=> Building science/py-abipy@py37 Started : Thursday, 23 JAN 2020 at 15:31:30 UTC Platform: 5.7-DEVELOPMENT DragonFly v5.7.0.1284.g34ca1-DEVELOPMENT #20: Fri Jan 17 02:50:51 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-abipy XDG_CONFIG_HOME=/construction/science/py-abipy HOME=/construction/science/py-abipy TMPDIR="/tmp" PATH=/construction/science/py-abipy/.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-abipy XDG_CONFIG_HOME=/construction/science/py-abipy HOME=/construction/science/py-abipy TMPDIR="/tmp" PATH=/construction/science/py-abipy/.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-abipy/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/py37-abipy" EXAMPLESDIR="share/examples/py37-abipy" DATADIR="share/py37-abipy" WWWDIR="www/py37-abipy" ETCDIR="etc/py37-abipy" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/py37-abipy DOCSDIR=/usr/local/share/doc/py37-abipy EXAMPLESDIR=/usr/local/share/examples/py37-abipy WWWDIR=/usr/local/www/py37-abipy ETCDIR=/usr/local/etc/py37-abipy -------------------------------------------------- -- /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-abipy-0.7.0 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.12.0.txz Installing pkg-1.12.0... Extracting pkg-1.12.0: .......... done ===> py37-abipy-0.7.0 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py37-abipy-0.7.0 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> Fetching all distfiles required by py37-abipy-0.7.0 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> Fetching all distfiles required by py37-abipy-0.7.0 for building => SHA256 Checksum OK for abinit-abipy-0.7.0_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> Fetching all distfiles required by py37-abipy-0.7.0 for building ===> Extracting for py37-abipy-0.7.0 => SHA256 Checksum OK for abinit-abipy-0.7.0_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for py37-abipy-0.7.0 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> py37-abipy-0.7.0 depends on package: py37-numpy>0 - not found ===> Installing existing package /packages/All/py37-numpy-1.16.5_2,1.txz Installing py37-numpy-1.16.5_2,1... `-- Installing gcc8-8.3.0_3... | `-- Installing binutils-2.33.1_1,1... | | `-- 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_1,1: .......... 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-0.2.20_11,1... `-- Extracting openblas-0.2.20_11,1: .......... done `-- Installing py37-setuptools-41.4.0_1... | `-- 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-41.4.0_1: .......... done `-- Installing suitesparse-5.4.0_4... | `-- Installing metis-5.1.0_8... | `-- Extracting metis-5.1.0_8: .......... done | `-- Installing tbb-2020.0... | `-- Extracting tbb-2020.0: .......... done `-- Extracting suitesparse-5.4.0_4: .......... done Extracting py37-numpy-1.16.5_2,1: .......... 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-abipy-0.7.0 depends on package: py37-numpy>0 - found ===> Returning to build of py37-abipy-0.7.0 ===> py37-abipy-0.7.0 depends on package: py37-apscheduler>=2.1.0 - not found ===> Installing existing package /packages/All/py37-apscheduler-3.6.3.txz Installing py37-apscheduler-3.6.3... `-- Installing py37-pytz-2019.3,1... `-- Extracting py37-pytz-2019.3,1: .......... done `-- Installing py37-six-1.13.0... `-- Extracting py37-six-1.13.0: ....... done `-- Installing py37-tzlocal-1.5.1... `-- Extracting py37-tzlocal-1.5.1: .......... done Extracting py37-apscheduler-3.6.3: .......... done ===> py37-abipy-0.7.0 depends on package: py37-apscheduler>=2.1.0 - found ===> Returning to build of py37-abipy-0.7.0 ===> py37-abipy-0.7.0 depends on package: py37-html2text>0 - not found ===> Installing existing package /packages/All/py37-html2text-2018.1.9_2.txz Installing py37-html2text-2018.1.9_2... Extracting