=> Building science/py-MDAnalysis@py36 Started : Friday, 20 JUL 2018 at 20:11:52 UTC Platform: 5.3-DEVELOPMENT DragonFly v5.3.0.242.g757c0-DEVELOPMENT #30: Tue May 8 14:06:27 PDT 2018 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.2-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.2-SYNTH UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 TERM=dumb PKG_CACHEDIR=/var/cache/pkg8 PKG_DBDIR=/var/db/pkg8 PORTSDIR=/xports LANG=C HOME=/root USER=root -------------------------------------------------- -- Options -------------------------------------------------- -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- PYTHON="/usr/local/bin/python3.6" XDG_DATA_HOME=/construction/science/py-MDAnalysis XDG_CONFIG_HOME=/construction/science/py-MDAnalysis HOME=/construction/science/py-MDAnalysis TMPDIR="/tmp" PATH=/construction/science/py-MDAnalysis/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/science/py-MDAnalysis XDG_CONFIG_HOME=/construction/science/py-MDAnalysis HOME=/construction/science/py-MDAnalysis TMPDIR="/tmp" PATH=/construction/science/py-MDAnalysis/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc50 LDSHARED="cc -shared" PYTHONDONTWRITEBYTECODE= PYTHONOPTIMIZE= PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS="" LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing" MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/science/py-MDAnalysis/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PORTDOCS="" PORTEXAMPLES="" PYTHON_INCLUDEDIR=include/python3.6m PYTHON_LIBDIR=lib/python3.6 PYTHON_PLATFORM=dragonfly5 PYTHON_PYOEXTENSION=opt-1.pyc PYTHON_SITELIBDIR=lib/python3.6/site-packages PYTHON_SUFFIX=36 PYTHON_VER=3.6 PYTHON_VERSION=python3.6 PYTHON2="@comment " PYTHON3="" OSREL=5.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/MDAnalysis" EXAMPLESDIR="share/examples/MDAnalysis" DATADIR="share/MDAnalysis" WWWDIR="www/MDAnalysis" ETCDIR="etc/MDAnalysis" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/MDAnalysis DOCSDIR=/usr/local/share/doc/MDAnalysis EXAMPLESDIR=/usr/local/share/examples/MDAnalysis WWWDIR=/usr/local/www/MDAnalysis ETCDIR=/usr/local/etc/MDAnalysis -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-5.2 USE_PACKAGE_DEPENDS_ONLY=yes PACKAGE_BUILDING=yes BATCH=yes PKG_CREATE_VERBOSE=yes PORTSDIR=/xports DISTDIR=/distfiles WRKDIRPREFIX=/construction PORT_DBDIR=/options PACKAGES=/packages MAKE_JOBS_NUMBER_LIMIT=5 LICENSES_ACCEPTED= NONE HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _PERL5_FROM_BIN=5.26.1 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500200 OSVERSION=9999999 OSREL=5.2 _OSRELEASE=5.2-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License GPLv2 accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> py36-MDAnalysis-0.18.0 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_1.txz Installing pkg-1.10.5_1... Extracting pkg-1.10.5_1: .......... done ===> py36-MDAnalysis-0.18.0 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py36-MDAnalysis-0.18.0 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by py36-MDAnalysis-0.18.0 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by py36-MDAnalysis-0.18.0 for building => SHA256 Checksum OK for MDAnalysis-0.18.0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by py36-MDAnalysis-0.18.0 for building ===> Extracting for py36-MDAnalysis-0.18.0 => SHA256 Checksum OK for MDAnalysis-0.18.0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for py36-MDAnalysis-0.18.0 ===> Applying ports patches for py36-MDAnalysis-0.18.0 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> py36-MDAnalysis-0.18.0 depends on package: py36-numpy>0 - not found ===> Installing existing package /packages/All/py36-numpy-1.14.3,1.txz Installing py36-numpy-1.14.3,1... `-- Installing gcc5-5.5.0_4... | `-- Installing binutils-2.30_3,1... | | `-- Installing gettext-runtime-0.19.8.1_1... | | `-- Installing indexinfo-0.3.1... | | `-- Extracting indexinfo-0.3.1: .... done | | `-- Extracting gettext-runtime-0.19.8.1_1: .......... done | `-- Extracting binutils-2.30_3,1: .......... done | `-- Installing gmp-6.1.2... | `-- Extracting gmp-6.1.2: .......... done | `-- Installing mpc-1.1.0_1... | | `-- Installing mpfr-4.0.1... | | `-- Extracting mpfr-4.0.1: .......... done | `-- Extracting mpc-1.1.0_1: ......... done `-- Extracting gcc5-5.5.0_4: .......... done `-- Installing openblas-0.2.20_2,1... `-- Extracting openblas-0.2.20_2,1: ......... done `-- Installing py36-setuptools-39.2.0... | `-- Installing python36-3.6.5... | | `-- Installing expat-2.2.5... | | `-- Extracting expat-2.2.5: .......... done | | `-- Installing libffi-3.2.1_2... | | `-- Extracting libffi-3.2.1_2: .......... done | | `-- Installing libressl-2.7.4... | | `-- Extracting libressl-2.7.4: .......... done | | `-- Installing ncurses-6.0.0s20171223_1... | | `-- Extracting ncurses-6.0.0s20171223_1: .......... done | | `-- Installing readline-7.0.3_1... | | `-- Extracting readline-7.0.3_1: .......... done | `-- Extracting python36-3.6.5: .......... done `-- Extracting py36-setuptools-39.2.0: .......... done `-- Installing suitesparse-5.2.0... | `-- Installing lapack-3.5.0_4... | | `-- Installing blas-3.5.0_4... | | `-- Extracting blas-3.5.0_4: ....... done | `-- Extracting lapack-3.5.0_4: .......... done | `-- Installing metis-5.1.0_4... | `-- Extracting metis-5.1.0_4: .......... done `-- Extracting suitesparse-5.2.0: .......... done Extracting py36-numpy-1.14.3,1: .......... done Message from gcc5-5.5.0_4: 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/gcc5 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Unsupported by upstream. Use GCC 6 or newer instead.. Message from python36-3.6.5: =========================================================================== 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 =========================================================================== Message from py36-setuptools-39.2.0: ******************************************************************* Only /usr/local/bin/easy_install-3.6 script has been installed since Python 3.6 is not the default Python version. ******************************************************************* Message from metis-5.1.0_4: ===> 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 ===> py36-MDAnalysis-0.18.0 depends on package: py36-numpy>0 - found ===> Returning to build of py36-MDAnalysis-0.18.0 ===> py36-MDAnalysis-0.18.0 depends on package: py36-setuptools>0 - found ===> py36-MDAnalysis-0.18.0 depends on file: /usr/local/bin/python3.6 - found -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for py36-MDAnalysis-0.18.0 Attempting to autodetect OpenMP support... Compiler supports OpenMP Will not attempt to use Cython. running config -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for py36-MDAnalysis-0.18.0 Attempting to autodetect OpenMP support... Compiler supports OpenMP Will not attempt to use Cython. running build running build_py creating build creating build/lib.dragonfly-5.2-SYNTH-x86_64-3.6 creating build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis copying MDAnalysis/due.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis copying MDAnalysis/units.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis copying MDAnalysis/exceptions.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis copying MDAnalysis/authors.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis copying MDAnalysis/KDTree.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis copying MDAnalysis/version.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis copying MDAnalysis/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis creating build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/tests copying MDAnalysis/tests/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/tests copying MDAnalysis/tests/datafiles.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/tests creating build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/XVG.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/core.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/base.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/auxiliary creating build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/visualization copying MDAnalysis/visualization/streamlines_3D.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/visualization copying MDAnalysis/visualization/streamlines.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/visualization copying MDAnalysis/visualization/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/visualization creating build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRR.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/PDB.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/base.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/MOL2.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/dummy.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/PDBQT.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/PQR.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/XTC.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/chain.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/DMS.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/MMTF.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRJ.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/GMS.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/DCD.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/memory.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/XDR.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/GSD.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/GRO.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/TXYZ.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/INPCRD.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/null.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/XYZ.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/CRD.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/core.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/LAMMPS.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/DLPoly.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRZ.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates creating build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/core copying MDAnalysis/core/qcprot.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/core copying MDAnalysis/core/topology.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/core copying MDAnalysis/core/groups.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/core copying MDAnalysis/core/distances.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/core copying MDAnalysis/core/units.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/core copying MDAnalysis/core/parallel.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/core copying MDAnalysis/core/AtomGroup.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/core copying MDAnalysis/core/topologyattrs.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/core copying MDAnalysis/core/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/core copying MDAnalysis/core/log.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/core copying MDAnalysis/core/util.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/core copying MDAnalysis/core/universe.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/core copying MDAnalysis/core/transformations.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/core copying MDAnalysis/core/_get_readers.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/core copying MDAnalysis/core/topologyobjects.