=> Building science/py-molmod@py37 Started : Saturday, 15 FEB 2020 at 16:56:45 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-molmod XDG_CONFIG_HOME=/construction/science/py-molmod HOME=/construction/science/py-molmod TMPDIR="/tmp" PATH=/construction/science/py-molmod/.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-molmod XDG_CONFIG_HOME=/construction/science/py-molmod HOME=/construction/science/py-molmod TMPDIR="/tmp" PATH=/construction/science/py-molmod/.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-molmod/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/molmod" EXAMPLESDIR="share/examples/molmod" DATADIR="share/molmod" WWWDIR="www/molmod" ETCDIR="etc/molmod" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/molmod DOCSDIR=/usr/local/share/doc/molmod EXAMPLESDIR=/usr/local/share/examples/molmod WWWDIR=/usr/local/www/molmod ETCDIR=/usr/local/etc/molmod -------------------------------------------------- -- /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-molmod-1.4.5 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-molmod-1.4.5 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py37-molmod-1.4.5 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> Fetching all distfiles required by py37-molmod-1.4.5 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> Fetching all distfiles required by py37-molmod-1.4.5 for building => SHA256 Checksum OK for molmod-1.4.5.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> Fetching all distfiles required by py37-molmod-1.4.5 for building ===> Extracting for py37-molmod-1.4.5 => SHA256 Checksum OK for molmod-1.4.5.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for py37-molmod-1.4.5 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> py37-molmod-1.4.5 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-molmod-1.4.5 depends on package: py37-numpy>=1.15,1<1.19,1 - found ===> Returning to build of py37-molmod-1.4.5 ===> py37-molmod-1.4.5 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-molmod-1.4.5 depends on executable: cython-3.7 - found ===> Returning to build of py37-molmod-1.4.5 ===> py37-molmod-1.4.5 depends on package: py37-setuptools>0 - found ===> py37-molmod-1.4.5 depends on file: /usr/local/bin/python3.7 - found -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for py37-molmod-1.4.5 Trying to get the version from git describe Trying to get the version from {} molmod/version.py Version according to molmod/version.py: 1.4.5 running config -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for py37-molmod-1.4.5 Trying to get the version from git describe Trying to get the version from {} molmod/version.py Version according to molmod/version.py: 1.4.5 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/molmod copying molmod/molecular_graphs.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod copying molmod/clusters.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod copying molmod/toyff.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod copying molmod/units.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod copying molmod/binning.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod copying molmod/transformations.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod copying molmod/utils.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod copying molmod/periodic.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod copying molmod/zmatrix.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod copying molmod/symmetry.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod copying molmod/isotopes.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod copying molmod/unit_cells.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod copying molmod/ic.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod copying molmod/version.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod copying molmod/log.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod copying molmod/randomize.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod copying molmod/minimizer.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod copying molmod/constants.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod copying molmod/pairff.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod copying molmod/graphs.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod copying molmod/similarity.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod copying molmod/molecules.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod copying molmod/vectors.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod copying molmod/__init__.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod copying molmod/quaternions.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod copying molmod/bonds.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod creating build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test copying molmod/test/test_binning.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test copying molmod/test/test_minimizer.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test copying molmod/test/test_molecular_graphs.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test copying molmod/test/test_toyff.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test copying molmod/test/test_randomize.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test copying molmod/test/test_graphs.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test copying molmod/test/common.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test copying molmod/test/test_log.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test copying molmod/test/test_transformations.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test copying molmod/test/test_pairff.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test copying molmod/test/test_symmetry.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test copying molmod/test/test_units.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test copying molmod/test/test_vectors.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test copying molmod/test/test_quaternions.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test copying molmod/test/test_utils.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test copying molmod/test/test_examples.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test copying molmod/test/test_similarity.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test copying molmod/test/test_molecules.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test copying molmod/test/test_ic.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test copying molmod/test/test_clusters.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test copying molmod/test/__init__.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test copying molmod/test/test_zmatrix.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test copying molmod/test/test_data.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test copying molmod/test/test_unit_cells.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test creating build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io copying molmod/io/xyz.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io copying molmod/io/__init__.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io copying molmod/io/cube.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io copying molmod/io/psf.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io copying molmod/io/number_state.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io copying molmod/io/common.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io copying molmod/io/pdb.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io copying molmod/io/cml.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io copying molmod/io/cp2k.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io copying molmod/io/sdf.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io copying molmod/io/cpmd.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io copying molmod/io/atrj.