=> Building biology/fastp Started : Tuesday, 23 JUL 2019 at 05:30:28 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/fastp XDG_CONFIG_HOME=/construction/biology/fastp HOME=/construction/biology/fastp TMPDIR="/tmp" PATH=/construction/biology/fastp/.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/fastp XDG_CONFIG_HOME=/construction/biology/fastp HOME=/construction/biology/fastp TMPDIR="/tmp" PATH=/construction/biology/fastp/.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/fastp/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- OSREL=5.6 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/fastp" EXAMPLESDIR="share/examples/fastp" DATADIR="share/fastp" WWWDIR="www/fastp" ETCDIR="etc/fastp" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/fastp DOCSDIR=/usr/local/share/doc/fastp EXAMPLESDIR=/usr/local/share/examples/fastp WWWDIR=/usr/local/www/fastp ETCDIR=/usr/local/etc/fastp -------------------------------------------------- -- /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 MIT accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> fastp-0.20.0 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 ===> fastp-0.20.0 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of fastp-0.20.0 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License MIT accepted by the user ===> Fetching all distfiles required by fastp-0.20.0 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License MIT accepted by the user ===> Fetching all distfiles required by fastp-0.20.0 for building => SHA256 Checksum OK for OpenGene-fastp-v0.20.0_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License MIT accepted by the user ===> Fetching all distfiles required by fastp-0.20.0 for building ===> Extracting for fastp-0.20.0 => SHA256 Checksum OK for OpenGene-fastp-v0.20.0_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for fastp-0.20.0 ===> Applying ports patches for fastp-0.20.0 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> fastp-0.20.0 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 ===> fastp-0.20.0 depends on executable: gmake - found ===> Returning to build of fastp-0.20.0 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for fastp-0.20.0 -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for fastp-0.20.0 gmake[1]: Entering directory '/construction/biology/fastp/fastp-0.20.0' c++ -c src/filter.cpp -o obj/filter.o -pipe -O2 -fno-strict-aliasing -std=c++11 -I./inc c++ -c src/main.cpp -o obj/main.o -pipe -O2 -fno-strict-aliasing -std=c++11 -I./inc c++ -c src/writer.cpp -o obj/writer.o -pipe -O2 -fno-strict-aliasing -std=c++11 -I./inc c++ -c src/fastqreader.cpp -o obj/fastqreader.o -pipe -O2 -fno-strict-aliasing -std=c++11 -I./inc c++ -c src/options.cpp -o obj/options.o -pipe -O2 -fno-strict-aliasing -std=c++11 -I./inc c++ -c src/evaluator.cpp -o obj/evaluator.o -pipe -O2 -fno-strict-aliasing -std=c++11 -I./inc c++ -c src/seprocessor.cpp -o obj/seprocessor.o -pipe -O2 -fno-strict-aliasing -std=c++11 -I./inc c++ -c src/nucleotidetree.cpp -o obj/nucleotidetree.o -pipe -O2 -fno-strict-aliasing -std=c++11 -I./inc c++ -c src/duplicate.cpp -o obj/duplicate.o -pipe -O2 -fno-strict-aliasing -std=c++11 -I./inc c++ -c src/peprocessor.cpp -o obj/peprocessor.o -pipe -O2 -fno-strict-aliasing -std=c++11 -I./inc c++ -c src/umiprocessor.cpp -o obj/umiprocessor.o -pipe -O2 -fno-strict-aliasing -std=c++11 -I./inc c++ -c src/polyx.cpp -o obj/polyx.o -pipe -O2 -fno-strict-aliasing -std=c++11 -I./inc c++ -c src/adaptertrimmer.cpp -o obj/adaptertrimmer.o -pipe -O2 -fno-strict-aliasing -std=c++11 -I./inc c++ -c src/htmlreporter.cpp -o obj/htmlreporter.o -pipe -O2 -fno-strict-aliasing -std=c++11 -I./inc c++ -c src/processor.cpp -o obj/processor.o -pipe -O2 -fno-strict-aliasing -std=c++11 -I./inc c++ -c src/overlapanalysis.cpp -o obj/overlapanalysis.o -pipe -O2 -fno-strict-aliasing -std=c++11 -I./inc c++ -c src/read.cpp -o obj/read.o -pipe -O2 -fno-strict-aliasing -std=c++11 -I./inc c++ -c src/jsonreporter.cpp -o obj/jsonreporter.o -pipe -O2 -fno-strict-aliasing -std=c++11 -I./inc c++ -c src/fastareader.cpp -o obj/fastareader.o -pipe -O2 -fno-strict-aliasing -std=c++11 -I./inc c++ -c src/filterresult.cpp -o obj/filterresult.o -pipe -O2 -fno-strict-aliasing -std=c++11 -I./inc c++ -c src/threadconfig.cpp -o obj/threadconfig.o -pipe -O2 -fno-strict-aliasing -std=c++11 -I./inc c++ -c src/unittest.cpp -o obj/unittest.o -pipe -O2 -fno-strict-aliasing -std=c++11 -I./inc c++ -c src/basecorrector.cpp -o obj/basecorrector.o -pipe -O2 -fno-strict-aliasing -std=c++11 -I./inc c++ -c src/sequence.cpp -o obj/sequence.o -pipe -O2 -fno-strict-aliasing -std=c++11 -I./inc c++ -c src/writerthread.cpp -o obj/writerthread.o -pipe -O2 -fno-strict-aliasing -std=c++11 -I./inc c++ -c src/stats.cpp -o obj/stats.o -pipe -O2 -fno-strict-aliasing -std=c++11 -I./inc c++ ./obj/filter.o ./obj/main.o ./obj/writer.o ./obj/fastqreader.o ./obj/options.o ./obj/evaluator.o ./obj/seprocessor.o ./obj/nucleotidetree.o ./obj/duplicate.o ./obj/peprocessor.o ./obj/umiprocessor.o ./obj/polyx.o ./obj/adaptertrimmer.o ./obj/htmlreporter.o ./obj/processor.o ./obj/overlapanalysis.o ./obj/read.o ./obj/jsonreporter.o ./obj/fastareader.o ./obj/filterresult.o ./obj/threadconfig.o ./obj/unittest.o ./obj/basecorrector.o ./obj/sequence.o ./obj/writerthread.o ./obj/stats.o -o fastp -lz -lpthread gmake[1]: Leaving directory '/construction/biology/fastp/fastp-0.20.0' -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for fastp-0.20.0 ===> Generating temporary packing list gmake[1]: Entering directory '/construction/biology/fastp/fastp-0.20.0' install fastp /construction/biology/fastp/stage/usr/local/bin/fastp Installed. gmake[1]: Leaving directory '/construction/biology/fastp/fastp-0.20.0' /usr/bin/strip /construction/biology/fastp/stage/usr/local/bin/fastp ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for fastp-0.20.0 file sizes/checksums [4]: . done packing files [4]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Tuesday, 23 JUL 2019 at 05:30:56 UTC Duration: 00:00:27