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/core copying MDAnalysis/core/selection.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/core creating build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/migration copying MDAnalysis/migration/test_dummy_old_MDA_code.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/migration copying MDAnalysis/migration/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/migration copying MDAnalysis/migration/test_dummy_torsion.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/migration copying MDAnalysis/migration/ten2eleven.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/migration creating build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis copying MDAnalysis/analysis/lineardensity.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis copying MDAnalysis/analysis/diffusionmap.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis copying MDAnalysis/analysis/x3dna.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis copying MDAnalysis/analysis/psa.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis copying MDAnalysis/analysis/helanal.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis copying MDAnalysis/analysis/density.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis copying MDAnalysis/analysis/leaflet.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis copying MDAnalysis/analysis/align.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis copying MDAnalysis/analysis/polymer.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis copying MDAnalysis/analysis/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis copying MDAnalysis/analysis/pca.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis copying MDAnalysis/analysis/waterdynamics.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis copying MDAnalysis/analysis/hole.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis copying MDAnalysis/analysis/nuclinfo.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis copying MDAnalysis/analysis/gnm.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis copying MDAnalysis/analysis/distances.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis copying MDAnalysis/analysis/rms.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis copying MDAnalysis/analysis/base.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis copying MDAnalysis/analysis/rdf.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis copying MDAnalysis/analysis/contacts.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis creating build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/selections copying MDAnalysis/selections/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/selections copying MDAnalysis/selections/pymol.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/selections copying MDAnalysis/selections/gromacs.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/selections copying MDAnalysis/selections/charmm.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/selections copying MDAnalysis/selections/jmol.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/selections copying MDAnalysis/selections/vmd.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/selections copying MDAnalysis/selections/base.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/selections creating build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib copying MDAnalysis/lib/util.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib copying MDAnalysis/lib/pkdtree.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib copying MDAnalysis/lib/NeighborSearch.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib copying MDAnalysis/lib/transformations.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib copying MDAnalysis/lib/mdamath.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib copying MDAnalysis/lib/distances.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib copying MDAnalysis/lib/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib copying MDAnalysis/lib/log.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib creating build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/CRDParser.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/PQRParser.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/MinimalParser.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/_elements.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/XYZParser.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/PSFParser.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/MOL2Parser.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/GROParser.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/DLPolyParser.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/base.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/TOPParser.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/HoomdXMLParser.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/tables.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/PDBQTParser.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/TXYZParser.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/DMSParser.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/LAMMPSParser.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/TPRParser.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/MMTFParser.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/guessers.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/ExtendedPDBParser.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/PDBParser.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/core.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/GSDParser.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/GMSParser.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology creating build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_torsionclasses.