------------------------------------------------------------------------------- -- Phase: Environment ------------------------------------------------------------------------------- NO_DEPENDS=1 FLAVOR=py39 UNAME_r=6.5 UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=unknown UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 LANG=C HOME=/root USER=root TERM=dumb SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: showconfig ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ENV ------------------------------------------------------------------------------- PYTHON="/usr/local/bin/python3.9" XDG_DATA_HOME=/construction/science/py-molmod XDG_CONFIG_HOME=/construction/science/py-molmod XDG_CACHE_HOME=/construction/science/py-molmod/.cache 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 PKG_CONFIG_LIBDIR=/construction/science/py-molmod/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ARGS ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ENV ------------------------------------------------------------------------------- XDG_DATA_HOME=/construction/science/py-molmod XDG_CONFIG_HOME=/construction/science/py-molmod XDG_CACHE_HOME=/construction/science/py-molmod/.cache 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 PKG_CONFIG_LIBDIR=/construction/science/py-molmod/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig 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" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ARGS ------------------------------------------------------------------------------- DESTDIR=/construction/science/py-molmod/stage SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: PLIST_SUB ------------------------------------------------------------------------------- PYTHON_INCLUDEDIR=include/python3.9 PYTHON_LIBDIR=lib/python3.9 PYTHON_PLATFORM=dragonfly6 PYTHON_SITELIBDIR=lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" OSREL=6.5 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" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: SUB_LIST ------------------------------------------------------------------------------- PYTHON_INCLUDEDIR=/usr/local/include/python3.9 PYTHON_LIBDIR=/usr/local/lib/python3.9 PYTHON_PLATFORM=dragonfly6 PYTHON_SITELIBDIR=/usr/local/lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" 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 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: /etc/make.conf ------------------------------------------------------------------------------- DPORTS_BUILDER=yes DISABLE_LICENSES=yes DEFAULT_VERSIONS=ssl=openssl FORCE_PACKAGE=yes DEVELOPER=yes DFLY_STING_XFAIL=yes USE_PACKAGE_DEPENDS_ONLY=yes PORTSDIR=/xports PORT_DBDIR=/options PKG_DBDIR=/var/db/pkg PKG_CACHEDIR=/var/cache/pkg PKG_COMPRESSION_FORMAT=.tgz DEVELOPER=1 WITH_CCACHE_BUILD=yes CCACHE_DIR=/ccache UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=600503 OSVERSION=9999999 OSREL=6.5 _OSRELEASE=6.5-SYNTH DISTDIR=/distfiles WRKDIRPREFIX=/construction BATCH=yes PACKAGE_BUILDING=yes PKG_CREATE_VERBOSE=yes MAKE_JOBS_NUMBER=13 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/metis-5.1.0_9.pkg ===== Message from metis-5.1.0_9: -- ===> NOTICE: The metis port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing Installing /packages/All/indexinfo-0.3.1.pkg Installing /packages/All/gmp-6.2.1.pkg Installing /packages/All/mpfr-4.2.0_1,1.pkg Installing /packages/All/mpc-1.3.1_1.pkg UNFLAVORED devel/binutils -> use devel/binutils@native Installing /packages/All/liblz4-1.9.4,1.pkg Installing /packages/All/zstd-1.5.5.pkg Installing /packages/All/gettext-runtime-0.21.1.pkg Installing /packages/All/binutils-2.40_4,1.pkg Installing /packages/All/gcc12-12.2.0_6.pkg ===== Message from gcc12-12.2.0_6: -- 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/gcc12 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. Installing /packages/All/openblas-0.3.20_1,1.pkg Installing /packages/All/suitesparse-config-7.0.1_1.pkg Installing /packages/All/suitesparse-amd-3.0.3_1.pkg Installing /packages/All/suitesparse-camd-3.0.3_1.pkg Installing /packages/All/suitesparse-colamd-3.0.3_1.pkg Installing /packages/All/suitesparse-ccolamd-3.0.3_1.pkg Installing /packages/All/suitesparse-cholmod-4.0.3_1.pkg Installing /packages/All/suitesparse-umfpack-6.1.0_1.pkg Installing /packages/All/libffi-3.4.4.pkg Installing /packages/All/expat-2.5.0.pkg Installing /packages/All/mpdecimal-2.5.1.pkg Installing /packages/All/ncurses-6.4.pkg ===== Message from ncurses-6.4: -- To get the terminfo database please install the terminfo-db package: pkg install terminfo-db Installing /packages/All/readline-8.2.1.pkg Installing /packages/All/openssl-1.1.1u,1.pkg Installing /packages/All/python39-3.9.17.pkg ===== Message from python39-3.9.17: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py39-gdbm databases/py-gdbm@py39 py39-sqlite3 databases/py-sqlite3@py39 py39-tkinter x11-toolkits/py-tkinter@py39 Installing /packages/All/py39-setuptools-63.1.0_1.pkg Installing /packages/All/py39-numpy-1.24.1_4,1.pkg Installing /packages/All/py39-cython-0.29.35.pkg Installing /packages/All/ccache-3.7.12_4.pkg Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for gcc create symlink for gcc (world) create symlink for g++ create symlink for g++ (world) create symlink for gcc12 create symlink for gcc12 (world) create symlink for g++12 create symlink for g++12 (world) create symlink for cpp12 create symlink for cpp12 (world) ===== Message from ccache-3.7.12_4: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. Installing /packages/All/py39-future-0.18.3.pkg UNFLAVORED devel/binutils -> use devel/binutils@native SUCCEEDED 00:00:10 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> py39-molmod-1.4.8_1 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> py39-molmod-1.4.8_1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py39-molmod-1.4.8_1 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> py39-molmod-1.4.8_1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py39-molmod-1.4.8_1 for building => SHA256 Checksum OK for molmod-1.4.8.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> py39-molmod-1.4.8_1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py39-molmod-1.4.8_1 for building ===> Extracting for py39-molmod-1.4.8_1 => SHA256 Checksum OK for molmod-1.4.8.tar.gz. Extracted Memory Use: 5.44M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for py39-molmod-1.4.8_1 SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> py39-molmod-1.4.8_1 depends on package: py39-numpy>=1.16,1<1.25,1 - found ===> py39-molmod-1.4.8_1 depends on executable: cython-3.9 - found ===> py39-molmod-1.4.8_1 depends on package: py39-setuptools>=63.1.0 - found ===> py39-molmod-1.4.8_1 depends on file: /usr/local/bin/python3.9 - found ===> py39-molmod-1.4.8_1 depends on file: /usr/local/bin/ccache - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> py39-molmod-1.4.8_1 depends on package: py39-numpy>=1.16,1<1.25,1 - found ===> py39-molmod-1.4.8_1 depends on executable: cython-3.9 - found ===> py39-molmod-1.4.8_1 depends on package: py39-setuptools>=63.1.0 - found ===> py39-molmod-1.4.8_1 depends on file: /usr/local/bin/python3.9 - found ===> py39-molmod-1.4.8_1 depends on file: /usr/local/bin/ccache - found ===> Configuring for py39-molmod-1.4.8_1 Trying to get the version from git describe Trying to get the version from {} molmod/version.py Version according to molmod/version.py: 1.4.8 running config SUCCEEDED 00:00:02 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for py39-molmod-1.4.8_1 Trying to get the version from git describe Trying to get the version from {} molmod/version.py Version according to molmod/version.py: 1.4.8 running build running build_py creating build creating build/lib.dragonfly-6.5-x86_64-cpython-39 creating build/lib.dragonfly-6.5-x86_64-cpython-39/molmod copying molmod/zmatrix.