=> Building science/py-gsd@py37 Started : Saturday, 15 FEB 2020 at 09:08:08 UTC Platform: 5.7-DEVELOPMENT DragonFly v5.7.0.1432.g9cd86-DEVELOPMENT #23: Thu Feb 13 14:43:04 PST 2020 root@sting.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.7-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.7-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/python3.7" XDG_DATA_HOME=/construction/science/py-gsd XDG_CONFIG_HOME=/construction/science/py-gsd HOME=/construction/science/py-gsd TMPDIR="/tmp" PATH=/construction/science/py-gsd/.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/science/py-gsd XDG_CONFIG_HOME=/construction/science/py-gsd HOME=/construction/science/py-gsd TMPDIR="/tmp" PATH=/construction/science/py-gsd/.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 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/science/py-gsd/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PYTHON_INCLUDEDIR=include/python3.7m PYTHON_LIBDIR=lib/python3.7 PYTHON_PLATFORM=dragonfly5 PYTHON_SITELIBDIR=lib/python3.7/site-packages PYTHON_SUFFIX=37 PYTHON_VER=3.7 PYTHON_VERSION=python3.7 PYTHON2="@comment " PYTHON3="" OSREL=5.7 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/gsd" EXAMPLESDIR="share/examples/gsd" DATADIR="share/gsd" WWWDIR="www/gsd" ETCDIR="etc/gsd" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/gsd DOCSDIR=/usr/local/share/doc/gsd EXAMPLESDIR=/usr/local/share/examples/gsd WWWDIR=/usr/local/www/gsd ETCDIR=/usr/local/etc/gsd -------------------------------------------------- -- /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=15 DPORTS_BUILDER= yes DISABLE_LICENSES= yes DEFAULT_VERSIONS= ssl=openssl FORCE_PACKAGE= yes DEVELOPER= yes HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _PERL5_FROM_BIN=5.30.1 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=32 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500709 OSVERSION=9999999 OSREL=5.7 _OSRELEASE=5.7-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> py37-gsd-1.10.0 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.12.0_1.txz Installing pkg-1.12.0_1... Extracting pkg-1.12.0_1: .......... done ===> py37-gsd-1.10.0 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py37-gsd-1.10.0 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- => gsd-v1.10.0.tar.gz doesn't seem to exist in /distfiles/. => Attempting to fetch http://glotzerlab.engin.umich.edu/Downloads/gsd/gsd-v1.10.0.tar.gz gsd-v1.10.0.tar.gz 84 kB 490 kBps 00s ===> Fetching all distfiles required by py37-gsd-1.10.0 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> Fetching all distfiles required by py37-gsd-1.10.0 for building => SHA256 Checksum OK for gsd-v1.10.0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> Fetching all distfiles required by py37-gsd-1.10.0 for building ===> Extracting for py37-gsd-1.10.0 => SHA256 Checksum OK for gsd-v1.10.0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for py37-gsd-1.10.0 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> py37-gsd-1.10.0 depends on package: py37-numpy>=1.15,1<1.19,1 - not found ===> Installing existing package /packages/All/py37-numpy-1.16.5_4,1.txz Installing py37-numpy-1.16.5_4,1... `-- Installing gcc8-8.3.0_3... | `-- Installing binutils-2.33.1_2,1... | | `-- 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 binutils-2.33.1_2,1: .......... done | `-- Installing gmp-6.1.2_1... | `-- Extracting gmp-6.1.2_1: .......... done | `-- Installing mpc-1.1.0_2... | | `-- Installing mpfr-4.0.2... | | `-- Extracting mpfr-4.0.2: .......... done | `-- Extracting mpc-1.1.0_2: ...... done `-- Extracting gcc8-8.3.0_3: .......... done `-- Installing openblas-0.3.7_2,1... `-- Extracting openblas-0.3.7_2,1: .......... done `-- Installing py37-setuptools-44.0.0... | `-- Installing python37-3.7.6... | | `-- Installing expat-2.2.8... | | `-- Extracting expat-2.2.8: .......... done | | `-- Installing libffi-3.2.1_3... | | `-- Extracting libffi-3.2.1_3: .......... done | | `-- Installing ncurses-6.1.20190525... | | `-- Extracting ncurses-6.1.20190525: .......... done | | `-- Installing openssl-1.1.1d,1... | | `-- Extracting openssl-1.1.1d,1: .......... done | | `-- Installing readline-8.0.1... | | `-- Extracting readline-8.0.1: .......... done | `-- Extracting python37-3.7.6: .......... done `-- Extracting py37-setuptools-44.0.0: .......... done `-- Installing suitesparse-5.4.0_5... | `-- Installing