=> Building biology/py-cutadapt@py27 Started : Thursday, 30 AUG 2018 at 10:55:18 UTC Platform: 5.3-DEVELOPMENT DragonFly 5.3-DEVELOPMENT #140: Wed Aug 29 22:06:30 PDT 2018 root@test.backplane.com:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.3-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.3-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 -------------------------------------------------- PYTHON="/usr/local/bin/python2.7" XDG_DATA_HOME=/construction/biology/py-cutadapt XDG_CONFIG_HOME=/construction/biology/py-cutadapt HOME=/construction/biology/py-cutadapt TMPDIR="/tmp" PATH=/construction/biology/py-cutadapt/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/biology/py-cutadapt XDG_CONFIG_HOME=/construction/biology/py-cutadapt HOME=/construction/biology/py-cutadapt TMPDIR="/tmp" PATH=/construction/biology/py-cutadapt/.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=gcc50 LDSHARED="cc -shared" PYTHONDONTWRITEBYTECODE= PYTHONOPTIMIZE= 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/py-cutadapt/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PORTDOCS="" PORTEXAMPLES="" PYTHON_INCLUDEDIR=include/python2.7 PYTHON_LIBDIR=lib/python2.7 PYTHON_PLATFORM=dragonfly5 PYTHON_PYOEXTENSION=pyo PYTHON_SITELIBDIR=lib/python2.7/site-packages PYTHON_SUFFIX=27 PYTHON_VER=2.7 PYTHON_VERSION=python2.7 PYTHON2="" PYTHON3="@comment " OSREL=5.3 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/cutadapt" EXAMPLESDIR="share/examples/cutadapt" DATADIR="share/cutadapt" WWWDIR="www/cutadapt" ETCDIR="etc/cutadapt" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/cutadapt DOCSDIR=/usr/local/share/doc/cutadapt EXAMPLESDIR=/usr/local/share/examples/cutadapt WWWDIR=/usr/local/www/cutadapt ETCDIR=/usr/local/etc/cutadapt -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=LiveSystem 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=12 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=32 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500316 OSVERSION=9999999 OSREL=5.3 _OSRELEASE=5.3-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License MIT accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> py27-cutadapt-1.14 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_1.txz Installing pkg-1.10.5_1... Extracting pkg-1.10.5_1: .......... done ===> py27-cutadapt-1.14 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py27-cutadapt-1.14 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License MIT accepted by the user ===> Fetching all distfiles required by py27-cutadapt-1.14 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License MIT accepted by the user ===> Fetching all distfiles required by py27-cutadapt-1.14 for building => SHA256 Checksum OK for cutadapt-1.14.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License MIT accepted by the user ===> Fetching all distfiles required by py27-cutadapt-1.14 for building ===> Extracting for py27-cutadapt-1.14 => SHA256 Checksum OK for cutadapt-1.14.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for py27-cutadapt-1.14 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> py27-cutadapt-1.14 depends on package: py27-setuptools>0 - not found ===> Installing existing package /packages/All/py27-setuptools-39.2.0.txz Installing py27-setuptools-39.2.0... `-- Installing python27-2.7.15... | `-- Installing expat-2.2.5... | `-- Extracting expat-2.2.5: .......... done | `-- Installing gettext-runtime-0.19.8.1_1... | | `-- Installing indexinfo-0.3.1... | | `-- Extracting indexinfo-0.3.1: .... done | `-- Extracting gettext-runtime-0.19.8.1_1: .......... done | `-- Installing