py37-html2text-2018.1.9_2: .......... done ===> py37-abipy-0.7.0 depends on package: py37-html2text>0 - found ===> Returning to build of py37-abipy-0.7.0 ===> py37-abipy-0.7.0 depends on package: py37-matplotlib>0 - not found ===> Installing existing package /packages/All/py37-matplotlib-2.2.4_1.txz Installing py37-matplotlib-2.2.4_1... `-- Installing fontconfig-2.12.6,1... | `-- Installing freetype2-2.10.1... | `-- Extracting freetype2-2.10.1: .......... done `-- Extracting fontconfig-2.12.6,1: .......... done Running fc-cache to build fontconfig cache... /usr/local/share/fonts: skipping, no such directory /usr/local/lib/X11/fonts: skipping, no such directory /var/db/fontconfig: cleaning cache directory fc-cache: succeeded `-- Installing png-1.6.37... `-- Extracting png-1.6.37: .......... done `-- Installing py37-cycler-0.10.0... `-- Extracting py37-cycler-0.10.0: ........ done `-- Installing py37-dateutil-2.8.0... `-- Extracting py37-dateutil-2.8.0: .......... done `-- Installing py37-kiwisolver-1.1.0... `-- Extracting py37-kiwisolver-1.1.0: ...... done `-- Installing py37-pyparsing-2.4.6... `-- Extracting py37-pyparsing-2.4.6: ....... done `-- Installing py37-tkinter-3.7.6_6... | `-- Installing tcl86-8.6.10... | `-- Extracting tcl86-8.6.10: .......... done | `-- Installing tk86-8.6.10_1... | | `-- Installing libX11-1.6.9,1... | | `-- Installing libXau-1.0.9... | | `-- Extracting libXau-1.0.9: .......... done | | `-- Installing libXdmcp-1.1.3... | | | `-- Installing xorgproto-2019.2... | | | `-- Extracting xorgproto-2019.2: .......... done | | `-- Extracting libXdmcp-1.1.3: ...... done | | `-- Installing libxcb-1.13.1... | | | `-- Installing libpthread-stubs-0.4... | | | `-- Extracting libpthread-stubs-0.4: . done | | | `-- Installing libxml2-2.9.10... | | | `-- Extracting libxml2-2.9.10: .......... done | | `-- Extracting libxcb-1.13.1: .......... done | | `-- Extracting libX11-1.6.9,1: .......... done | | `-- Installing libXScrnSaver-1.2.3_2... | | `-- Installing libXext-1.3.4,1... | | `-- Extracting libXext-1.3.4,1: .......... done | | `-- Extracting libXScrnSaver-1.2.3_2: .......... done | | `-- Installing libXft-2.3.3... | | `-- Installing libXrender-0.9.10_2... | | `-- Extracting libXrender-0.9.10_2: ....... done | | `-- Extracting libXft-2.3.3: ......... done | `-- Extracting tk86-8.6.10_1: .......... done `-- Extracting py37-tkinter-3.7.6_6: ..... done `-- Installing py37-tornado-5.1.1... `-- Extracting py37-tornado-5.1.1: .......... done Extracting py37-matplotlib-2.2.4_1: .......... done ===== Message from freetype2-2.10.1: -- The 2.7.x series now uses the new subpixel hinting mode (V40 port's option) as the default, emulating a modern version of ClearType. This change inevitably leads to different rendering results, and you might change port's options to adapt it to your taste (or use the new "FREETYPE_PROPERTIES" environment variable). The environment variable "FREETYPE_PROPERTIES" can be used to control the driver properties. Example: FREETYPE_PROPERTIES=truetype:interpreter-version=35 \ cff:no-stem-darkening=1 \ autofitter:warping=1 This allows to select, say, the subpixel hinting mode at runtime for a given application. If LONG_PCF_NAMES port's option was enabled, the PCF family names may include the foundry and information whether they contain wide characters. For example, "Sony Fixed" or "Misc Fixed Wide", instead of "Fixed". This can be disabled at run time with using pcf:no-long-family-names property, if needed. Example: FREETYPE_PROPERTIES=pcf:no-long-family-names=1 How to recreate fontconfig cache with using such environment variable, if needed: # env FREETYPE_PROPERTIES=pcf:no-long-family-names=1 fc-cache -fsv The controllable properties are listed in the section "Controlling