 file sizes/checksums [4]: 0% file sizes/checksums [4]: 100% packing files [4]: 0% packing files [4]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:02 TOTAL TIME 00:00:47