------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/metis-5.1.0_8.tgz Message from metis-5.1.0_8: ===> 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://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port Installing /packages/All/indexinfo-0.3.1.tgz Installing /packages/All/gmp-6.1.2_1.tgz Installing /packages/All/mpfr-4.0.2.tgz Installing /packages/All/mpc-1.1.0_2.tgz Installing /packages/All/gettext-runtime-0.20.1.tgz Installing /packages/All/binutils-2.32_1,1.tgz Installing /packages/All/gcc8-8.3.0_3.tgz Message from gcc8-8.3.0_3: To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc8 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. Installing /packages/All/blas-3.5.0_6.tgz Installing /packages/All/lapack-3.5.0_8.tgz Installing /packages/All/openblas-0.2.20_10,1.tgz Installing /packages/All/suitesparse-5.2.0_4.tgz Installing /packages/All/expat-2.2.6_1.tgz Installing /packages/All/libffi-3.2.1_3.tgz Installing /packages/All/ncurses-6.1.20190525.tgz Installing /packages/All/readline-8.0.0.tgz Installing /packages/All/openssl-1.0.2s,1.tgz Message from openssl-1.0.2s,1: Edit /usr/local/openssl/openssl.cnf to fit your needs. Installing /packages/All/python36-3.6.9.tgz Message from python36-3.6.9: =========================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py36-gdbm databases/py-gdbm@py36 py36-sqlite3 databases/py-sqlite3@py36 py36-tkinter x11-toolkits/py-tkinter@py36 =========================================================================== Installing /packages/All/py36-setuptools-41.0.1.tgz Installing /packages/All/py36-numpy-1.16.4_1,1.tgz Installing /packages/All/py36-cython-0.29_1.tgz Installing /packages/All/py36-future-0.17.1_1.tgz SUCCEEDED 00:00:15 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- x SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- x SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- x SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- x===> Fetching all distfiles required by py36-molmod-1.4.4_2 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- x===> Fetching all distfiles required by py36-molmod-1.4.4_2 for building => SHA256 Checksum OK for molmod-1.4.4.tar.gz. SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- x SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- x===> Fetching all distfiles required by py36-molmod-1.4.4_2 for building ===> Extracting for py36-molmod-1.4.4_2 => SHA256 Checksum OK for molmod-1.4.4.tar.gz. Extracted Memory Use: 5.45M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- x SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- x===> Patching for py36-molmod-1.4.4_2 SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- x SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- x SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- x===> Configuring for py36-molmod-1.4.4_2 Trying to get the version from git describe Trying to get the version from {} molmod/version.py Version according to molmod/version.py: 1.4.4 running config SUCCEEDED 00:00:03 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- x===> Building for py36-molmod-1.4.4_2 Trying to get the version from git describe Trying to get the version from {} molmod/version.py Version according to molmod/version.py: 1.4.4 running build running build_py creating build creating build/lib.dragonfly-5.7-x86_64-3.6 creating build/lib.dragonfly-5.7-x86_64-3.6/molmod copying molmod/utils.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod copying molmod/vectors.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod copying molmod/units.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod copying molmod/zmatrix.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod copying molmod/unit_cells.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod copying molmod/version.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod copying molmod/ic.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod copying molmod/log.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod copying molmod/symmetry.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod copying molmod/constants.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod copying molmod/binning.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod copying molmod/randomize.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod copying molmod/molecular_graphs.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod copying molmod/minimizer.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod copying molmod/similarity.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod copying molmod/pairff.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod copying molmod/bonds.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod copying molmod/__init__.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod copying molmod/toyff.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod copying molmod/transformations.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod copying molmod/isotopes.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod copying molmod/molecules.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod copying molmod/clusters.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod copying molmod/periodic.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod copying molmod/quaternions.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod copying molmod/graphs.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod creating build/lib.dragonfly-5.7-x86_64-3.6/molmod/test copying molmod/test/test_minimizer.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/test copying molmod/test/test_vectors.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/test copying molmod/test/test_molecular_graphs.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/test copying molmod/test/test_quaternions.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/test copying molmod/test/test_toyff.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/test copying molmod/test/common.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/test copying molmod/test/test_units.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/test copying molmod/test/test_transformations.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/test copying molmod/test/test_randomize.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/test copying molmod/test/test_similarity.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/test copying molmod/test/test_molecules.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/test copying molmod/test/__init__.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/test copying molmod/test/test_utils.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/test copying molmod/test/test_pairff.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/test copying molmod/test/test_symmetry.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/test copying molmod/test/test_ic.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/test copying molmod/test/test_clusters.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/test copying molmod/test/test_unit_cells.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/test copying molmod/test/test_binning.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/test copying molmod/test/test_log.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/test copying molmod/test/test_data.