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io copying molmod/io/dlpoly.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io copying molmod/io/fchk.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io copying molmod/io/gamess.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io copying molmod/io/crystal.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io copying molmod/io/gromacs.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io copying molmod/io/chk.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io copying molmod/io/lammps.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io creating build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/test copying molmod/io/test/test_gamess.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/test copying molmod/io/test/test_psf.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/test copying molmod/io/test/test_lammps.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/test copying molmod/io/test/test_dlpoly.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/test copying molmod/io/test/test_pdb.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/test copying molmod/io/test/test_cpmd.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/test copying molmod/io/test/test_crystal.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/test copying molmod/io/test/test_chk.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/test copying molmod/io/test/test_atrj.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/test copying molmod/io/test/__init__.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/test copying molmod/io/test/test_fchk.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/test copying molmod/io/test/test_cml.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/test copying molmod/io/test/test_number_state.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/test copying molmod/io/test/test_xyz.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/test copying molmod/io/test/test_cube.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/test copying molmod/io/test/test_sdf.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/test copying molmod/io/test/test_cp2k.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/test copying molmod/io/test/test_gromacs.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/test running egg_info writing molmod.egg-info/PKG-INFO writing dependency_links to molmod.egg-info/dependency_links.txt writing requirements to molmod.egg-info/requires.txt writing top-level names to molmod.egg-info/top_level.txt reading manifest file 'molmod.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files matching 'ext.c' found under directory 'molmod' writing manifest file 'molmod.egg-info/SOURCES.txt' copying molmod/common.c -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod copying molmod/common.h -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod copying molmod/ext.pyx -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod copying molmod/ff.c -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod copying molmod/ff.h -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod copying molmod/ff.pxd -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod copying molmod/graphs.c -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod copying molmod/graphs.h -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod copying molmod/graphs.pxd -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod copying molmod/molecules.c -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod copying molmod/molecules.h -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod copying molmod/molecules.pxd -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod copying molmod/similarity.c -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod copying molmod/similarity.h -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod copying molmod/similarity.pxd -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod copying molmod/unit_cells.c -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod copying molmod/unit_cells.h -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod copying molmod/unit_cells.pxd -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod creating build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data copying molmod/data/bonds.csv -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data copying molmod/data/bonds.ods -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data copying molmod/data/mass.mas03 -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data copying molmod/data/nubtab03.asc -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data copying molmod/data/periodic.csv -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data copying molmod/data/periodic.ods -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data copying molmod/data/toyff_angles.txt -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data creating build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/1LJL_Cys10.cml -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/1TOH.b3lyp.fchk -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/1TOH.b3lyp.trim.fchk -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/5ringOH.xyz -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/CID_22898828.sdf -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/PCGamess_PUNCH -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/SID_31646545.sdf -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/SID_31646548.sdf -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/SID_40363570.sdf -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/SID_40363571.sdf -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/SID_41893278.sdf -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/SID_41893280.sdf -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/SID_54258192.sdf -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/SID_55127927.sdf -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/SID_55488598.sdf -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/SID_56274343.sdf -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/TRAJECTORY_H2_CPMD -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/alanine.cube -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/argon.xyz -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/bartek.atrj -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/benzene.xyz -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/butane.xyz -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/caplayer.cml -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/crystal_api.out -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/cyclopentane.xyz -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/dinitrogen.xyz -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/dlpoly_HISTORY -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/dlpoly_HISTORY_an2 -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/dlpoly_OUTPUT -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/dopamine.xyz -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/ethane.xyz -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/ethene.xyz -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/ethene_ethyl_trans.xyz -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/example.sdf -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/formol.xyz -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/funny.xyz -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/h3zrosihohosioh3.xyz -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/il2.pdb -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/lammps_dump.txt -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/lau.xyz -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/octane.xyz -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/oh3siozroh3.xyz -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/opt_5ring10T.xyz -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/opt_5ring12T.xyz -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/opt_6_6ring.xyz -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/opt_6ring.xyz -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/osih2osihosih2osih2ozrh2oh.xyz -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/pentapeptide.psf -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/precursor.xyz -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/probes.xyz -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/tea.xyz -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/tetra.xyz -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/thf.psf -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/thf.xyz -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/thf_64.cell -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/thf_single.xyz -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/tpa.xyz -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/water.xyz -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/water2.gro -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/water_md.inp -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test copying molmod/data/test/zr4o8-3.xyz -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test creating build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples creating build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/000_units copying molmod/examples/000_units/a_reaction.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/000_units copying molmod/examples/000_units/b_chbond.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/000_units copying molmod/examples/000_units/c_h2rot.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/000_units creating build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/001_molecules copying molmod/examples/001_molecules/a_convert.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/001_molecules copying molmod/examples/001_molecules/b_com.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/001_molecules copying molmod/examples/001_molecules/c_carbon.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/001_molecules copying molmod/examples/001_molecules/d_size.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/001_molecules copying molmod/examples/001_molecules/e_shape.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/001_molecules copying molmod/examples/001_molecules/ibuprofen.sdf -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/001_molecules creating build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/002_graphs copying molmod/examples/002_graphs/a_graphs.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/002_graphs copying molmod/examples/002_graphs/b_neighbors.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/002_graphs copying molmod/examples/002_graphs/c_distances.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/002_graphs copying molmod/examples/002_graphs/caffeine.xyz -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/002_graphs copying molmod/examples/002_graphs/d_symmetries.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/002_graphs copying molmod/examples/002_graphs/ethanol.xyz -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/002_graphs creating build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/003_internal_coordinates copying molmod/examples/003_internal_coordinates/a_bond_length.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/003_internal_coordinates copying molmod/examples/003_internal_coordinates/b_bending_angles.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/003_internal_coordinates copying molmod/examples/003_internal_coordinates/c_ff_hessian.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/003_internal_coordinates copying molmod/examples/003_internal_coordinates/d_dft_hessian.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/003_internal_coordinates copying molmod/examples/003_internal_coordinates/dopamine.fchk -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/003_internal_coordinates copying molmod/examples/003_internal_coordinates/dopamine.xyz -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/003_internal_coordinates copying molmod/examples/003_internal_coordinates/propane.xyz -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/003_internal_coordinates creating build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/004_patterns copying molmod/examples/004_patterns/a_propane_types.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/004_patterns copying molmod/examples/004_patterns/b_dopamine_types.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/004_patterns copying molmod/examples/004_patterns/dopamine.xyz -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/004_patterns copying molmod/examples/004_patterns/mfi_fragment.xyz -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/004_patterns copying molmod/examples/004_patterns/propane.xyz -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/004_patterns running build_ext cythoning molmod/ext.pyx to molmod/ext.c building 'molmod.ext' extension creating build/temp.dragonfly-5.7-SYNTH-x86_64-3.7 creating build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/molmod 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/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include/python3.7m -c molmod/ext.c -o build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/ext.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 molmod/ext.c:598: /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 " \ ^~~~~~~ molmod/ext.c: In function '__pyx_pf_6molmod_3ext_ff_dm_quad': molmod/ext.c:2929:40: warning: comparison of integer expressions of different signedness: 'Py_ssize_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] __pyx_t_3 = (((__pyx_v_dm0.shape[0]) != __pyx_v_natom) != 0); ^~ molmod/ext.c:2935:40: warning: comparison of integer expressions of different signedness: 'Py_ssize_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] __pyx_t_3 = (((__pyx_v_dm0.shape[1]) != __pyx_v_natom) != 0); ^~ molmod/ext.c:2969:40: warning: comparison of integer expressions of different signedness: 'Py_ssize_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] __pyx_t_3 = (((__pyx_v_dmk.shape[0]) != __pyx_v_natom) != 0); ^~ molmod/ext.c:2975:40: warning: comparison of integer expressions of different signedness: 'Py_ssize_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] __pyx_t_3 = (((__pyx_v_dmk.shape[1]) != __pyx_v_natom) != 0); ^~ molmod/ext.c: In function '__pyx_pf_6molmod_3ext_2ff_dm_reci': molmod/ext.c:3686:42: warning: comparison of integer expressions of different signedness: 'Py_ssize_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] __pyx_t_1 = (((__pyx_v_radii.shape[0]) != __pyx_v_natom) != 0); ^~ molmod/ext.c:3718:40: warning: comparison of integer expressions of different signedness: 'Py_ssize_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] __pyx_t_3 = (((__pyx_v_dm0.shape[0]) != __pyx_v_natom) != 0); ^~ molmod/ext.c:3724:40: warning: comparison of integer expressions of different signedness: 'Py_ssize_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] __pyx_t_3 = (((__pyx_v_dm0.shape[1]) != __pyx_v_natom) != 0); ^~ molmod/ext.c: In function '__pyx_pf_6molmod_3ext_4ff_bond_quad': molmod/ext.c:4591:44: warning: comparison of integer expressions of different signedness: 'Py_ssize_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] __pyx_t_1 = (((__pyx_v_lengths.shape[0]) != __pyx_v_npair) != 0); ^~ molmod/ext.c: In function '__pyx_pf_6molmod_3ext_6ff_bond_hyper': molmod/ext.c:5336:44: warning: comparison of integer expressions of different signedness: 'Py_ssize_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] __pyx_t_1 = (((__pyx_v_lengths.shape[0]) != __pyx_v_npair) != 0); ^~ molmod/ext.c: In function '__pyx_pf_6molmod_3ext_8graphs_floyd_warshall': molmod/ext.c:5861:39: warning: comparison of integer expressions of different signedness: 'Py_ssize_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] __pyx_t_1 = (((__pyx_v_dm.shape[1]) != __pyx_v_nvertex) != 0); ^~ molmod/ext.c: In function '__pyx_pf_6molmod_3ext_12similarity_table_labels': molmod/ext.c:6695:39: warning: passing argument 2 of 'similarity_table_labels' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] similarity_table_labels(__pyx_v_n, (&(*((long const *) ( /* dim=0 */ ((char *) (((long const *) __pyx_v_labels.data) + __pyx_t_6)) )))), (&(*__Pyx_BufPtrStrided2d(long *, __pyx_pybuffernd_labels_table.rcbuffer->pybuffer.buf, __pyx_t_8, __pyx_pybuffernd_labels_table.diminfo[0].strides, __pyx_t_9, __pyx_pybuffernd_labels_table.diminfo[1].strides)))); ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from molmod/ext.c:603: molmod/similarity.h:30:46: note: expected 'long int *' but argument is of type 'const long int *' void similarity_table_labels(size_t n, long *labels, long* labels_table); ~~~~~~^~~~~~ molmod/ext.c: In function '__pyx_pf_6molmod_3ext_14similarity_table_distances': molmod/ext.c:6820:52: warning: comparison of integer expressions of different signedness: 'Py_ssize_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] __pyx_t_1 = (((__pyx_v_distance_matrix.shape[1]) != __pyx_v_n) != 0); ^~ molmod/ext.c:6918:42: warning: passing argument 2 of 'similarity_table_distances' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] similarity_table_distances(__pyx_v_n, (&(*((double const *) ( /* dim=1 */ ((char *) (((double const *) ( /* dim=0 */ (__pyx_v_distance_matrix.data + __pyx_t_7 * __pyx_v_distance_matrix.strides[0]) )) + __pyx_t_8)) )))), (&(*__Pyx_BufPtrStrided1d(double *, __pyx_pybuffernd_distances_table.rcbuffer->pybuffer.buf, __pyx_t_10, __pyx_pybuffernd_distances_table.diminfo[0].strides)))); ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from molmod/ext.c:603: molmod/similarity.h:31:51: note: expected 'double *' but argument is of type 'const double *' void similarity_table_distances(size_t n, double *distance_matrix, double *distances_table); ~~~~~~~~^~~~~~~~~~~~~~~ molmod/ext.c: In function '__pyx_pf_6molmod_3ext_16similarity_measure': molmod/ext.c:7168:47: warning: comparison of integer expressions of different signedness: 'Py_ssize_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] __pyx_t_1 = (((__pyx_v_distances1.shape[0]) != __pyx_v_n1) != 0); ^~ molmod/ext.c:7232:47: warning: comparison of integer expressions of different signedness: 'Py_ssize_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] __pyx_t_1 = (((__pyx_v_distances2.shape[0]) != __pyx_v_n2) != 0); ^~ 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/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include/python3.7m -c molmod/common.c -o build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/common.o 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/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include/python3.7m -c molmod/ff.c -o build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/ff.o 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/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include/python3.7m -c molmod/graphs.c -o build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/graphs.o 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/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include/python3.7m -c molmod/similarity.c -o build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/similarity.o molmod/similarity.c:29: warning: "M_PI" redefined #define M_PI 3.14159265358979323846 In file included from molmod/similarity.c:26: /usr/include/math.h:137: note: this is the location of the previous definition #define M_PI ((double)3.14159265358979323846) /* pi */ 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/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include/python3.7m -c molmod/molecules.c -o build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/molecules.o 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/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include/python3.7m -c molmod/unit_cells.c -o build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/unit_cells.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/ext.o build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/common.o build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/ff.o build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/graphs.o build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/similarity.o build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/molecules.o build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/unit_cells.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/ext.so /usr/local/lib/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /construction/science/py-molmod/molmod-1.4.5/molmod/ext.pyx tree = Parsing.p_module(s, pxd, full_module_name) -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> py37-molmod-1.4.5 depends on package: py37-numpy>=1.15,1<1.19,1 - found ===> py37-molmod-1.4.5 depends on package: py37-future>0 - not found ===> Installing existing package /packages/All/py37-future-0.18.2.txz Installing py37-future-0.18.2... Extracting py37-future-0.18.2: .......... done ===> py37-molmod-1.4.5 depends on package: py37-future>0 - found ===> Returning to build of py37-molmod-1.4.5 ===> py37-molmod-1.4.5 depends on executable: cython-3.7 - found ===> py37-molmod-1.4.5 depends on package: py37-setuptools>0 - found ===> py37-molmod-1.4.5 depends on file: /usr/local/bin/python3.7 - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for py37-molmod-1.4.5 ===> Generating temporary packing list Trying to get the version from git describe Trying to get the version from {} molmod/version.py Version according to molmod/version.py: 1.4.5 running install running build running build_py running egg_info writing molmod.egg-info/PKG-INFO writing dependency_links to molmod.egg-info/dependency_links.txt writing requirements to molmod.egg-info/requires.txt writing top-level names to molmod.egg-info/top_level.txt reading manifest file 'molmod.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'molmod.egg-info/SOURCES.txt' running build_ext skipping 'molmod/ext.c' Cython extension (up-to-date) running install_lib creating /construction/science/py-molmod/stage/usr/local/lib/python3.7 creating /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages creating /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/molecular_graphs.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/clusters.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/toyff.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/units.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/binning.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/transformations.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/utils.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/periodic.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/zmatrix.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/symmetry.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/isotopes.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/unit_cells.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/ic.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/version.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/log.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/randomize.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/minimizer.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/constants.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/pairff.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/graphs.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/similarity.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/molecules.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/vectors.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/__init__.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/quaternions.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/bonds.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod creating /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test/test_binning.