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_agmethods.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_framenumberingzerobased2.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_torsions.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_numframes.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_writer.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_mdaimports.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_agsetterpluralization.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_calctorsions.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_framenumberingzerobased.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_selectatoms.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_agmethods2.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_camelcase.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_agcountmethods.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/migration/fixes creating build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/legacy copying MDAnalysis/analysis/legacy/x3dna.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/legacy copying MDAnalysis/analysis/legacy/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/legacy creating build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/hbonds copying MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/hbonds copying MDAnalysis/analysis/hbonds/hbond_analysis.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/hbonds copying MDAnalysis/analysis/hbonds/wbridge_analysis.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/hbonds copying MDAnalysis/analysis/hbonds/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/hbonds creating build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/bootstrap.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/covariance.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/utils.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/confdistmatrix.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/similarity.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore creating build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore/dimensionality_reduction creating build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/cluster.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore/clustering creating build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/formats creating build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/obj.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/setting.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/utils.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology/tpr running build_ext building 'MDAnalysis.lib.formats.libdcd' extension creating build/temp.dragonfly-5.2-SYNTH-x86_64-3.6 creating build/temp.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis creating build/temp.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib creating build/temp.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/formats cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.6/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -I/usr/local/include/python3.6m -c MDAnalysis/lib/formats/libdcd.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/formats/libdcd.o -std=c99 -ffast-math -funroll-loops In file included from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1816:0, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/lib/formats/libdcd.c:595: /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it by " \ ^ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/formats/libdcd.o -L/usr/local/lib -lpython3.6m -o build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/formats/libdcd.so building 'MDAnalysis.lib.c_distances' extension cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.6/site-packages/numpy/core/include -IMDAnalysis/lib/include -I/usr/local/include/python3.6m -c MDAnalysis/lib/c_distances.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/c_distances.o -std=c99 -ffast-math -funroll-loops In file included from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1816:0, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/lib/c_distances.c:596: /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it by " \ ^ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/c_distances.o -L/usr/local/lib -lm -lpython3.6m -o build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/c_distances.so building 'MDAnalysis.lib.c_distances_openmp' extension cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -DPARALLEL -I/usr/local/lib/python3.6/site-packages/numpy/core/include -IMDAnalysis/lib/include -I/usr/local/include/python3.6m -c MDAnalysis/lib/c_distances_openmp.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/c_distances_openmp.o -fopenmp -std=c99 -ffast-math -funroll-loops In file included from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1816:0, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/lib/c_distances_openmp.c:607: /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it by " \ ^ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/c_distances_openmp.o -L/usr/local/lib -lm -lgomp -lpython3.6m -o build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/c_distances_openmp.so -fopenmp building 'MDAnalysis.lib.qcprot' extension 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 MDAnalysis/lib/qcprot.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/qcprot.o -std=c99 -ffast-math -funroll-loops In file included from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1816:0, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/lib/qcprot.c:591: /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it by " \ ^ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/qcprot.o -L/usr/local/lib -lpython3.6m -o build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/qcprot.so building 'MDAnalysis.lib._transformations' extension creating build/temp.