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/test copying molmod/test/test_examples.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/test copying molmod/test/test_zmatrix.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/test copying molmod/test/test_graphs.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/test creating build/lib.dragonfly-5.7-x86_64-3.6/molmod/io copying molmod/io/cpmd.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/io copying molmod/io/number_state.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/io copying molmod/io/atrj.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/io copying molmod/io/gromacs.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/io copying molmod/io/psf.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/io copying molmod/io/fchk.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/io copying molmod/io/pdb.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/io copying molmod/io/crystal.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/io copying molmod/io/cml.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/io copying molmod/io/common.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/io copying molmod/io/xyz.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/io copying molmod/io/cube.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/io copying molmod/io/lammps.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/io copying molmod/io/gamess.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/io copying molmod/io/cp2k.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/io copying molmod/io/chk.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/io copying molmod/io/dlpoly.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/io copying molmod/io/sdf.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/io copying molmod/io/__init__.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/io creating build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/test copying molmod/io/test/test_cp2k.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/test copying molmod/io/test/test_pdb.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/test copying molmod/io/test/test_dlpoly.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/test copying molmod/io/test/__init__.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/test copying molmod/io/test/test_gamess.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/test copying molmod/io/test/test_lammps.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/test copying molmod/io/test/test_cml.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/test copying molmod/io/test/test_atrj.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/test copying molmod/io/test/test_sdf.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/test copying molmod/io/test/test_gromacs.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/test copying molmod/io/test/test_number_state.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/test copying molmod/io/test/test_fchk.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/test copying molmod/io/test/test_xyz.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/test copying molmod/io/test/test_cube.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/test copying molmod/io/test/test_cpmd.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/test copying molmod/io/test/test_chk.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/test copying molmod/io/test/test_crystal.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/test copying molmod/io/test/test_psf.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/test running egg_info writing molmod.egg-info/PKG-INFO writing dependency_links to molmod.egg-info/dependency_links.txt writing requirements to molmod.egg-info/requires.txt writing top-level names to molmod.egg-info/top_level.txt reading manifest file 'molmod.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files matching 'ext.c' found under directory 'molmod' writing manifest file 'molmod.egg-info/SOURCES.txt' copying molmod/common.c -> build/lib.dragonfly-5.7-x86_64-3.6/molmod copying molmod/common.h -> build/lib.dragonfly-5.7-x86_64-3.6/molmod copying molmod/ext.pyx -> build/lib.dragonfly-5.7-x86_64-3.6/molmod copying molmod/ff.c -> build/lib.dragonfly-5.7-x86_64-3.6/molmod copying molmod/ff.h -> build/lib.dragonfly-5.7-x86_64-3.6/molmod copying molmod/ff.pxd -> build/lib.dragonfly-5.7-x86_64-3.6/molmod copying molmod/graphs.c -> build/lib.dragonfly-5.7-x86_64-3.6/molmod copying molmod/graphs.h -> build/lib.dragonfly-5.7-x86_64-3.6/molmod copying molmod/graphs.pxd -> build/lib.dragonfly-5.7-x86_64-3.6/molmod copying molmod/molecules.c -> build/lib.dragonfly-5.7-x86_64-3.6/molmod copying molmod/molecules.h -> build/lib.dragonfly-5.7-x86_64-3.6/molmod copying molmod/molecules.pxd -> build/lib.dragonfly-5.7-x86_64-3.6/molmod copying molmod/similarity.c -> build/lib.dragonfly-5.7-x86_64-3.6/molmod copying molmod/similarity.h -> build/lib.dragonfly-5.7-x86_64-3.6/molmod copying molmod/similarity.pxd -> build/lib.dragonfly-5.7-x86_64-3.6/molmod copying molmod/unit_cells.c -> build/lib.dragonfly-5.7-x86_64-3.6/molmod copying molmod/unit_cells.h -> build/lib.dragonfly-5.7-x86_64-3.6/molmod copying molmod/unit_cells.pxd -> build/lib.dragonfly-5.7-x86_64-3.6/molmod creating build/lib.dragonfly-5.7-x86_64-3.6/molmod/data copying molmod/data/bonds.csv -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data copying molmod/data/bonds.ods -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data copying molmod/data/mass.mas03 -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data copying molmod/data/nubtab03.asc -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data copying molmod/data/periodic.csv -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data copying molmod/data/periodic.ods -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data copying molmod/data/toyff_angles.txt -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data creating build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/1LJL_Cys10.cml -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/1TOH.b3lyp.fchk -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/1TOH.b3lyp.trim.fchk -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/5ringOH.xyz -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/CID_22898828.sdf -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/PCGamess_PUNCH -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/SID_31646545.sdf -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/SID_31646548.sdf -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/SID_40363570.sdf -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/SID_40363571.sdf -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/SID_41893278.sdf -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/SID_41893280.sdf -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/SID_54258192.sdf -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/SID_55127927.sdf -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/SID_55488598.sdf -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/SID_56274343.sdf -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/TRAJECTORY_H2_CPMD -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/alanine.cube -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/argon.xyz -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/bartek.atrj -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/benzene.xyz -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/butane.xyz -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/caplayer.cml -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/crystal_api.out -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/cyclopentane.xyz -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/dinitrogen.xyz -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/dlpoly_HISTORY -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/dlpoly_HISTORY_an2 -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/dlpoly_OUTPUT -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/dopamine.xyz -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/ethane.xyz -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/ethene.xyz -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/ethene_ethyl_trans.xyz -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/example.sdf -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/formol.xyz -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/funny.xyz -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/h3zrosihohosioh3.xyz -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/il2.pdb -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/lammps_dump.txt -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/lau.xyz -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/octane.xyz -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/oh3siozroh3.xyz -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/opt_5ring10T.xyz -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/opt_5ring12T.xyz -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/opt_6_6ring.xyz -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/opt_6ring.xyz -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/osih2osihosih2osih2ozrh2oh.xyz -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/pentapeptide.psf -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/precursor.xyz -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/probes.xyz -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/tea.xyz -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/tetra.xyz -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/thf.psf -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/thf.xyz -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/thf_64.cell -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/thf_single.xyz -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/tpa.xyz -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/water.xyz -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/water2.gro -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/water_md.inp -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test copying molmod/data/test/zr4o8-3.xyz -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test creating build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples creating build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/000_units copying molmod/examples/000_units/a_reaction.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/000_units copying molmod/examples/000_units/b_chbond.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/000_units copying molmod/examples/000_units/c_h2rot.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/000_units creating build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/001_molecules copying molmod/examples/001_molecules/a_convert.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/001_molecules copying molmod/examples/001_molecules/b_com.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/001_molecules copying molmod/examples/001_molecules/c_carbon.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/001_molecules copying molmod/examples/001_molecules/d_size.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/001_molecules copying molmod/examples/001_molecules/e_shape.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/001_molecules copying molmod/examples/001_molecules/ibuprofen.sdf -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/001_molecules creating build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/002_graphs copying molmod/examples/002_graphs/a_graphs.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/002_graphs copying molmod/examples/002_graphs/b_neighbors.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/002_graphs copying molmod/examples/002_graphs/c_distances.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/002_graphs copying molmod/examples/002_graphs/caffeine.xyz -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/002_graphs copying molmod/examples/002_graphs/d_symmetries.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/002_graphs copying molmod/examples/002_graphs/ethanol.xyz -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/002_graphs creating build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/003_internal_coordinates copying molmod/examples/003_internal_coordinates/a_bond_length.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/003_internal_coordinates copying molmod/examples/003_internal_coordinates/b_bending_angles.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/003_internal_coordinates copying molmod/examples/003_internal_coordinates/c_ff_hessian.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/003_internal_coordinates copying molmod/examples/003_internal_coordinates/d_dft_hessian.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/003_internal_coordinates copying molmod/examples/003_internal_coordinates/dopamine.fchk -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/003_internal_coordinates copying molmod/examples/003_internal_coordinates/dopamine.xyz -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/003_internal_coordinates copying molmod/examples/003_internal_coordinates/propane.xyz -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/003_internal_coordinates creating build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/004_patterns copying molmod/examples/004_patterns/a_propane_types.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/004_patterns copying molmod/examples/004_patterns/b_dopamine_types.py -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/004_patterns copying molmod/examples/004_patterns/dopamine.xyz -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/004_patterns copying molmod/examples/004_patterns/mfi_fragment.xyz -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/004_patterns copying molmod/examples/004_patterns/propane.xyz -> build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/004_patterns running build_ext cythoning molmod/ext.pyx to molmod/ext.c /usr/local/lib/python3.6/site-packages/Cython/Compiler/Main.py:367: 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-1.4.4/molmod/ext.pyx tree = Parsing.p_module(s, pxd, full_module_name) building 'molmod.ext' extension creating build/temp.dragonfly-5.7-x86_64-3.6 creating build/temp.dragonfly-5.7-x86_64-3.6/molmod cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/usr/local/include/python3.6m -c molmod/ext.c -o build/temp.dragonfly-5.7-x86_64-3.6/molmod/ext.o In file included from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4, from