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod copying molmod/molecules.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod copying molmod/quaternions.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod copying molmod/toyff.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod copying molmod/pairff.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod copying molmod/clusters.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod copying molmod/randomize.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod copying molmod/units.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod copying molmod/molecular_graphs.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod copying molmod/minimizer.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod copying molmod/constants.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod copying molmod/periodic.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod copying molmod/symmetry.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod copying molmod/transformations.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod copying molmod/graphs.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod copying molmod/ic.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod copying molmod/vectors.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod copying molmod/utils.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod copying molmod/binning.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod copying molmod/similarity.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod copying molmod/version.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod copying molmod/isotopes.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod copying molmod/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod copying molmod/unit_cells.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod copying molmod/bonds.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod copying molmod/log.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod creating build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test copying molmod/test/test_units.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test copying molmod/test/test_examples.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test copying molmod/test/test_symmetry.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test copying molmod/test/test_ic.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test copying molmod/test/test_similarity.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test copying molmod/test/test_data.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test copying molmod/test/test_vectors.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test copying molmod/test/test_graphs.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test copying molmod/test/test_clusters.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test copying molmod/test/test_zmatrix.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test copying molmod/test/common.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test copying molmod/test/test_pairff.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test copying molmod/test/test_molecular_graphs.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test copying molmod/test/test_toyff.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test copying molmod/test/test_minimizer.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test copying molmod/test/test_binning.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test copying molmod/test/test_unit_cells.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test copying molmod/test/test_quaternions.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test copying molmod/test/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test copying molmod/test/test_log.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test copying molmod/test/test_transformations.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test copying molmod/test/test_utils.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test copying molmod/test/test_molecules.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test copying molmod/test/test_randomize.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test creating build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io copying molmod/io/cube.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io copying molmod/io/crystal.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io copying molmod/io/cml.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io copying molmod/io/xyz.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io copying molmod/io/dlpoly.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io copying molmod/io/common.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io copying molmod/io/sdf.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io copying molmod/io/atrj.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io copying molmod/io/number_state.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io copying molmod/io/gromacs.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io copying molmod/io/psf.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io copying molmod/io/fchk.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io copying molmod/io/cp2k.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io copying molmod/io/chk.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io copying molmod/io/lammps.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io copying molmod/io/gamess.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io copying molmod/io/cpmd.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io copying molmod/io/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io copying molmod/io/pdb.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io creating build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/test copying molmod/io/test/test_psf.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/test copying molmod/io/test/test_atrj.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/test copying molmod/io/test/test_cp2k.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/test copying molmod/io/test/test_gromacs.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/test copying molmod/io/test/test_dlpoly.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/test copying molmod/io/test/test_gamess.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/test copying molmod/io/test/test_cpmd.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/test copying molmod/io/test/test_cube.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/test copying molmod/io/test/test_chk.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/test copying molmod/io/test/test_lammps.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/test copying molmod/io/test/test_pdb.