=> Building biology/smithwaterman Started : Tuesday, 23 JUL 2019 at 23:50:58 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=5.6-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.6-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/smithwaterman XDG_CONFIG_HOME=/construction/biology/smithwaterman HOME=/construction/biology/smithwaterman TMPDIR="/tmp" PATH=/construction/biology/smithwaterman/.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/smithwaterman XDG_CONFIG_HOME=/construction/biology/smithwaterman HOME=/construction/biology/smithwaterman TMPDIR="/tmp" PATH=/construction/biology/smithwaterman/.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/smithwaterman/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- OSREL=5.6 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/smithwaterman" EXAMPLESDIR="share/examples/smithwaterman" DATADIR="share/smithwaterman" WWWDIR="www/smithwaterman" ETCDIR="etc/smithwaterman" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/smithwaterman DOCSDIR=/usr/local/share/doc/smithwaterman EXAMPLESDIR=/usr/local/share/examples/smithwaterman WWWDIR=/usr/local/www/smithwaterman ETCDIR=/usr/local/etc/smithwaterman -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-5.6 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 LICENSES_ACCEPTED= NONE 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=500601 OSVERSION=9999999 OSREL=5.6 _OSRELEASE=5.6-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License GPLv2 accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> smithwaterman-g20160702 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 ===> smithwaterman-g20160702 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of smithwaterman-g20160702 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by smithwaterman-g20160702 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by smithwaterman-g20160702 for building => SHA256 Checksum OK for ekg-smithwaterman-g20160702-2610e259611ae4cde8f03c72499d28f03f6d38a7_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by smithwaterman-g20160702 for building ===> Extracting for smithwaterman-g20160702 => SHA256 Checksum OK for ekg-smithwaterman-g20160702-2610e259611ae4cde8f03c72499d28f03f6d38a7_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for smithwaterman-g20160702 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> smithwaterman-g20160702 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 ===> smithwaterman-g20160702 depends on executable: gmake - found ===> Returning to build of smithwaterman-g20160702 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for smithwaterman-g20160702 -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for smithwaterman-g20160702 gmake[1]: Entering directory '/construction/biology/smithwaterman/smithwaterman-2610e259611ae4cde8f03c72499d28f03f6d38a7' c++ -pipe -O2 -fno-strict-aliasing -fPIC -c -o disorder.o disorder.cpp -I. c++ -pipe -O2 -fno-strict-aliasing -fPIC -c -o BandedSmithWaterman.o BandedSmithWaterman.cpp -I. c++ -pipe -O2 -fno-strict-aliasing -fPIC -c -o Repeats.o Repeats.cpp -I. c++ -pipe -O2 -fno-strict-aliasing -fPIC -c -o LeftAlign.o LeftAlign.cpp -I. c++ -pipe -O2 -fno-strict-aliasing -fPIC -c -o IndelAllele.o IndelAllele.cpp -I. c++ -pipe -O2 -fno-strict-aliasing -fPIC -c -o smithwaterman.o smithwaterman.cpp -I. c++ -pipe -O2 -fno-strict-aliasing -fPIC -c -o SmithWatermanGotoh.o SmithWatermanGotoh.cpp -I. c++ -pipe -O2 -fno-strict-aliasing smithwaterman.o BandedSmithWaterman.o SmithWatermanGotoh.o Repeats.o LeftAlign.o IndelAllele.o disorder.o -I. -o smithwaterman ar rs libsw.a disorder.o BandedSmithWaterman.o SmithWatermanGotoh.o Repeats.o LeftAlign.o IndelAllele.o c++ -shared -Wl,-soname,libsw.so.1 -o libsw.so.1 disorder.o BandedSmithWaterman.o SmithWatermanGotoh.o Repeats.o LeftAlign.o IndelAllele.o ld -r disorder.o BandedSmithWaterman.o SmithWatermanGotoh.o Repeats.o LeftAlign.o IndelAllele.o -o sw.o -L. /usr/libexec/binutils227/elf/ar: creating libsw.a gmake[1]: Leaving directory '/construction/biology/smithwaterman/smithwaterman-2610e259611ae4cde8f03c72499d28f03f6d38a7' -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for smithwaterman-g20160702 ===> Generating temporary packing list gmake[1]: Entering directory '/construction/biology/smithwaterman/smithwaterman-2610e259611ae4cde8f03c72499d28f03f6d38a7' mkdir -p /construction/biology/smithwaterman/stage/usr/local/bin mkdir -p /construction/biology/smithwaterman/stage/usr/local/include/smithwaterman mkdir -p /construction/biology/smithwaterman/stage/usr/local/lib install -c smithwaterman /construction/biology/smithwaterman/stage/usr/local/bin install -c *.h /construction/biology/smithwaterman/stage/usr/local/include/smithwaterman install -c libsw.a libsw.so.1 /construction/biology/smithwaterman/stage/usr/local/lib strip /construction/biology/smithwaterman/stage/usr/local/bin/smithwaterman /construction/biology/smithwaterman/stage/usr/local/lib/libsw.so.1 gmake[1]: Leaving directory '/construction/biology/smithwaterman/smithwaterman-2610e259611ae4cde8f03c72499d28f03f6d38a7' /bin/sh /xports/Mk/Scripts/relative_link.sh /construction/biology/smithwaterman/stage/usr/local/lib/libsw.so.1 /construction/biology/smithwaterman/stage/usr/local/lib/libsw.so ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for smithwaterman-g20160702 file sizes/checksums [15]: . done packing files [15]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Tuesday, 23 JUL 2019 at 23:51:16 UTC Duration: 00:00:18