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test/test_minimizer.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test/test_molecular_graphs.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test/test_toyff.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test/test_randomize.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test/test_graphs.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test/common.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test/test_log.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test/test_transformations.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test/test_pairff.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test/test_symmetry.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test/test_units.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test/test_vectors.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test/test_quaternions.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test/test_utils.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test/test_examples.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test/test_similarity.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test/test_molecules.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test/test_ic.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test/test_clusters.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test/__init__.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test/test_zmatrix.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test/test_data.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/test/test_unit_cells.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test creating /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/xyz.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/__init__.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/cube.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/psf.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/number_state.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/common.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/pdb.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/cml.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/cp2k.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/sdf.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/cpmd.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/atrj.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/dlpoly.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/fchk.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/gamess.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/crystal.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/gromacs.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/chk.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/lammps.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io creating /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/test/test_gamess.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/test/test_psf.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/test/test_lammps.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/test/test_dlpoly.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/test/test_pdb.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/test/test_cpmd.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/test/test_crystal.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/test/test_chk.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/test/test_atrj.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/test/__init__.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/test/test_fchk.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/test/test_cml.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/test/test_number_state.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/test/test_xyz.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/test/test_cube.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/test/test_sdf.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/test/test_cp2k.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/io/test/test_gromacs.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/common.c -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/common.h -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/ext.pyx -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/ff.c -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/ff.h -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/ff.pxd -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/graphs.c -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/graphs.h -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/graphs.pxd -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/molecules.c -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/molecules.h -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/molecules.pxd -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/similarity.c -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/similarity.h -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/similarity.pxd -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/unit_cells.c -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/unit_cells.h -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/unit_cells.pxd -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod creating /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/bonds.csv -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/bonds.ods -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/mass.mas03 -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/nubtab03.asc -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/periodic.csv -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/periodic.ods -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/toyff_angles.txt -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data creating /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/1LJL_Cys10.cml -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/1TOH.b3lyp.fchk -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/1TOH.b3lyp.trim.fchk -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/5ringOH.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/CID_22898828.sdf -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/PCGamess_PUNCH -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/SID_31646545.sdf -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/SID_31646548.sdf -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/SID_40363570.sdf -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/SID_40363571.sdf -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/SID_41893278.sdf -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/SID_41893280.sdf -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/SID_54258192.sdf -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/SID_55127927.sdf -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/SID_55488598.sdf -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/SID_56274343.sdf -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/TRAJECTORY_H2_CPMD -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/alanine.cube -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/argon.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/bartek.atrj -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/benzene.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/butane.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/caplayer.cml -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/crystal_api.out -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/cyclopentane.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/dinitrogen.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/dlpoly_HISTORY -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/dlpoly_HISTORY_an2 -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/dlpoly_OUTPUT -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/dopamine.