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/test copying molmod/io/test/test_number_state.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/test copying molmod/io/test/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/test copying molmod/io/test/test_sdf.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/test copying molmod/io/test/test_xyz.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/test copying molmod/io/test/test_crystal.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/test copying molmod/io/test/test_fchk.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/test copying molmod/io/test/test_cml.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/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' adding license file 'LICENSE.txt' writing manifest file 'molmod.egg-info/SOURCES.txt' /usr/local/lib/python3.9/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'molmod.data' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'molmod.data' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'molmod.data' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'molmod.data' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/local/lib/python3.9/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'molmod.data.test' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'molmod.data.test' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'molmod.data.test' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'molmod.data.test' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/local/lib/python3.9/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'molmod.examples' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'molmod.examples' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'molmod.examples' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'molmod.examples' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) copying molmod/common.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod copying molmod/common.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod copying molmod/ext.pyx -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod copying molmod/ff.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod copying molmod/ff.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod copying molmod/ff.pxd -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod copying molmod/graphs.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod copying molmod/graphs.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod copying molmod/graphs.pxd -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod copying molmod/molecules.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod copying molmod/molecules.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod copying molmod/molecules.pxd -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod copying molmod/similarity.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod copying molmod/similarity.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod copying molmod/similarity.pxd -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod copying molmod/unit_cells.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod copying molmod/unit_cells.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod copying molmod/unit_cells.pxd -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod creating build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data copying molmod/data/bonds.csv -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data copying molmod/data/bonds.ods -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data copying molmod/data/mass.mas03 -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data copying molmod/data/nubtab03.asc -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data copying molmod/data/periodic.csv -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data copying molmod/data/periodic.ods -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data copying molmod/data/toyff_angles.txt -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data creating build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/1LJL_Cys10.cml -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/1TOH.b3lyp.fchk -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/1TOH.b3lyp.trim.fchk -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/5ringOH.xyz -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/CID_22898828.sdf -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/PCGamess_PUNCH -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/SID_31646545.sdf -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/SID_31646548.sdf -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/SID_40363570.sdf -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/SID_40363571.sdf -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/SID_41893278.sdf -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/SID_41893280.sdf -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/SID_54258192.sdf -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/SID_55127927.sdf -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/SID_55488598.sdf -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/SID_56274343.sdf -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/TRAJECTORY_H2_CPMD -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/alanine.cube -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/argon.xyz -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/bartek.atrj -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/benzene.xyz -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/butane.xyz -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/caplayer.cml -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/crystal_api.out -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/cyclopentane.xyz -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/dinitrogen.xyz -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/dlpoly_HISTORY -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/dlpoly_HISTORY_an2 -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/dlpoly_OUTPUT -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/dopamine.xyz -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/ethane.xyz -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/ethene.xyz -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/ethene_ethyl_trans.xyz -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/example.sdf -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/formol.xyz -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/funny.xyz -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/h3zrosihohosioh3.xyz -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/il2.pdb -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/lammps_dump.txt -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/lau.xyz -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/octane.xyz -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/oh3siozroh3.xyz -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/opt_5ring10T.xyz -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/opt_5ring12T.xyz -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/opt_6_6ring.xyz -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/opt_6ring.xyz -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/osih2osihosih2osih2ozrh2oh.xyz -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/pentapeptide.psf -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/precursor.xyz -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/probes.xyz -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/tea.xyz -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/tetra.xyz -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/thf.psf -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/thf.xyz -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/thf_64.cell -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/thf_single.xyz -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/tpa.xyz -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/water.xyz -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/water2.gro -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/water_md.inp -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test copying molmod/data/test/zr4o8-3.xyz -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test creating build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples creating build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/000_units copying molmod/examples/000_units/a_reaction.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/000_units copying molmod/examples/000_units/b_chbond.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/000_units copying molmod/examples/000_units/c_h2rot.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/000_units creating build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/001_molecules copying molmod/examples/001_molecules/a_convert.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/001_molecules copying molmod/examples/001_molecules/b_com.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/001_molecules copying molmod/examples/001_molecules/c_carbon.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/001_molecules copying molmod/examples/001_molecules/d_size.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/001_molecules copying molmod/examples/001_molecules/e_shape.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/001_molecules copying molmod/examples/001_molecules/ibuprofen.sdf -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/001_molecules creating build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/002_graphs copying molmod/examples/002_graphs/a_graphs.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/002_graphs copying molmod/examples/002_graphs/b_neighbors.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/002_graphs copying molmod/examples/002_graphs/c_distances.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/002_graphs copying molmod/examples/002_graphs/caffeine.xyz -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/002_graphs copying molmod/examples/002_graphs/d_symmetries.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/002_graphs copying molmod/examples/002_graphs/ethanol.xyz -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/002_graphs creating build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/003_internal_coordinates copying molmod/examples/003_internal_coordinates/a_bond_length.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/003_internal_coordinates copying molmod/examples/003_internal_coordinates/b_bending_angles.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/003_internal_coordinates copying molmod/examples/003_internal_coordinates/c_ff_hessian.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/003_internal_coordinates copying molmod/examples/003_internal_coordinates/d_dft_hessian.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/003_internal_coordinates copying molmod/examples/003_internal_coordinates/dopamine.fchk -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/003_internal_coordinates copying molmod/examples/003_internal_coordinates/dopamine.xyz -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/003_internal_coordinates copying molmod/examples/003_internal_coordinates/propane.xyz -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/003_internal_coordinates creating build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/004_patterns copying molmod/examples/004_patterns/a_propane_types.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/004_patterns copying molmod/examples/004_patterns/b_dopamine_types.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/004_patterns copying molmod/examples/004_patterns/dopamine.xyz -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/004_patterns copying molmod/examples/004_patterns/mfi_fragment.xyz -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/004_patterns copying molmod/examples/004_patterns/propane.xyz -> build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/004_patterns running build_ext cythoning molmod/ext.pyx to molmod/ext.c /usr/local/lib/python3.9/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-1.4.8/molmod/ext.pyx tree = Parsing.p_module(s, pxd, full_module_name) building 'molmod.ext' extension creating build/temp.dragonfly-6.5-x86_64-cpython-39 creating build/temp.dragonfly-6.5-x86_64-cpython-39/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/python3.9/site-packages/numpy/core/include -I/usr/local/include/python3.9 -c molmod/common.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/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/python3.9/site-packages/numpy/core/include -I/usr/local/include/python3.9 -c molmod/ext.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/molmod/ext.o In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1940, from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5, from molmod/ext.c:750: /usr/local/lib/python3.9/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:3083:40: 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:3089:40: 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:3123:40: 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:3129:40: 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:3839:42: 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:3871:40: 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:3877:40: 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:4743:44: 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:5487:44: 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:6018:39: 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:6860:39: 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:761: 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:6991:52: 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:7089:42: 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:761: 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:7345:47: 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:7409:47: 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/python3.9/site-packages/numpy/core/include -I/usr/local/include/python3.9 -c molmod/ff.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/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/python3.9/site-packages/numpy/core/include -I/usr/local/include/python3.9 -c molmod/graphs.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/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/python3.9/site-packages/numpy/core/include -I/usr/local/include/python3.9 -c molmod/molecules.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/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/python3.9/site-packages/numpy/core/include -I/usr/local/include/python3.9 -c molmod/similarity.