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/src creating build/temp.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/src/transformations 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 MDAnalysis/lib/src/transformations/transformations.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/src/transformations/transformations.o -std=c99 -ffast-math -funroll-loops In file included from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1816:0, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/lib/src/transformations/transformations.c:73: /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it by " \ ^ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/src/transformations/transformations.o -L/usr/local/lib -lm -lpython3.6m -o build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/_transformations.so building 'MDAnalysis.lib.formats.libmdaxdr' extension creating build/temp.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/formats/src cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/local/lib/python3.6/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/local/include/python3.6m -c MDAnalysis/lib/formats/libmdaxdr.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/formats/libmdaxdr.o -std=c99 -ffast-math -funroll-loops In file included from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1816:0, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/lib/formats/libmdaxdr.c:617: /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it by " \ ^ cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/local/lib/python3.6/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/local/include/python3.6m -c MDAnalysis/lib/formats/src/xdrfile.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/formats/src/xdrfile.o -std=c99 -ffast-math -funroll-loops MDAnalysis/lib/formats/src/xdrfile.c:2528:3: warning: initialization from incompatible pointer type [-Wincompatible-pointer-types] xdrstdio_getpos, /* get offset in the stream */ ^ MDAnalysis/lib/formats/src/xdrfile.c:2528:3: note: (near initialization for 'xdrstdio_ops.x_getpostn') MDAnalysis/lib/formats/src/xdrfile.c:2529:3: warning: initialization from incompatible pointer type [-Wincompatible-pointer-types] xdrstdio_setpos, /* set offset in the stream */ ^ MDAnalysis/lib/formats/src/xdrfile.c:2529:3: note: (near initialization for 'xdrstdio_ops.x_setpostn') cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/local/lib/python3.6/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/local/include/python3.6m -c MDAnalysis/lib/formats/src/xdrfile_xtc.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/formats/src/xdrfile_xtc.o -std=c99 -ffast-math -funroll-loops cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/local/lib/python3.6/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/local/include/python3.6m -c MDAnalysis/lib/formats/src/xdrfile_trr.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/formats/src/xdrfile_trr.o -std=c99 -ffast-math -funroll-loops cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/local/lib/python3.6/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/local/include/python3.6m -c MDAnalysis/lib/formats/src/trr_seek.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/formats/src/trr_seek.o -std=c99 -ffast-math -funroll-loops cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/local/lib/python3.6/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/local/include/python3.6m -c MDAnalysis/lib/formats/src/xtc_seek.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/formats/src/xtc_seek.o -std=c99 -ffast-math -funroll-loops cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/formats/libmdaxdr.o build/temp.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/formats/src/xdrfile.o build/temp.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/formats/src/xdrfile_xtc.o build/temp.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/formats/src/xdrfile_trr.o build/temp.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/formats/src/trr_seek.o build/temp.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/formats/src/xtc_seek.o -L/usr/local/lib -lpython3.6m -o build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/formats/libmdaxdr.so building 'MDAnalysis.lib.formats.cython_util' extension 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 MDAnalysis/lib/formats/cython_util.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/formats/cython_util.o -std=c99 -ffast-math -funroll-loops In file included from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1816:0, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/lib/formats/cython_util.c:591: /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it by " \ ^ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/formats/cython_util.o -L/usr/local/lib -lpython3.6m -o build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/formats/cython_util.so building 'MDAnalysis.analysis.encore.cutils' extension creating build/temp.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis creating build/temp.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore 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 MDAnalysis/analysis/encore/cutils.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore/cutils.o -std=c99 -ffast-math -funroll-loops In file included from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1816:0, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/analysis/encore/cutils.c:591: /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it by " \ ^ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore/cutils.o -L/usr/local/lib -lpython3.6m -o build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore/cutils.so building 'MDAnalysis.analysis.encore.clustering.affinityprop' extension creating build/temp.