metis-5.1.0_8... | `-- Extracting metis-5.1.0_8: .......... done | `-- Installing tbb-2020.1... | `-- Extracting tbb-2020.1: .......... done `-- Extracting suitesparse-5.4.0_5: .......... done Extracting py37-numpy-1.16.5_4,1: .......... done ===== Message from gcc8-8.3.0_3: -- 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. ===== Message from python37-3.7.6: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py37-gdbm databases/py-gdbm@py37 py37-sqlite3 databases/py-sqlite3@py37 py37-tkinter x11-toolkits/py-tkinter@py37 ===> py37-gsd-1.10.0 depends on package: py37-numpy>=1.15,1<1.19,1 - found ===> Returning to build of py37-gsd-1.10.0 ===> py37-gsd-1.10.0 depends on executable: cython-3.7 - not found ===> Installing existing package /packages/All/py37-cython-0.29.13_1.txz Installing py37-cython-0.29.13_1... Extracting py37-cython-0.29.13_1: .......... done ===> py37-gsd-1.10.0 depends on executable: cython-3.7 - found ===> Returning to build of py37-gsd-1.10.0 ===> py37-gsd-1.10.0 depends on package: py37-setuptools>0 - found ===> py37-gsd-1.10.0 depends on file: /usr/local/bin/python3.7 - found -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for py37-gsd-1.10.0 Compiling gsd/fl.pyx because it changed. [1/1] Cythonizing gsd/fl.pyx running config -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for py37-gsd-1.10.0 running build running build_py creating build creating build/lib.dragonfly-5.7-SYNTH-x86_64-3.7 creating build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/gsd copying gsd/hoomd.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/gsd copying gsd/pygsd.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/gsd copying gsd/__init__.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/gsd running build_ext building 'gsd.fl' extension creating build/temp.dragonfly-5.7-SYNTH-x86_64-3.7 creating build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/gsd cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I./gsd -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include/python3.7m -c gsd/fl.c -o build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/gsd/fl.o In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from gsd/fl.c:623: /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I./gsd -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include/python3.7m -c gsd/gsd.c -o build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/gsd/gsd.o gsd/gsd.c: In function '__gsd_expand_index': gsd/gsd.c:161:50: warning: comparison of integer expressions of different signedness: 'ssize_t' {aka 'long int'} and 'long unsigned int' [-Wsign-compare] if (bytes_written == -1 || bytes_written != sizeof(struct gsd_index_entry) * handle->header.index_allocated_entries) ^~ gsd/gsd.c:189:48: warning: comparison of integer expressions of different signedness: 'ssize_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] if (bytes_read == -1 || bytes_read != bytes_to_copy) ^~ gsd/gsd.c:197:54: warning: comparison of integer expressions of different signedness: 'ssize_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] if (bytes_written == -1 || bytes_written != bytes_to_copy) ^~ gsd/gsd.c:216:54: warning: comparison of integer expressions of different signedness: 'ssize_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] if (bytes_written == -1 || bytes_written != bytes_to_copy) ^~ gsd/gsd.c: In function '__is_entry_valid': gsd/gsd.c:375:33: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int64_t' {aka 'long int'} [-Wsign-compare] if ((entry.location + size) > handle->file_size) ^ gsd/gsd.c: In function '__gsd_read_header': gsd/gsd.c:457:117: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int64_t' {aka 'long int'} [-Wsign-compare] if (handle->header.index_location + sizeof(struct gsd_index_entry) * handle->header.index_allocated_entries > handle->file_size) ^ gsd/gsd.c:470:44: warning: comparison of integer expressions of different signedness: 'ssize_t' {aka 'long int'} and 'long unsigned int' [-Wsign-compare] if (bytes_read == -1 || bytes_read != sizeof(struct gsd_index_entry) * handle->header.index_allocated_entries) ^~ gsd/gsd.c:496:122: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int64_t' {aka 'long int'} [-Wsign-compare] if (handle->header.namelist_location + sizeof(struct gsd_namelist_entry) * handle->header.namelist_allocated_entries > handle->file_size) ^ gsd/gsd.c:509:40: warning: comparison of integer expressions of different signedness: 'ssize_t' {aka 'long int'} and 'long unsigned int' [-Wsign-compare] if (bytes_read == -1 || bytes_read != sizeof(struct gsd_namelist_entry) * handle->header.namelist_allocated_entries) ^~ gsd/gsd.c: In function 'gsd_end_frame': gsd/gsd.c:915:50: warning: comparison of integer expressions of different signedness: 'ssize_t' {aka 'long int'} and 'long unsigned int' [-Wsign-compare] if (bytes_written == -1 || bytes_written != sizeof(struct gsd_index_entry)*entries_to_write) ^~ gsd/gsd.c: In function 'gsd_write_chunk': gsd/gsd.c:982:46: warning: comparison of integer expressions of different signedness: 'ssize_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] if (bytes_written == -1 || bytes_written != size) ^~ gsd/gsd.c: In function 'gsd_read_chunk': gsd/gsd.c:1115:34: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int64_t' {aka 'long int'} [-Wsign-compare] if ((chunk->location + size) > handle->file_size) ^ gsd/gsd.c:1121:40: warning: comparison of integer expressions of different signedness: 'ssize_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] if (bytes_read == -1 || bytes_read != size) ^~ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/gsd/fl.o build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/gsd/gsd.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/gsd/fl.so -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> py37-gsd-1.10.0 depends on package: py37-numpy>=1.15,1<1.19,1 - found ===> py37-gsd-1.10.0 depends on package: py37-setuptools>0 - found ===> py37-gsd-1.10.0 depends on file: /usr/local/bin/python3.7 - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for py37-gsd-1.10.0 ===> Generating temporary packing list running install running build running build_py running build_ext running install_lib creating /construction/science/py-gsd/stage/usr/local/lib/python3.7 creating /construction/science/py-gsd/stage/usr/local/lib/python3.7/site-packages creating /construction/science/py-gsd/stage/usr/local/lib/python3.7/site-packages/gsd copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/gsd/fl.so -> /construction/science/py-gsd/stage/usr/local/lib/python3.7/site-packages/gsd copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/gsd/__init__.py -> /construction/science/py-gsd/stage/usr/local/lib/python3.7/site-packages/gsd copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/gsd/pygsd.py -> /construction/science/py-gsd/stage/usr/local/lib/python3.7/site-packages/gsd copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/gsd/hoomd.py -> /construction/science/py-gsd/stage/usr/local/lib/python3.7/site-packages/gsd byte-compiling /construction/science/py-gsd/stage/usr/local/lib/python3.7/site-packages/gsd/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/science/py-gsd/stage/usr/local/lib/python3.7/site-packages/gsd/pygsd.py to pygsd.cpython-37.pyc byte-compiling /construction/science/py-gsd/stage/usr/local/lib/python3.7/site-packages/gsd/hoomd.py to hoomd.cpython-37.pyc writing byte-compilation script '/tmp/tmp5ocp6gvr.py' /usr/local/bin/python3.7 /tmp/tmp5ocp6gvr.py removing /tmp/tmp5ocp6gvr.py running install_egg_info running egg_info creating gsd.egg-info writing gsd.egg-info/PKG-INFO writing dependency_links to gsd.egg-info/dependency_links.txt writing requirements to gsd.egg-info/requires.txt writing top-level names to gsd.egg-info/top_level.txt writing manifest file 'gsd.egg-info/SOURCES.txt' reading manifest file 'gsd.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'ChangeLog.md' writing manifest file 'gsd.egg-info/SOURCES.txt' Copying gsd.egg-info to /construction/science/py-gsd/stage/usr/local/lib/python3.7/site-packages/gsd-1.10.0-py3.7.egg-info running install_scripts writing list of installed files to '/construction/science/py-gsd/.PLIST.pymodtmp' ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Error: /usr/local/lib/python3.7/site-packages/gsd/fl.so is linked to /usr/local/lib/libintl.so.8 from devel/gettext-runtime but it is not declared as a dependency Warning: you need USES+=gettext-runtime Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for py37-gsd-1.10.0 file sizes/checksums [15]: . done packing files [15]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Saturday, 15 FEB 2020 at 09:09:20 UTC Duration: 00:01:11