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/ethane.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/ethene.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/ethene_ethyl_trans.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/example.sdf -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/formol.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/funny.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/h3zrosihohosioh3.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/il2.pdb -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/lammps_dump.txt -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/lau.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/octane.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/oh3siozroh3.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/opt_5ring10T.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/opt_5ring12T.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/opt_6_6ring.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/opt_6ring.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/osih2osihosih2osih2ozrh2oh.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/pentapeptide.psf -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/precursor.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/probes.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/tea.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/tetra.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/thf.psf -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/thf.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/thf_64.cell -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/thf_single.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/tpa.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/water.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/water2.gro -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/water_md.inp -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/data/test/zr4o8-3.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/data/test creating /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples creating /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/000_units copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/000_units/a_reaction.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/000_units copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/000_units/b_chbond.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/000_units copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/000_units/c_h2rot.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/000_units creating /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/001_molecules copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/001_molecules/a_convert.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/001_molecules copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/001_molecules/b_com.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/001_molecules copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/001_molecules/c_carbon.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/001_molecules copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/001_molecules/d_size.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/001_molecules copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/001_molecules/e_shape.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/001_molecules copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/001_molecules/ibuprofen.sdf -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/001_molecules creating /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/002_graphs copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/002_graphs/a_graphs.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/002_graphs copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/002_graphs/b_neighbors.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/002_graphs copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/002_graphs/c_distances.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/002_graphs copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/002_graphs/caffeine.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/002_graphs copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/002_graphs/d_symmetries.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/002_graphs copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/002_graphs/ethanol.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/002_graphs creating /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/003_internal_coordinates copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/003_internal_coordinates/a_bond_length.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/003_internal_coordinates copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/003_internal_coordinates/b_bending_angles.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/003_internal_coordinates copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/003_internal_coordinates/c_ff_hessian.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/003_internal_coordinates copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/003_internal_coordinates/d_dft_hessian.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/003_internal_coordinates copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/003_internal_coordinates/dopamine.fchk -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/003_internal_coordinates copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/003_internal_coordinates/dopamine.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/003_internal_coordinates copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/003_internal_coordinates/propane.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/003_internal_coordinates creating /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/004_patterns copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/004_patterns/a_propane_types.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/004_patterns copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/004_patterns/b_dopamine_types.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/004_patterns copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/004_patterns/dopamine.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/004_patterns copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/004_patterns/mfi_fragment.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/004_patterns copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/examples/004_patterns/propane.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/004_patterns copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/molmod/ext.so -> /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/molecular_graphs.py to molecular_graphs.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/clusters.py to clusters.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/toyff.py to toyff.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/units.py to units.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/binning.py to binning.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/transformations.py to transformations.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/utils.py to utils.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/periodic.py to periodic.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/zmatrix.py to zmatrix.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/symmetry.py to symmetry.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/isotopes.py to isotopes.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/unit_cells.py to unit_cells.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/ic.py to ic.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/version.py to version.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/log.py to log.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/randomize.py to randomize.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/minimizer.py to minimizer.