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/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:135: 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/python3.9/site-packages/numpy/core/include -I/usr/local/include/python3.9 -c molmod/unit_cells.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/molmod/unit_cells.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/molmod/common.o build/temp.dragonfly-6.5-x86_64-cpython-39/molmod/ext.o build/temp.dragonfly-6.5-x86_64-cpython-39/molmod/ff.o build/temp.dragonfly-6.5-x86_64-cpython-39/molmod/graphs.o build/temp.dragonfly-6.5-x86_64-cpython-39/molmod/molecules.o build/temp.dragonfly-6.5-x86_64-cpython-39/molmod/similarity.o build/temp.dragonfly-6.5-x86_64-cpython-39/molmod/unit_cells.o -L/usr/local/lib -o build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/ext.cpython-39.so SUCCEEDED 00:00:22 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- ===> py39-molmod-1.4.8_1 depends on package: py39-numpy>=1.16,1<1.25,1 - found ===> py39-molmod-1.4.8_1 depends on package: py39-future>0 - found ===> py39-molmod-1.4.8_1 depends on executable: cython-3.9 - found ===> py39-molmod-1.4.8_1 depends on package: py39-setuptools>=63.1.0 - found ===> py39-molmod-1.4.8_1 depends on file: /usr/local/bin/python3.9 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for py39-molmod-1.4.8_1 ===> py39-molmod-1.4.8_1 depends on package: py39-numpy>=1.16,1<1.25,1 - found ===> py39-molmod-1.4.8_1 depends on package: py39-future>0 - found ===> py39-molmod-1.4.8_1 depends on executable: cython-3.9 - found ===> py39-molmod-1.4.8_1 depends on package: py39-setuptools>=63.1.0 - found ===> py39-molmod-1.4.8_1 depends on file: /usr/local/bin/python3.9 - found ===> 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: 1.4.8 running install /usr/local/lib/python3.9/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( 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' adding license file 'LICENSE.txt' writing manifest file 'molmod.egg-info/SOURCES.txt' /usr/local/lib/python3.9/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'molmod.data' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'molmod.data' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'molmod.data' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'molmod.data' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/local/lib/python3.9/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'molmod.data.test' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'molmod.data.test' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'molmod.data.test' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'molmod.data.test' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/local/lib/python3.9/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'molmod.examples' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'molmod.examples' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'molmod.examples' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'molmod.examples' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) running build_ext skipping 'molmod/ext.c' Cython extension (up-to-date) running install_lib creating /construction/science/py-molmod/stage/usr/local/lib/python3.9 creating /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages creating /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/ext.cpython-39.so -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/zmatrix.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/molecules.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/quaternions.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/toyff.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/pairff.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/clusters.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/randomize.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/units.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/molecular_graphs.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/minimizer.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/constants.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/periodic.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/symmetry.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/transformations.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/graphs.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/ic.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/vectors.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/utils.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/binning.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/similarity.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/version.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/isotopes.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/__init__.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/unit_cells.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/bonds.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/log.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod creating /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test/test_units.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test/test_examples.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test/test_symmetry.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test/test_ic.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test/test_similarity.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test/test_data.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test/test_vectors.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test/test_graphs.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test/test_clusters.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test/test_zmatrix.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test/common.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test/test_pairff.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test/test_molecular_graphs.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test/test_toyff.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test/test_minimizer.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test/test_binning.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test/test_unit_cells.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test/test_quaternions.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test/__init__.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test/test_log.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test/test_transformations.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test/test_utils.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test/test_molecules.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/test/test_randomize.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test creating /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/cube.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/crystal.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/cml.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/xyz.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/dlpoly.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/common.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/sdf.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/atrj.