molmod/ext.c:610: /usr/local/lib/python3.6/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_12similarity_table_labels': molmod/ext.c:6680:39: 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:615: 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:6903:42: 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:615: 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); ~~~~~~~~^~~~~~~~~~~~~~~ cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/usr/local/include/python3.6m -c molmod/common.c -o build/temp.dragonfly-5.7-x86_64-3.6/molmod/common.o cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/usr/local/include/python3.6m -c molmod/ff.c -o build/temp.dragonfly-5.7-x86_64-3.6/molmod/ff.o cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/usr/local/include/python3.6m -c molmod/graphs.c -o build/temp.dragonfly-5.7-x86_64-3.6/molmod/graphs.o cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/usr/local/include/python3.6m -c molmod/similarity.c -o build/temp.dragonfly-5.7-x86_64-3.6/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:138: note: this is the location of the previous definition #define M_PI ((double)3.14159265358979323846) /* pi */ cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/usr/local/include/python3.6m -c molmod/molecules.c -o build/temp.dragonfly-5.7-x86_64-3.6/molmod/molecules.o cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/usr/local/include/python3.6m -c molmod/unit_cells.c -o build/temp.dragonfly-5.7-x86_64-3.6/molmod/unit_cells.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-x86_64-3.6/molmod/ext.o build/temp.dragonfly-5.7-x86_64-3.6/molmod/common.o build/temp.dragonfly-5.7-x86_64-3.6/molmod/ff.o build/temp.dragonfly-5.7-x86_64-3.6/molmod/graphs.o build/temp.dragonfly-5.7-x86_64-3.6/molmod/similarity.o build/temp.dragonfly-5.7-x86_64-3.6/molmod/molecules.o build/temp.dragonfly-5.7-x86_64-3.6/molmod/unit_cells.o -L/usr/local/lib -lpython3.6m -o build/lib.dragonfly-5.7-x86_64-3.6/molmod/ext.so SUCCEEDED 00:00:22 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- x SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- x===> Staging for py36-molmod-1.4.4_2 ===> 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: 1.4.4 running install running build running build_py running egg_info writing molmod.egg-info/PKG-INFO writing dependency_links to molmod.egg-info/dependency_links.txt writing requirements to molmod.egg-info/requires.txt writing top-level names to molmod.egg-info/top_level.txt reading manifest file 'molmod.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'molmod.egg-info/SOURCES.txt' running build_ext skipping 'molmod/ext.c' Cython extension (up-to-date) running install_lib creating /construction/science/py-molmod/stage/usr/local/lib/python3.6 creating /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages creating /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/ext.so -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod creating /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples creating /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/000_units copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/000_units/c_h2rot.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/000_units copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/000_units/b_chbond.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/000_units copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/000_units/a_reaction.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/000_units creating /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/004_patterns copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/004_patterns/b_dopamine_types.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/004_patterns copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/004_patterns/propane.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/004_patterns copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/004_patterns/a_propane_types.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/004_patterns copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/004_patterns/dopamine.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/004_patterns copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/004_patterns/mfi_fragment.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/004_patterns creating /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/001_molecules copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/001_molecules/e_shape.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/001_molecules copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/001_molecules/d_size.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/001_molecules copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/001_molecules/b_com.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/001_molecules copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/001_molecules/ibuprofen.sdf -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/001_molecules copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/001_molecules/a_convert.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/001_molecules copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/001_molecules/c_carbon.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/001_molecules creating /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/002_graphs copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/002_graphs/a_graphs.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/002_graphs copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/002_graphs/c_distances.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/002_graphs copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/002_graphs/ethanol.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/002_graphs copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/002_graphs/d_symmetries.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/002_graphs copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/002_graphs/caffeine.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/002_graphs copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/002_graphs/b_neighbors.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/002_graphs creating /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/003_internal_coordinates copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/003_internal_coordinates/d_dft_hessian.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/003_internal_coordinates copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/003_internal_coordinates/propane.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/003_internal_coordinates copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/003_internal_coordinates/dopamine.fchk -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/003_internal_coordinates copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/003_internal_coordinates/dopamine.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/003_internal_coordinates copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/003_internal_coordinates/b_bending_angles.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/003_internal_coordinates copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/003_internal_coordinates/c_ff_hessian.