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/constants.py to constants.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/pairff.py to pairff.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/graphs.py to graphs.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/similarity.py to similarity.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/molecules.py to molecules.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/vectors.py to vectors.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/quaternions.py to quaternions.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/bonds.py to bonds.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test/test_binning.py to test_binning.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test/test_minimizer.py to test_minimizer.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test/test_molecular_graphs.py to test_molecular_graphs.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test/test_toyff.py to test_toyff.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test/test_randomize.py to test_randomize.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test/test_graphs.py to test_graphs.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test/common.py to common.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test/test_log.py to test_log.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test/test_transformations.py to test_transformations.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test/test_pairff.py to test_pairff.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test/test_symmetry.py to test_symmetry.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test/test_units.py to test_units.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test/test_vectors.py to test_vectors.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test/test_quaternions.py to test_quaternions.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test/test_utils.py to test_utils.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test/test_examples.py to test_examples.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test/test_similarity.py to test_similarity.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test/test_molecules.py to test_molecules.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test/test_ic.py to test_ic.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test/test_clusters.py to test_clusters.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test/test_zmatrix.py to test_zmatrix.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test/test_data.py to test_data.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/test/test_unit_cells.py to test_unit_cells.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/xyz.py to xyz.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/cube.py to cube.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/psf.py to psf.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/number_state.py to number_state.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/common.py to common.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/pdb.py to pdb.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/cml.py to cml.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/cp2k.py to cp2k.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/sdf.py to sdf.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/cpmd.py to cpmd.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/atrj.py to atrj.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/dlpoly.py to dlpoly.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/fchk.py to fchk.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/gamess.py to gamess.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/crystal.py to crystal.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/gromacs.py to gromacs.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/chk.py to chk.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/lammps.py to lammps.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/test/test_gamess.py to test_gamess.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/test/test_psf.py to test_psf.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/test/test_lammps.py to test_lammps.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/test/test_dlpoly.py to test_dlpoly.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/test/test_pdb.py to test_pdb.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/test/test_cpmd.py to test_cpmd.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/test/test_crystal.py to test_crystal.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/test/test_chk.py to test_chk.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/test/test_atrj.py to test_atrj.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/test/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/test/test_fchk.py to test_fchk.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/test/test_cml.py to test_cml.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/test/test_number_state.py to test_number_state.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/test/test_xyz.py to test_xyz.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/test/test_cube.py to test_cube.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/test/test_sdf.py to test_sdf.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/test/test_cp2k.py to test_cp2k.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/io/test/test_gromacs.py to test_gromacs.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/000_units/a_reaction.py to a_reaction.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/000_units/b_chbond.py to b_chbond.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/000_units/c_h2rot.py to c_h2rot.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/001_molecules/a_convert.py to a_convert.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/001_molecules/b_com.py to b_com.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/001_molecules/c_carbon.py to c_carbon.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/001_molecules/d_size.py to d_size.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/001_molecules/e_shape.py to e_shape.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/002_graphs/a_graphs.py to a_graphs.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/002_graphs/b_neighbors.py to b_neighbors.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/002_graphs/c_distances.py to c_distances.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/002_graphs/d_symmetries.py to d_symmetries.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/003_internal_coordinates/a_bond_length.py to a_bond_length.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/003_internal_coordinates/b_bending_angles.py to b_bending_angles.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/003_internal_coordinates/c_ff_hessian.py to c_ff_hessian.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/003_internal_coordinates/d_dft_hessian.py to d_dft_hessian.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/004_patterns/a_propane_types.py to a_propane_types.cpython-37.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod/examples/004_patterns/b_dopamine_types.py to b_dopamine_types.cpython-37.pyc writing byte-compilation script '/tmp/tmp9zwdkztz.py' /usr/local/bin/python3.7 /tmp/tmp9zwdkztz.py removing /tmp/tmp9zwdkztz.py running install_egg_info Copying molmod.egg-info to /construction/science/py-molmod/stage/usr/local/lib/python3.7/site-packages/molmod-1.4.5-py3.7.egg-info running install_scripts writing list of installed files to '/construction/science/py-molmod/.PLIST.pymodtmp' ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Error: /usr/local/lib/python3.7/site-packages/molmod/ext.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-molmod-1.4.5 file sizes/checksums [417]: ..... done packing files [417]: ..... done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Saturday, 15 FEB 2020 at 16:57:54 UTC Duration: 00:01:09