=> Building biology/minimap2 Started : Sunday, 7 JUL 2019 at 04:23:47 UTC Platform: 5.7-DEVELOPMENT DragonFly v5.7.0.83.g49866-DEVELOPMENT #40: Sun Jun 30 03:00:04 PDT 2019 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.4-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.4-SYNTH UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 TERM=dumb PKG_CACHEDIR=/var/cache/pkg8 PKG_DBDIR=/var/db/pkg8 PORTSDIR=/xports LANG=C HOME=/root USER=root -------------------------------------------------- -- Options -------------------------------------------------- -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- MAKE=gmake XDG_DATA_HOME=/construction/biology/minimap2 XDG_CONFIG_HOME=/construction/biology/minimap2 HOME=/construction/biology/minimap2 TMPDIR="/tmp" PATH=/construction/biology/minimap2/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/biology/minimap2 XDG_CONFIG_HOME=/construction/biology/minimap2 HOME=/construction/biology/minimap2 TMPDIR="/tmp" PATH=/construction/biology/minimap2/.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 PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS=" -pipe -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" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/biology/minimap2/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- OSREL=5.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/minimap2" EXAMPLESDIR="share/examples/minimap2" DATADIR="share/minimap2" WWWDIR="www/minimap2" ETCDIR="etc/minimap2" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/minimap2 DOCSDIR=/usr/local/share/doc/minimap2 EXAMPLESDIR=/usr/local/share/examples/minimap2 WWWDIR=/usr/local/www/minimap2 ETCDIR=/usr/local/etc/minimap2 -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-5.4 USE_PACKAGE_DEPENDS_ONLY=yes PACKAGE_BUILDING=yes BATCH=yes PKG_CREATE_VERBOSE=yes PORTSDIR=/xports DISTDIR=/distfiles WRKDIRPREFIX=/construction PORT_DBDIR=/options PACKAGES=/packages MAKE_JOBS_NUMBER_LIMIT=5 HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _PERL5_FROM_BIN=5.28.1 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500400 OSVERSION=9999999 OSREL=5.4 _OSRELEASE=5.4-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License MIT accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> minimap2-2.17 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.11.1.txz Installing pkg-1.11.1... Extracting pkg-1.11.1: .......... done ===> minimap2-2.17 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of minimap2-2.17 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License MIT accepted by the user ===> Fetching all distfiles required by minimap2-2.17 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License MIT accepted by the user ===> Fetching all distfiles required by minimap2-2.17 for building => SHA256 Checksum OK for lh3-minimap2-v2.17_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License MIT accepted by the user ===> Fetching all distfiles required by minimap2-2.17 for building ===> Extracting for minimap2-2.17 => SHA256 Checksum OK for lh3-minimap2-v2.17_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for minimap2-2.17 ===> Applying ports patches for minimap2-2.17 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> minimap2-2.17 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_3.txz Installing gmake-4.2.1_3... `-- Installing gettext-runtime-0.20.1... | `-- Installing indexinfo-0.3.1... | `-- Extracting indexinfo-0.3.1: .... done `-- Extracting gettext-runtime-0.20.1: .......... done Extracting gmake-4.2.1_3: .......... done ===> minimap2-2.17 depends on executable: gmake - found ===> Returning to build of minimap2-2.17 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for minimap2-2.17 -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for minimap2-2.17 gmake[1]: Entering