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/003_internal_coordinates copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/examples/003_internal_coordinates/a_bond_length.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/003_internal_coordinates copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/utils.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/vectors.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/units.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/zmatrix.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/unit_cells.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/version.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/ic.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/log.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/symmetry.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/constants.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/binning.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/randomize.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/molecular_graphs.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/minimizer.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/similarity.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/pairff.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/bonds.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/__init__.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/toyff.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/transformations.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/isotopes.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/molecules.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/clusters.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/periodic.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/quaternions.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/graphs.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod creating /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/test/test_minimizer.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/test/test_vectors.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/test/test_molecular_graphs.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/test/test_quaternions.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/test/test_toyff.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/test/common.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/test/test_units.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/test/test_transformations.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/test/test_randomize.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/test/test_similarity.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/test/test_molecules.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/test/__init__.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/test/test_utils.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/test/test_pairff.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/test/test_symmetry.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/test/test_ic.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/test/test_clusters.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/test/test_unit_cells.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/test/test_binning.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/test/test_log.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/test/test_data.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/test/test_examples.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/test/test_zmatrix.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/test/test_graphs.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test creating /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/cpmd.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/number_state.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/atrj.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/gromacs.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/psf.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/fchk.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/pdb.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/crystal.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/cml.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/common.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/xyz.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/cube.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/lammps.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/gamess.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/cp2k.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/chk.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/dlpoly.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/sdf.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/__init__.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io creating /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/test/test_cp2k.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/test/test_pdb.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/test/test_dlpoly.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/test/__init__.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/test/test_gamess.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/test/test_lammps.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/test/test_cml.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/test/test_atrj.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/test/test_sdf.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/test/test_gromacs.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/test/test_number_state.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/test/test_fchk.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/test/test_xyz.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/test/test_cube.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/test/test_cpmd.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/test/test_chk.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/test/test_crystal.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/io/test/test_psf.py -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/common.c -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/common.h -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/ext.pyx -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/ff.c -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/ff.h -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/ff.pxd -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/graphs.c -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/graphs.h -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/graphs.pxd -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/molecules.c -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/molecules.h -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/molecules.pxd -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/similarity.c -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/similarity.h -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/similarity.pxd -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/unit_cells.c -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/unit_cells.h -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/unit_cells.pxd -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod creating /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/bonds.csv -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/bonds.ods -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/mass.mas03 -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/nubtab03.asc -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/periodic.csv -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/periodic.ods -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/toyff_angles.txt -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data creating /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/water.