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/number_state.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/gromacs.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/psf.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/fchk.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/cp2k.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/chk.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/lammps.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/gamess.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/cpmd.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/__init__.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/pdb.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io creating /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/test/test_psf.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/test/test_atrj.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/test/test_cp2k.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/test/test_gromacs.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/test/test_dlpoly.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/test/test_gamess.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/test/test_cpmd.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/test/test_cube.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/test/test_chk.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/test/test_lammps.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/test/test_pdb.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/test/test_number_state.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/test/__init__.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/test/test_sdf.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/test/test_xyz.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/test/test_crystal.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/test/test_fchk.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/io/test/test_cml.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/common.c -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/common.h -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/ext.pyx -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/ff.c -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/ff.h -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/ff.pxd -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/graphs.c -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/graphs.h -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/graphs.pxd -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/molecules.c -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/molecules.h -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/molecules.pxd -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/similarity.c -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/similarity.h -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/similarity.pxd -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/unit_cells.c -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/unit_cells.h -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/unit_cells.pxd -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod creating /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/bonds.csv -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/bonds.ods -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/mass.mas03 -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/nubtab03.asc -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/periodic.csv -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/periodic.ods -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/toyff_angles.txt -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data creating /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/1LJL_Cys10.cml -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/1TOH.b3lyp.fchk -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/1TOH.b3lyp.trim.fchk -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/5ringOH.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/CID_22898828.sdf -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/PCGamess_PUNCH -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/SID_31646545.sdf -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/SID_31646548.sdf -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/SID_40363570.sdf -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/SID_40363571.sdf -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/SID_41893278.sdf -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/SID_41893280.sdf -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/SID_54258192.sdf -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/SID_55127927.sdf -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/SID_55488598.sdf -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/SID_56274343.sdf -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/TRAJECTORY_H2_CPMD -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/alanine.cube -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/argon.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/bartek.atrj -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/benzene.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/butane.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/caplayer.cml -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/crystal_api.out -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/cyclopentane.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/dinitrogen.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/dlpoly_HISTORY -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/dlpoly_HISTORY_an2 -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/dlpoly_OUTPUT -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/dopamine.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/ethane.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/ethene.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/ethene_ethyl_trans.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/example.sdf -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/formol.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/funny.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/h3zrosihohosioh3.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/il2.pdb -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/lammps_dump.txt -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/lau.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/octane.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/oh3siozroh3.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/opt_5ring10T.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/opt_5ring12T.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/opt_6_6ring.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/opt_6ring.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/osih2osihosih2osih2ozrh2oh.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/pentapeptide.psf -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/precursor.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/probes.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/tea.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/tetra.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/thf.psf -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/thf.