directory '/construction/biology/minimap2/minimap2-2.17' cc -c -pipe -O2 -fno-strict-aliasing -Wc++-compat -DHAVE_KALLOC main.c -o main.o cc -c -pipe -O2 -fno-strict-aliasing -Wc++-compat -DHAVE_KALLOC kthread.c -o kthread.o cc -c -pipe -O2 -fno-strict-aliasing -Wc++-compat -DHAVE_KALLOC kalloc.c -o kalloc.o cc -c -pipe -O2 -fno-strict-aliasing -Wc++-compat -DHAVE_KALLOC misc.c -o misc.o cc -c -pipe -O2 -fno-strict-aliasing -Wc++-compat -DHAVE_KALLOC bseq.c -o bseq.o cc -c -pipe -O2 -fno-strict-aliasing -Wc++-compat -DHAVE_KALLOC sketch.c -o sketch.o cc -c -pipe -O2 -fno-strict-aliasing -Wc++-compat -DHAVE_KALLOC sdust.c -o sdust.o cc -c -pipe -O2 -fno-strict-aliasing -Wc++-compat -DHAVE_KALLOC options.c -o options.o cc -c -pipe -O2 -fno-strict-aliasing -Wc++-compat -DHAVE_KALLOC index.c -o index.o cc -c -pipe -O2 -fno-strict-aliasing -Wc++-compat -DHAVE_KALLOC chain.c -o chain.o cc -c -pipe -O2 -fno-strict-aliasing -Wc++-compat -DHAVE_KALLOC align.c -o align.o cc -c -pipe -O2 -fno-strict-aliasing -Wc++-compat -DHAVE_KALLOC hit.c -o hit.o cc -c -pipe -O2 -fno-strict-aliasing -Wc++-compat -DHAVE_KALLOC map.c -o map.o cc -c -pipe -O2 -fno-strict-aliasing -Wc++-compat -DHAVE_KALLOC format.c -o format.o cc -c -pipe -O2 -fno-strict-aliasing -Wc++-compat -DHAVE_KALLOC pe.c -o pe.o cc -c -pipe -O2 -fno-strict-aliasing -Wc++-compat -DHAVE_KALLOC esterr.c -o esterr.o cc -c -pipe -O2 -fno-strict-aliasing -Wc++-compat -DHAVE_KALLOC splitidx.c -o splitidx.o cc -c -pipe -O2 -fno-strict-aliasing -Wc++-compat -msse2 -DHAVE_KALLOC ksw2_ll_sse.c -o ksw2_ll_sse.o cc -c -pipe -O2 -fno-strict-aliasing -Wc++-compat -msse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_extz2_sse.c -o ksw2_extz2_sse41.o cc -c -pipe -O2 -fno-strict-aliasing -Wc++-compat -msse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_extd2_sse.c -o ksw2_extd2_sse41.o cc -c -pipe -O2 -fno-strict-aliasing -Wc++-compat -msse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_exts2_sse.c -o ksw2_exts2_sse41.o cc -c -pipe -O2 -fno-strict-aliasing -Wc++-compat -msse2 -mno-sse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY ksw2_extz2_sse.c -o ksw2_extz2_sse2.o cc -c -pipe -O2 -fno-strict-aliasing -Wc++-compat -msse2 -mno-sse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY ksw2_extd2_sse.c -o ksw2_extd2_sse2.o cc -c -pipe -O2 -fno-strict-aliasing -Wc++-compat -msse2 -mno-sse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY ksw2_exts2_sse.c -o ksw2_exts2_sse2.o cc -c -pipe -O2 -fno-strict-aliasing -Wc++-compat -msse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_dispatch.c -o ksw2_dispatch.o ar -csru libminimap2.a kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o chain.o align.o hit.o map.o format.o pe.o esterr.o splitidx.o ksw2_ll_sse.o ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') cc -pipe -O2 -fno-strict-aliasing -Wc++-compat main.o -o minimap2 -L. -lminimap2 -lm -lz -lpthread gmake[1]: Leaving directory '/construction/biology/minimap2/minimap2-2.17' -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for minimap2-2.17 ===> Generating temporary packing list gmake[1]: Entering directory '/construction/biology/minimap2/minimap2-2.17' mkdir -p /construction/biology/minimap2/stage/usr/local/bin mkdir -p /construction/biology/minimap2/stage/usr/local/man/man1 install -c minimap2 /construction/biology/minimap2/stage/usr/local/bin install -c minimap2.1 /construction/biology/minimap2/stage/usr/local/man/man1 strip /construction/biology/minimap2/stage/usr/local/bin/minimap2 gmake[1]: Leaving directory '/construction/biology/minimap2/minimap2-2.17' ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for minimap2-2.17 file sizes/checksums [5]: . done packing files [5]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Sunday, 7 JUL 2019 at 04:23:58 UTC Duration: 00:00:10