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/tpa.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/zr4o8-3.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/water_md.inp -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/water2.gro -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/thf_single.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/opt_6ring.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/opt_5ring10T.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/precursor.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/opt_5ring12T.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/thf_64.cell -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/pentapeptide.psf -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/tea.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/thf.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/osih2osihosih2osih2ozrh2oh.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/thf.psf -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/oh3siozroh3.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/opt_6_6ring.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/tetra.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/probes.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/lau.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/octane.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/alanine.cube -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/argon.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/dlpoly_OUTPUT -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/dlpoly_HISTORY_an2 -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/ethane.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/dlpoly_HISTORY -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/dopamine.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/crystal_api.out -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/caplayer.cml -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/dinitrogen.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/formol.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/example.sdf -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/lammps_dump.txt -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/h3zrosihohosioh3.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/il2.pdb -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/ethene_ethyl_trans.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/funny.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/ethene.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/butane.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/cyclopentane.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/benzene.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/bartek.atrj -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/PCGamess_PUNCH -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/SID_54258192.sdf -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/TRAJECTORY_H2_CPMD -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/SID_56274343.sdf -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/SID_55488598.sdf -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/SID_40363571.sdf -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/SID_31646548.sdf -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/SID_41893280.sdf -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/SID_55127927.sdf -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/SID_41893278.sdf -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/SID_31646545.sdf -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/SID_40363570.sdf -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/1LJL_Cys10.cml -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/1TOH.b3lyp.fchk -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/1TOH.b3lyp.trim.fchk -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/5ringOH.xyz -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test copying build/lib.dragonfly-5.7-x86_64-3.6/molmod/data/test/CID_22898828.sdf -> /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/data/test byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/000_units/c_h2rot.py to c_h2rot.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/000_units/b_chbond.py to b_chbond.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/000_units/a_reaction.py to a_reaction.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/004_patterns/b_dopamine_types.py to b_dopamine_types.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/004_patterns/a_propane_types.py to a_propane_types.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/001_molecules/e_shape.py to e_shape.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/001_molecules/d_size.py to d_size.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/001_molecules/b_com.py to b_com.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/001_molecules/a_convert.py to a_convert.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/001_molecules/c_carbon.py to c_carbon.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/002_graphs/a_graphs.py to a_graphs.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/002_graphs/c_distances.py to c_distances.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/002_graphs/d_symmetries.py to d_symmetries.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/002_graphs/b_neighbors.py to b_neighbors.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/003_internal_coordinates/d_dft_hessian.py to d_dft_hessian.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/003_internal_coordinates/b_bending_angles.py to b_bending_angles.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/003_internal_coordinates/c_ff_hessian.py to c_ff_hessian.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/examples/003_internal_coordinates/a_bond_length.py to a_bond_length.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/utils.py to utils.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/vectors.py to vectors.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/units.py to units.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/zmatrix.py to zmatrix.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/unit_cells.py to unit_cells.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/version.py to version.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/ic.py to ic.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/log.py to log.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/symmetry.py to symmetry.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/constants.py to constants.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/binning.py to binning.