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/thf_64.cell -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/thf_single.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/tpa.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/water.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/water2.gro -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/water_md.inp -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/data/test/zr4o8-3.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/data/test creating /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples creating /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/000_units copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/000_units/a_reaction.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/000_units copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/000_units/b_chbond.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/000_units copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/000_units/c_h2rot.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/000_units creating /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/001_molecules copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/001_molecules/a_convert.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/001_molecules copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/001_molecules/b_com.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/001_molecules copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/001_molecules/c_carbon.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/001_molecules copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/001_molecules/d_size.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/001_molecules copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/001_molecules/e_shape.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/001_molecules copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/001_molecules/ibuprofen.sdf -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/001_molecules creating /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/002_graphs copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/002_graphs/a_graphs.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/002_graphs copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/002_graphs/b_neighbors.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/002_graphs copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/002_graphs/c_distances.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/002_graphs copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/002_graphs/caffeine.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/002_graphs copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/002_graphs/d_symmetries.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/002_graphs copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/002_graphs/ethanol.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/002_graphs creating /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/003_internal_coordinates copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/003_internal_coordinates/a_bond_length.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/003_internal_coordinates copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/003_internal_coordinates/b_bending_angles.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/003_internal_coordinates copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/003_internal_coordinates/c_ff_hessian.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/003_internal_coordinates copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/003_internal_coordinates/d_dft_hessian.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/003_internal_coordinates copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/003_internal_coordinates/dopamine.fchk -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/003_internal_coordinates copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/003_internal_coordinates/dopamine.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/003_internal_coordinates copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/003_internal_coordinates/propane.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/003_internal_coordinates creating /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/004_patterns copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/004_patterns/a_propane_types.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/004_patterns copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/004_patterns/b_dopamine_types.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/004_patterns copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/004_patterns/dopamine.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/004_patterns copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/004_patterns/mfi_fragment.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/004_patterns copying build/lib.dragonfly-6.5-x86_64-cpython-39/molmod/examples/004_patterns/propane.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/004_patterns byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/zmatrix.py to zmatrix.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/molecules.py to molecules.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/quaternions.py to quaternions.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/toyff.py to toyff.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/pairff.py to pairff.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/clusters.py to clusters.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/randomize.py to randomize.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/units.py to units.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/molecular_graphs.py to molecular_graphs.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/minimizer.py to minimizer.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/constants.py to constants.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/periodic.py to periodic.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/symmetry.py to symmetry.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/transformations.py to transformations.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/graphs.py to graphs.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/ic.py to ic.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/vectors.py to vectors.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/utils.py to utils.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/binning.py to binning.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/similarity.py to similarity.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/version.py to version.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/isotopes.py to isotopes.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/unit_cells.py to unit_cells.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/bonds.py to bonds.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/log.py to log.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test/test_units.py to test_units.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test/test_examples.py to test_examples.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test/test_symmetry.py to test_symmetry.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test/test_ic.py to test_ic.