FreeType Modules" in the reference's table of contents (/usr/local/share/doc/freetype2/reference/site/index.html, if documentation was installed). ===> py37-abipy-0.7.0 depends on package: py37-matplotlib>0 - found ===> Returning to build of py37-abipy-0.7.0 ===> py37-abipy-0.7.0 depends on package: py37-monty>0 - not found ===> Installing existing package /packages/All/py37-monty-3.0.2.txz Installing py37-monty-3.0.2... Extracting py37-monty-3.0.2: .......... done ===> py37-abipy-0.7.0 depends on package: py37-monty>0 - found ===> Returning to build of py37-abipy-0.7.0 ===> py37-abipy-0.7.0 depends on package: py37-netCDF4>0 - not found ===> Installing existing package /packages/All/py37-netCDF4-1.3.1_7.txz Installing py37-netCDF4-1.3.1_7... `-- Installing hdf5-1.10.6... | `-- Installing hdf-szip-2.1.1... | `-- Extracting hdf-szip-2.1.1: ....... done `-- Extracting hdf5-1.10.6: .......... done `-- Installing netcdf-4.7.3... | `-- Installing curl-7.68.0... | | `-- Installing ca_root_nss-3.49.1... | | `-- Extracting ca_root_nss-3.49.1: ..... done | | `-- Installing libnghttp2-1.40.0... | | `-- Extracting libnghttp2-1.40.0: ....... done | `-- Extracting curl-7.68.0: .......... done | `-- Installing pkgconf-1.6.3,1... | `-- Extracting pkgconf-1.6.3,1: .......... done `-- Extracting netcdf-4.7.3: .......... done `-- Installing py37-cython-0.29.13_1... `-- Extracting py37-cython-0.29.13_1: .......... done Extracting py37-netCDF4-1.3.1_7: .......... done ===== Message from ca_root_nss-3.49.1: -- FreeBSD does not, and can not warrant that the certification authorities whose certificates are included in this package have in any way been audited for trustworthiness or RFC 3647 compliance. Assessment and verification of trust is the complete responsibility of the system administrator. This package installs symlinks to support root certificates discovery by default for software that uses OpenSSL. This enables SSL Certificate Verification by client software without manual intervention. If you prefer to do this manually, replace the following symlinks with either an empty file or your site-local certificate bundle. * /etc/ssl/cert.pem * /usr/local/etc/ssl/cert.pem * /usr/local/openssl/cert.pem ===> py37-abipy-0.7.0 depends on package: py37-netCDF4>0 - found ===> Returning to build of py37-abipy-0.7.0 ===> py37-abipy-0.7.0 depends on package: py37-pandas>0 - not found ===> Installing existing package /packages/All/py37-pandas-0.24.2_1,1.txz Installing py37-pandas-0.24.2_1,1... `-- Installing py37-bottleneck-1.3.1... `-- Extracting py37-bottleneck-1.3.1: .......... done `-- Installing py37-numexpr-2.7.1... `-- Extracting py37-numexpr-2.7.1: .......... done `-- Installing py37-sqlite3-3.7.6_7... | `-- Installing sqlite3-3.30.1... | `-- Extracting sqlite3-3.30.1: ......... done `-- Extracting py37-sqlite3-3.7.6_7: ..... done Extracting py37-pandas-0.24.2_1,1: .......... done ===== Message from py37-pandas-0.24.2_1,1: -- Install math/py-statsmodels to enable parts of pandas.stats. Install devel/py-xarray to enable the to_xarray() function. ===> py37-abipy-0.7.0 depends on package: py37-pandas>0 - found ===> Returning to build of py37-abipy-0.7.0 ===> py37-abipy-0.7.0 depends on package: py37-pydispatcher>=2.0.5 - not found ===> Installing existing package /packages/All/py37-pydispatcher-2.0.5.txz Installing py37-pydispatcher-2.0.5... 