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/randomize.py to randomize.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/molecular_graphs.py to molecular_graphs.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/minimizer.py to minimizer.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/similarity.py to similarity.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/pairff.py to pairff.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/bonds.py to bonds.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/toyff.py to toyff.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/transformations.py to transformations.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/isotopes.py to isotopes.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/molecules.py to molecules.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/clusters.py to clusters.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/periodic.py to periodic.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/quaternions.py to quaternions.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/graphs.py to graphs.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test/test_minimizer.py to test_minimizer.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test/test_vectors.py to test_vectors.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test/test_molecular_graphs.py to test_molecular_graphs.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test/test_quaternions.py to test_quaternions.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test/test_toyff.py to test_toyff.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test/common.py to common.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test/test_units.py to test_units.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test/test_transformations.py to test_transformations.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test/test_randomize.py to test_randomize.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test/test_similarity.py to test_similarity.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test/test_molecules.py to test_molecules.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test/test_utils.py to test_utils.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test/test_pairff.py to test_pairff.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test/test_symmetry.py to test_symmetry.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test/test_ic.py to test_ic.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test/test_clusters.py to test_clusters.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test/test_unit_cells.py to test_unit_cells.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test/test_binning.py to test_binning.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test/test_log.py to test_log.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test/test_data.py to test_data.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test/test_examples.py to test_examples.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test/test_zmatrix.py to test_zmatrix.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/test/test_graphs.py to test_graphs.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/cpmd.py to cpmd.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/number_state.py to number_state.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/atrj.py to atrj.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/gromacs.py to gromacs.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/psf.py to psf.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/fchk.py to fchk.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/pdb.py to pdb.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/crystal.py to crystal.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/cml.py to cml.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/common.py to common.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/xyz.py to xyz.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/cube.py to cube.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/lammps.py to lammps.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/gamess.py to gamess.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/cp2k.py to cp2k.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/chk.py to chk.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/dlpoly.py to dlpoly.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/sdf.py to sdf.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/test/test_cp2k.py to test_cp2k.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/test/test_pdb.py to test_pdb.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/test/test_dlpoly.py to test_dlpoly.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/test/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/test/test_gamess.py to test_gamess.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/test/test_lammps.py to test_lammps.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/test/test_cml.py to test_cml.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/test/test_atrj.py to test_atrj.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/test/test_sdf.py to test_sdf.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/test/test_gromacs.py to test_gromacs.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/test/test_number_state.py to test_number_state.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/test/test_fchk.py to test_fchk.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/test/test_xyz.py to test_xyz.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/test/test_cube.py to test_cube.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/test/test_cpmd.py to test_cpmd.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/test/test_chk.py to test_chk.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/test/test_crystal.py to test_crystal.cpython-36.pyc byte-compiling /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod/io/test/test_psf.py to test_psf.cpython-36.pyc writing byte-compilation script '/tmp/tmpfsueiclz.py' /usr/local/bin/python3.6 /tmp/tmpfsueiclz.py removing /tmp/tmpfsueiclz.py running install_egg_info Copying molmod.egg-info to /construction/science/py-molmod/stage/usr/local/lib/python3.6/site-packages/molmod-1.4.4-py3.6.egg-info running install_scripts writing list of installed files to '/construction/science/py-molmod/.PLIST.pymodtmp' ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Error: /usr/local/lib/python3.6/site-packages/molmod/ext.so is linked to /usr/local/lib/libintl.so.8 from devel/gettext-runtime but it is not declared as a dependency Warning: you need USES+=gettext-runtime Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:05 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- x====> 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 00:00:01 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- x===> Building package for py36-molmod-1.4.4_2 file sizes/checksums [417]: 0% file sizes/checksums [417]: 23% file sizes/checksums [417]: 47% file sizes/checksums [417]: 71% file sizes/checksums [417]: 95% file sizes/checksums [417]: 100% packing files [417]: 0% packing files [417]: 23% packing files [417]: 47% packing files [417]: 71% packing files [417]: 95% packing files [417]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:01 TOTAL TIME 00:00:49