libffi-3.2.1_2... | `-- Extracting libffi-3.2.1_2: .......... done | `-- Installing libressl-2.7.4... | `-- Extracting libressl-2.7.4: .......... done | `-- Installing ncurses-6.0.0s20171223_1... | `-- Extracting ncurses-6.0.0s20171223_1: .......... done | `-- Installing readline-7.0.3_1... | `-- Extracting readline-7.0.3_1: .......... done `-- Extracting python27-2.7.15: .......... done Extracting py27-setuptools-39.2.0: .......... done Message from python27-2.7.15: =========================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: bsddb databases/py-bsddb gdbm databases/py-gdbm sqlite3 databases/py-sqlite3 tkinter x11-toolkits/py-tkinter =========================================================================== ===> py27-cutadapt-1.14 depends on package: py27-setuptools>0 - found ===> Returning to build of py27-cutadapt-1.14 ===> py27-cutadapt-1.14 depends on file: /usr/local/bin/python2.7 - found -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for py27-cutadapt-1.14 running config -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for py27-cutadapt-1.14 running build running build_py creating build creating build/lib.dragonfly-5.3-SYNTH-x86_64-2.7 creating build/lib.dragonfly-5.3-SYNTH-x86_64-2.7/cutadapt copying cutadapt/modifiers.py -> build/lib.dragonfly-5.3-SYNTH-x86_64-2.7/cutadapt copying cutadapt/compat.py -> build/lib.dragonfly-5.3-SYNTH-x86_64-2.7/cutadapt copying cutadapt/adapters.py -> build/lib.dragonfly-5.3-SYNTH-x86_64-2.7/cutadapt copying cutadapt/colorspace.py -> build/lib.dragonfly-5.3-SYNTH-x86_64-2.7/cutadapt copying cutadapt/report.py -> build/lib.dragonfly-5.3-SYNTH-x86_64-2.7/cutadapt copying cutadapt/seqio.py -> build/lib.dragonfly-5.3-SYNTH-x86_64-2.7/cutadapt copying cutadapt/_version.py -> build/lib.dragonfly-5.3-SYNTH-x86_64-2.7/cutadapt copying cutadapt/qualtrim.py -> build/lib.dragonfly-5.3-SYNTH-x86_64-2.7/cutadapt copying cutadapt/__init__.py -> build/lib.dragonfly-5.3-SYNTH-x86_64-2.7/cutadapt copying cutadapt/align.py -> build/lib.dragonfly-5.3-SYNTH-x86_64-2.7/cutadapt copying cutadapt/filters.py -> build/lib.dragonfly-5.3-SYNTH-x86_64-2.7/cutadapt creating build/lib.dragonfly-5.3-SYNTH-x86_64-2.7/cutadapt/scripts copying cutadapt/scripts/__init__.py -> build/lib.dragonfly-5.3-SYNTH-x86_64-2.7/cutadapt/scripts copying cutadapt/scripts/cutadapt.py -> build/lib.dragonfly-5.3-SYNTH-x86_64-2.7/cutadapt/scripts UPDATING build/lib.dragonfly-5.3-SYNTH-x86_64-2.7/cutadapt/_version.py set build/lib.dragonfly-5.3-SYNTH-x86_64-2.7/cutadapt/_version.py to '1.14' running build_ext building 'cutadapt._align' extension creating build/temp.dragonfly-5.3-SYNTH-x86_64-2.7 creating build/temp.dragonfly-5.3-SYNTH-x86_64-2.7/cutadapt cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/include/python2.7 -c cutadapt/_align.c -o build/temp.dragonfly-5.3-SYNTH-x86_64-2.7/cutadapt/_align.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.3-SYNTH-x86_64-2.7/cutadapt/_align.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.3-SYNTH-x86_64-2.7/cutadapt/_align.so building 'cutadapt._qualtrim' extension cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/include/python2.7 -c cutadapt/_qualtrim.c -o build/temp.dragonfly-5.3-SYNTH-x86_64-2.7/cutadapt/_qualtrim.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.3-SYNTH-x86_64-2.7/cutadapt/_qualtrim.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.3-SYNTH-x86_64-2.7/cutadapt/_qualtrim.so building 'cutadapt._seqio' extension cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/include/python2.7 -c cutadapt/_seqio.c -o build/temp.dragonfly-5.3-SYNTH-x86_64-2.7/cutadapt/_seqio.