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test/test_similarity.py to test_similarity.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test/test_data.py to test_data.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test/test_vectors.py to test_vectors.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test/test_graphs.py to test_graphs.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test/test_clusters.py to test_clusters.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test/test_zmatrix.py to test_zmatrix.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test/common.py to common.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test/test_pairff.py to test_pairff.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test/test_molecular_graphs.py to test_molecular_graphs.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test/test_toyff.py to test_toyff.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test/test_minimizer.py to test_minimizer.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test/test_binning.py to test_binning.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test/test_unit_cells.py to test_unit_cells.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test/test_quaternions.py to test_quaternions.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test/test_log.py to test_log.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test/test_transformations.py to test_transformations.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test/test_utils.py to test_utils.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test/test_molecules.py to test_molecules.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/test/test_randomize.py to test_randomize.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/cube.py to cube.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/crystal.py to crystal.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/cml.py to cml.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/xyz.py to xyz.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/dlpoly.py to dlpoly.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/common.py to common.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/sdf.py to sdf.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/atrj.py to atrj.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/number_state.py to number_state.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/gromacs.py to gromacs.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/psf.py to psf.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/fchk.py to fchk.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/cp2k.py to cp2k.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/chk.py to chk.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/lammps.py to lammps.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/gamess.py to gamess.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/cpmd.py to cpmd.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/pdb.py to pdb.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/test/test_psf.py to test_psf.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/test/test_atrj.py to test_atrj.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/test/test_cp2k.py to test_cp2k.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/test/test_gromacs.py to test_gromacs.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/test/test_dlpoly.py to test_dlpoly.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/test/test_gamess.py to test_gamess.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/test/test_cpmd.py to test_cpmd.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/test/test_cube.py to test_cube.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/test/test_chk.py to test_chk.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/test/test_lammps.py to test_lammps.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/test/test_pdb.py to test_pdb.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/test/test_number_state.py to test_number_state.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/test/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/test/test_sdf.py to test_sdf.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/test/test_xyz.py to test_xyz.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/test/test_crystal.py to test_crystal.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/test/test_fchk.py to test_fchk.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/io/test/test_cml.py to test_cml.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/000_units/a_reaction.py to a_reaction.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/000_units/b_chbond.py to b_chbond.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/000_units/c_h2rot.py to c_h2rot.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/001_molecules/a_convert.py to a_convert.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/001_molecules/b_com.py to b_com.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/001_molecules/c_carbon.py to c_carbon.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/001_molecules/d_size.py to d_size.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/001_molecules/e_shape.py to e_shape.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/002_graphs/a_graphs.py to a_graphs.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/002_graphs/b_neighbors.py to b_neighbors.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/002_graphs/c_distances.py to c_distances.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/002_graphs/d_symmetries.py to d_symmetries.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/003_internal_coordinates/a_bond_length.py to a_bond_length.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/003_internal_coordinates/b_bending_angles.py to b_bending_angles.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/003_internal_coordinates/c_ff_hessian.py to c_ff_hessian.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/003_internal_coordinates/d_dft_hessian.py to d_dft_hessian.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/004_patterns/a_propane_types.py to a_propane_types.cpython-39.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod/examples/004_patterns/b_dopamine_types.py to b_dopamine_types.cpython-39.pyc writing byte-compilation script '/tmp/tmp7il4fhov.py' /usr/local/bin/python3.9 /tmp/tmp7il4fhov.py removing /tmp/tmp7il4fhov.py running install_egg_info Copying molmod.egg-info to /construction/science/py-molmod/stage/usr/local/lib/python3.9/site-packages/molmod-1.4.8-py3.9.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) Warning: 'lib/python3.9/site-packages/molmod/ext.cpython-39.so' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD} Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:05 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for py39-molmod-1.4.8_1 file sizes/checksums [416]: 0% file sizes/checksums [416]: 24% file sizes/checksums [416]: 48% file sizes/checksums [416]: 72% file sizes/checksums [416]: 96% file sizes/checksums [416]: 100% Service unavailablepacking files [416]: 0% packing files [416]: 24% packing files [416]: 48% packing files [416]: 72% packing files [416]: 96% packing files [416]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:02 TOTAL TIME 00:00:43