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Extracting dejavu-2.37_1: .......... done | | | `-- Installing font-bh-ttf-1.0.3_4... | | | `-- Extracting font-bh-ttf-1.0.3_4: .......... done | | | `-- Installing font-misc-ethiopic-1.0.3_4... | | | `-- Extracting font-misc-ethiopic-1.0.3_4: ... done | | | `-- Installing font-misc-meltho-1.0.3_4... | | | `-- Extracting font-misc-meltho-1.0.3_4: .......... done | | `-- Extracting pango-1.42.4_3: .......... done | | `-- Extracting graphviz-2.42.2_3: .......... done | `-- Extracting py37-pygraphviz-1.5: .......... done | `-- Installing py37-scikit-sparse-0.4.4_3... | | `-- Installing py37-scipy-1.2.2_1... | | `-- Extracting py37-scipy-1.2.2_1: .......... done | `-- Extracting py37-scikit-sparse-0.4.4_3: .......... done | `-- Installing py37-yaml-5.2... | `-- Extracting py37-yaml-5.2: .......... done `-- Extracting py37-networkx-2.1,1: .......... done `-- Installing py37-palettable-3.3.0... `-- Extracting py37-palettable-3.3.0: .......... done `-- Installing py37-requests-2.22.0... | `-- Installing py37-certifi-2019.11.28... | `-- Extracting py37-certifi-2019.11.28: .......... done | `-- Installing py37-chardet-3.0.4_3... | `-- Extracting py37-chardet-3.0.4_3: .......... done | `-- Installing py37-idna-2.8... | `-- Extracting py37-idna-2.8: .......... done | `-- Installing py37-urllib3-1.25.6,1... | | `-- Installing py37-cryptography-2.6.1... | | `-- Installing py37-asn1crypto-0.24.0... | | `-- Extracting py37-asn1crypto-0.24.0: .......... done | | `-- Installing py37-cffi-1.13.2... | | | `-- Installing py37-pycparser-2.19... | | | `-- Extracting py37-pycparser-2.19: .......... done | | `-- Extracting py37-cffi-1.13.2: .......... done | | `-- Extracting py37-cryptography-2.6.1: .......... done | | `-- Installing py37-openssl-19.0.0... | | `-- Extracting py37-openssl-19.0.0: .......... done | | `-- Installing py37-pysocks-1.7.1... | | `-- Extracting py37-pysocks-1.7.1: .......... done | `-- Extracting py37-urllib3-1.25.6,1: .......... done `-- Extracting py37-requests-2.22.0: .......... done `-- Installing py37-ruamel.yaml-0.15.87... `-- Extracting py37-ruamel.yaml-0.15.87: .......... done `-- Installing py37-spglib-1.14.1... `-- Extracting py37-spglib-1.14.1: .......... done `-- Installing py37-sympy-1.5... | `-- Installing py37-mpmath-1.1.0... | `-- Extracting py37-mpmath-1.1.0: .......... done `-- Extracting py37-sympy-1.5: .......... done `-- Installing py37-tabulate-0.8.6... `-- Extracting py37-tabulate-0.8.6: .......... done Extracting py37-pymatgen-2019.2.28_1: .......... done ===== Message from dejavu-2.37_1: -- Make sure that the freetype module is loaded. If it is not, add the following line to the "Modules" section of your X Windows configuration file: Load "freetype" Add the following line to the "Files" section of X Windows configuration file: FontPath "/usr/local/share/fonts/dejavu/" Note: your X Windows configuration file is typically /etc/X11/XF86Config if you are using XFree86, and /etc/X11/xorg.conf if you are using X.Org. ===== Message from py37-urllib3-1.25.6,1: -- Since version 1.25 HTTPS connections are now verified by default which is done via "cert_reqs = 'CERT_REQUIRED'". While certificate verification can be disabled via "cert_reqs = 'CERT_NONE'", it's highly recommended to leave it on. Various consumers of net/py-urllib3 already have implemented routines that either explicitly enable or disable HTTPS certificate verification (e.g. via configuration settings, CLI arguments, etc.). Yet it may happen that there are still some consumers which don't explicitly enable/disable certificate verification for HTTPS connections which could then lead to errors (as is often the case with self-signed certificates). In case of an error one should try first to temporarily disable certificate verification of the problematic urllib3 consumer to see if that approach will remedy the issue. ===> py37-abipy-0.7.0 depends on package: py37-pymatgen>=2019.10.16 - not found *** Error code 1 Stop. make: stopped in /xports/science/py-abipy -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Thursday, 23 JAN 2020 at 15:35:00 UTC Duration: 00:03:29