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.3-SYNTH-x86_64-2.7/cutadapt/_seqio.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.3-SYNTH-x86_64-2.7/cutadapt/_seqio.so -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> py27-cutadapt-1.14 depends on package: py27-xopen>0 - not found ===> Installing existing package /packages/All/py27-xopen-0.2.1.txz Installing py27-xopen-0.2.1... Extracting py27-xopen-0.2.1: .......... done ===> py27-cutadapt-1.14 depends on package: py27-xopen>0 - found ===> Returning to build of py27-cutadapt-1.14 ===> py27-cutadapt-1.14 depends on package: py27-setuptools>0 - found ===> py27-cutadapt-1.14 depends on file: /usr/local/bin/python2.7 - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for py27-cutadapt-1.14 ===> Generating temporary packing list running install running build running build_py UPDATING build/lib.dragonfly-5.3-SYNTH-x86_64-2.7/cutadapt/_version.py set build/lib.dragonfly-5.3-SYNTH-x86_64-2.7/cutadapt/_version.py to '1.14' running build_ext running install_lib creating /construction/biology/py-cutadapt/stage/usr/local/lib/python2.7 creating /construction/biology/py-cutadapt/stage/usr/local/lib/python2.7/site-packages creating /construction/biology/py-cutadapt/stage/usr/local/lib/python2.7/site-packages/cutadapt copying build/lib.dragonfly-5.3-SYNTH-x86_64-2.7/cutadapt/modifiers.py -> /construction/biology/py-cutadapt/stage/usr/local/lib/python2.7/site-packages/cutadapt copying build/lib.dragonfly-5.3-SYNTH-x86_64-2.7/cutadapt/_version.py -> /construction/biology/py-cutadapt/stage/usr/local/lib/python2.7/site-packages/cutadapt copying build/lib.dragonfly-5.3-SYNTH-x86_64-2.7/cutadapt/colorspace.py -> /construction/biology/py-cutadapt/stage/usr/local/lib/python2.7/site-packages/cutadapt copying build/lib.dragonfly-5.3-SYNTH-x86_64-2.7/cutadapt/seqio.py -> /construction/biology/py-cutadapt/stage/usr/local/lib/python2.7/site-packages/cutadapt creating /construction/biology/py-cutadapt/stage/usr/local/lib/python2.7/site-packages/cutadapt/scripts copying build/lib.dragonfly-5.3-SYNTH-x86_64-2.7/cutadapt/scripts/cutadapt.py -> /construction/biology/py-cutadapt/stage/usr/local/lib/python2.7/site-packages/cutadapt/scripts copying build/lib.dragonfly-5.3-SYNTH-x86_64-2.7/cutadapt/scripts/__init__.py -> /construction/biology/py-cutadapt/stage/usr/local/lib/python2.7/site-packages/cutadapt/scripts copying build/lib.dragonfly-5.3-SYNTH-x86_64-2.7/cutadapt/align.py -> /construction/biology/py-cutadapt/stage/usr/local/lib/python2.7/site-packages/cutadapt copying build/lib.dragonfly-5.3-SYNTH-x86_64-2.7/cutadapt/report.py -> /construction/biology/py-cutadapt/stage/usr/local/lib/python2.7/site-packages/cutadapt copying build/lib.dragonfly-5.3-SYNTH-x86_64-2.7/cutadapt/qualtrim.py -> /construction/biology/py-cutadapt/stage/usr/local/lib/python2.7/site-packages/cutadapt copying build/lib.dragonfly-5.3-SYNTH-x86_64-2.7/cutadapt/__init__.py -> /construction/biology/py-cutadapt/stage/usr/local/lib/python2.7/site-packages/cutadapt copying build/lib.dragonfly-5.3-SYNTH-x86_64-2.7/cutadapt/adapters.py -> /construction/biology/py-cutadapt/stage/usr/local/lib/python2.7/site-packages/cutadapt copying build/lib.dragonfly-5.3-SYNTH-x86_64-2.7/cutadapt/compat.py -> /construction/biology/py-cutadapt/stage/usr/local/lib/python2.7/site-packages/cutadapt copying build/lib.dragonfly-5.3-SYNTH-x86_64-2.7/cutadapt/filters.py -> /construction/biology/py-cutadapt/stage/usr/local/lib/python2.7/site-packages/cutadapt copying build/lib.dragonfly-5.3-SYNTH-x86_64-2.7/cutadapt/_align.so -> /construction/biology/py-cutadapt/stage/usr/local/lib/python2.7/site-packages/cutadapt copying build/lib.dragonfly-5.3-SYNTH-x86_64-2.7/cutadapt/_qualtrim.so -> /construction/biology/py-cutadapt/stage/usr/local/lib/python2.7/site-packages/cutadapt copying build/lib.dragonfly-5.3-SYNTH-x86_64-2.7/cutadapt/_seqio.so -> /construction/biology/py-cutadapt/stage/usr/local/lib/python2.7/site-packages/cutadapt byte-compiling /construction/biology/py-cutadapt/stage/usr/local/lib/python2.7/site-packages/cutadapt/modifiers.py to modifiers.pyc byte-compiling /construction/biology/py-cutadapt/stage/usr/local/lib/python2.7/site-packages/cutadapt/_version.py to _version.pyc byte-compiling /construction/biology/py-cutadapt/stage/usr/local/lib/python2.7/site-packages/cutadapt/colorspace.py to colorspace.pyc byte-compiling /construction/biology/py-cutadapt/stage/usr/local/lib/python2.7/site-packages/cutadapt/seqio.py to seqio.pyc byte-compiling /construction/biology/py-cutadapt/stage/usr/local/lib/python2.7/site-packages/cutadapt/scripts/cutadapt.py to cutadapt.pyc byte-compiling /construction/biology/py-cutadapt/stage/usr/local/lib/python2.7/site-packages/cutadapt/scripts/__init__.py to __init__.pyc byte-compiling /construction/biology/py-cutadapt/stage/usr/local/lib/python2.7/site-packages/cutadapt/align.py to align.pyc byte-compiling /construction/biology/py-cutadapt/stage/usr/local/lib/python2.7/site-packages/cutadapt/report.py to report.pyc byte-compiling /construction/biology/py-cutadapt/stage/usr/local/lib/python2.7/site-packages/cutadapt/qualtrim.py to qualtrim.pyc byte-compiling /construction/biology/py-cutadapt/stage/usr/local/lib/python2.7/site-packages/cutadapt/__init__.py to __init__.pyc byte-compiling /construction/biology/py-cutadapt/stage/usr/local/lib/python2.7/site-packages/cutadapt/adapters.py to adapters.pyc byte-compiling /construction/biology/py-cutadapt/stage/usr/local/lib/python2.7/site-packages/cutadapt/compat.py to compat.pyc byte-compiling /construction/biology/py-cutadapt/stage/usr/local/lib/python2.7/site-packages/cutadapt/filters.py to filters.pyc writing byte-compilation script '/tmp/tmpAvCoJm.py' /usr/local/bin/python2.7 -O /tmp/tmpAvCoJm.py removing /tmp/tmpAvCoJm.py running install_egg_info running egg_info writing requirements to cutadapt.egg-info/requires.txt writing cutadapt.egg-info/PKG-INFO writing top-level names to cutadapt.egg-info/top_level.txt writing dependency_links to cutadapt.egg-info/dependency_links.txt writing entry points to cutadapt.egg-info/entry_points.txt reading manifest file 'cutadapt.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'bin/_preamble.py' writing manifest file 'cutadapt.egg-info/SOURCES.txt' Copying cutadapt.egg-info to /construction/biology/py-cutadapt/stage/usr/local/lib/python2.7/site-packages/cutadapt-1.14-py2.7.egg-info running install_scripts Installing cutadapt script to /construction/biology/py-cutadapt/stage/usr/local/bin writing list of installed files to '/construction/biology/py-cutadapt/.PLIST.pymodtmp' ====> Compressing man pages (compress-man) if [ -d "/construction/biology/py-cutadapt/stage/usr/local/lib/python2.7/site-packages/cutadapt-1.14-py2.7.egg-info" ]; then /bin/ls /construction/biology/py-cutadapt/stage/usr/local/lib/python2.7/site-packages/cutadapt-1.14-py2.7.egg-info | while read f; do echo lib/python2.7/site-packages/cutadapt-1.14-py2.7.egg-info/${f} >> /construction/biology/py-cutadapt/.PLIST.mktmp; done; fi; -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for py27-cutadapt-1.14 file sizes/checksums [52]: . done packing files [52]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Thursday, 30 AUG 2018 at 10:55:39 UTC Duration: 00:00:20