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore/clustering creating build/temp.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore/clustering/src cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.6/site-packages/numpy/core/include -IMDAnalysis/analysis/encore/clustering/include -I/usr/local/include/python3.6m -c MDAnalysis/analysis/encore/clustering/affinityprop.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore/clustering/affinityprop.o -std=c99 -ffast-math -funroll-loops In file included from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1816:0, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/analysis/encore/clustering/affinityprop.c:597: /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it by " \ ^ cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.6/site-packages/numpy/core/include -IMDAnalysis/analysis/encore/clustering/include -I/usr/local/include/python3.6m -c MDAnalysis/analysis/encore/clustering/src/ap.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore/clustering/src/ap.o -std=c99 -ffast-math -funroll-loops cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore/clustering/affinityprop.o build/temp.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore/clustering/src/ap.o -L/usr/local/lib -lm -lpython3.6m -o build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore/clustering/affinityprop.so building 'MDAnalysis.analysis.encore.dimensionality_reduction.stochasticproxembed' extension creating build/temp.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore/dimensionality_reduction creating build/temp.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore/dimensionality_reduction/src cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.6/site-packages/numpy/core/include -IMDAnalysis/analysis/encore/dimensionality_reduction/include -I/usr/local/include/python3.6m -c MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.o -std=c99 -ffast-math -funroll-loops In file included from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1816:0, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c:597: /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it by " \ ^ cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.6/site-packages/numpy/core/include -IMDAnalysis/analysis/encore/dimensionality_reduction/include -I/usr/local/include/python3.6m -c MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.o -std=c99 -ffast-math -funroll-loops cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.o build/temp.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.o -L/usr/local/lib -lm -lpython3.6m -o build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.so -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> py36-MDAnalysis-0.18.0 depends on package: py36-numpy>0 - found ===> py36-MDAnalysis-0.18.0 depends on package: py36-biopython>=1.59 - not found ===> Installing existing package /packages/All/py36-biopython-1.71_1.txz Installing py36-biopython-1.71_1... `-- Installing py36-reportlab-3.2.0... | `-- Installing adobe-cmaps-20051217_3... | | `-- Installing fontconfig-2.12.6,1... | | `-- Installing freetype2-2.9.1... | | `-- Extracting freetype2-2.9.1: .......... done | | `-- Extracting fontconfig-2.12.6,1: .......... done Running fc-cache to build fontconfig cache... /usr/local/share/fonts: skipping, no such directory /usr/local/lib/X11/fonts: skipping, no such directory /var/db/fontconfig: cleaning cache directory fc-cache: succeeded | | `-- Installing mkfontdir-1.0.7... | | `-- Installing mkfontscale-1.1.3... | | | `-- Installing libfontenc-1.1.3_1... | | | `-- Installing xproto-7.0.31... | | | `-- Extracting xproto-7.0.31: .......... done | | | `-- Extracting libfontenc-1.1.3_1: ......... done | | `-- Extracting mkfontscale-1.1.3: ..... done | | `-- Extracting mkfontdir-1.0.7: ..... done | `-- Extracting adobe-cmaps-20051217_3: .......... done | `-- Installing py36-pillow-5.0.0... | | `-- Installing jpeg-turbo-1.5.3... | | `-- Extracting jpeg-turbo-1.5.3: .......... done | | `-- Installing openjpeg-2.3.0... | | `-- Installing lcms2-2.9... | | | `-- Installing tiff-4.0.9_1... | | | `-- Installing jbigkit-2.1_1... | | | `-- Extracting jbigkit-2.1_1: .......... done | | | `-- Extracting tiff-4.0.9_1: .......... done | | `-- Extracting lcms2-2.9: .......... done | | `-- Installing png-1.6.34... | | `-- Extracting png-1.6.34: .......... done | | `-- Extracting openjpeg-2.3.0: .......... done | | `-- Installing py36-tkinter-3.6.5_6... | | `-- Installing tcl86-8.6.8... | | `-- Extracting tcl86-8.6.8: .......... done | | `-- Installing tk86-8.6.8_2... | | | `-- Installing libX11-1.6.5,1... | | | `-- Installing kbproto-1.0.7... | | | `-- Extracting kbproto-1.0.7: .......... done | | | `-- Installing libXau-1.0.8_3... | | | `-- Extracting libXau-1.0.8_3: .......... done | | | `-- Installing libXdmcp-1.1.2... | | | `-- Extracting libXdmcp-1.1.2: ......... done | | | `-- Installing libxcb-1.13... | | | | `-- Installing libpthread-stubs-0.4... | | | | `-- Extracting libpthread-stubs-0.4: .... done | | | | `-- Installing libxml2-2.9.7... | | | | `-- Extracting libxml2-2.9.7: .......... done | | | `-- Extracting libxcb-1.13: .......... done | | | `-- Extracting libX11-1.6.5,1: .......... done | | | `-- Installing libXScrnSaver-1.2.2_3... | | | `-- Installing libXext-1.3.3_1,1... | | | | `-- Installing xextproto-7.3.0... | | | | `-- Extracting xextproto-7.3.0: .......... done | | | `-- Extracting libXext-1.3.3_1,1: .......... done | | | `-- Installing scrnsaverproto-1.2.2... | | | `-- Extracting scrnsaverproto-1.2.2: ... done | | | `-- Extracting libXScrnSaver-1.2.2_3: .......... done | | | `-- Installing libXft-2.3.2_1... | | | `-- Installing libXrender-0.9.10... | | | | `-- Installing renderproto-0.11.1... | | | | `-- Extracting renderproto-0.11.1: .... done | | | `-- Extracting libXrender-0.9.10: .......... done | | | `-- Extracting libXft-2.3.2_1: .......... done | | `-- Extracting tk86-8.6.8_2: .......... done | | `-- Extracting py36-tkinter-3.6.5_6: ........ done | | `-- Installing webp-1.0.0... | | `-- Installing giflib-5.1.4... | | `-- Extracting giflib-5.1.4: .......... done | | `-- Extracting webp-1.0.0: .......... done | `-- Extracting py36-pillow-5.0.0: .......... done `-- Extracting py36-reportlab-3.2.0: .......... done Extracting py36-biopython-1.71_1: .......... done Message from freetype2-2.9.1: The 2.7.x series now uses the new subpixel hinting mode (V40 port's option) as the default, emulating a modern version of ClearType. This change inevitably leads to different rendering results, and you might change port's options to adapt it to your taste (or use the new "FREETYPE_PROPERTIES" environment variable). The environment variable "FREETYPE_PROPERTIES" can be used to control the driver properties. Example: FREETYPE_PROPERTIES=truetype:interpreter-version=35 \ cff:no-stem-darkening=1 \ autofitter:warping=1 This allows to select, say, the subpixel hinting mode at runtime for a given application. The controllable properties are listed in the section "Controlling FreeType Modules" in the reference's table of contents (/usr/local/share/doc/freetype2/reference/ft2-toc.html, if documentation was installed). ===> py36-MDAnalysis-0.18.0 depends on package: py36-biopython>=1.59 - found ===> Returning to build of py36-MDAnalysis-0.18.0 ===> py36-MDAnalysis-0.18.0 depends on package: py36-duecredit>0 - not found ===> Installing existing package /packages/All/py36-duecredit-0.6.4.txz Installing py36-duecredit-0.6.4... `-- Installing py36-citeproc-py-0.4.0... | `-- Installing py36-lxml-4.1.1... | | `-- Installing libxslt-1.1.32... | | `-- Installing libgcrypt-1.8.3... | | | `-- Installing libgpg-error-1.31... | | | `-- Extracting libgpg-error-1.31: .......... done | | `-- Extracting libgcrypt-1.8.3: .......... done | | `-- Extracting libxslt-1.1.32: .......... done | `-- Extracting py36-lxml-4.1.1: .......... done `-- Extracting py36-citeproc-py-0.4.0: ......... done `-- Installing py36-requests-2.18.4... | `-- Installing py36-certifi-2018.4.16... | `-- Extracting py36-certifi-2018.4.16: .......... done | `-- Installing py36-chardet-3.0.4... | `-- Extracting py36-chardet-3.0.4: .......... done | `-- Installing py36-idna-2.6... | `-- Extracting py36-idna-2.6: .......... done | `-- Installing py36-urllib3-1.22,1... | | `-- Installing py36-cryptography-2.1.4... | | `-- Installing py36-asn1crypto-0.22.0... | | `-- Extracting py36-asn1crypto-0.22.0: .......... done | | `-- Installing py36-cffi-1.11.5... | | | `-- Installing py36-pycparser-2.18... | | | `-- Extracting py36-pycparser-2.18: .......... done | | `-- Extracting py36-cffi-1.11.5: .......... done | | `-- Installing py36-six-1.11.0... | | `-- Extracting py36-six-1.11.0: .......... done | | `-- Extracting py36-cryptography-2.1.4: .......... done | | `-- Installing py36-openssl-17.5.0_1... | | `-- Extracting py36-openssl-17.5.0_1: .......... done | | `-- Installing py36-pysocks-1.6.8... | | `-- Extracting py36-pysocks-1.6.8: .......... done | `-- Extracting py36-urllib3-1.22,1: .......... done `-- Extracting py36-requests-2.18.4: .......... done Extracting py36-duecredit-0.6.4: .......... done Message from py36-urllib3-1.22,1: Be careful, support of IPv6 is broken with PySocks 1.5.7. ===> py36-MDAnalysis-0.18.0 depends on package: py36-duecredit>0 - found ===> Returning to build of py36-MDAnalysis-0.18.0 ===> py36-MDAnalysis-0.18.0 depends on package: py36-GridDataFormats>=0.4.0 - not found ===> Installing existing package /packages/All/py36-GridDataFormats-0.4.0.txz Installing py36-GridDataFormats-0.4.0... Extracting py36-GridDataFormats-0.4.0: .......... done ===> py36-MDAnalysis-0.18.0 depends on package: py36-GridDataFormats>=0.4.0 - found ===> Returning to build of py36-MDAnalysis-0.18.0 ===> py36-MDAnalysis-0.18.0 depends on package: py36-gsd>=1.4.0 - not found ===> Installing existing package /packages/All/py36-gsd-1.5.2.txz Installing py36-gsd-1.5.2... Extracting py36-gsd-1.5.2: .......... done ===> py36-MDAnalysis-0.18.0 depends on package: py36-gsd>=1.4.0 - found ===> Returning to build of py36-MDAnalysis-0.18.0 ===> py36-MDAnalysis-0.18.0 depends on package: py36-joblib>0 - not found ===> Installing existing package /packages/All/py36-joblib-0.9.4.txz Installing py36-joblib-0.9.4... Extracting py36-joblib-0.9.4: .......... done ===> py36-MDAnalysis-0.18.0 depends on package: py36-joblib>0 - found ===> Returning to build of py36-MDAnalysis-0.18.0 ===> py36-MDAnalysis-0.18.0 depends on package: py36-matplotlib>=1.5.1 - not found ===> Installing existing package /packages/All/py36-matplotlib-2.1.2_2.txz Installing py36-matplotlib-2.1.2_2... `-- Installing py36-cycler-0.10.0... `-- Extracting py36-cycler-0.10.0: .......... done `-- Installing py36-dateutil-2.6.1... `-- Extracting py36-dateutil-2.6.1: .......... done `-- Installing py36-pyparsing-2.2.0... `-- Extracting py36-pyparsing-2.2.0: .......... done `-- Installing py36-pytz-2018.5,1... `-- Extracting py36-pytz-2018.5,1: .......... done `-- Installing py36-tornado-5.0.2... `-- Extracting py36-tornado-5.0.2: .......... done Extracting py36-matplotlib-2.1.2_2: .......... done ===> py36-MDAnalysis-0.18.0 depends on package: py36-matplotlib>=1.5.1 - found ===> Returning to build of py36-MDAnalysis-0.18.0 ===> py36-MDAnalysis-0.18.0 depends on package: py36-mmtf-python>=1.0.0 - not found ===> Installing existing package /packages/All/py36-mmtf-python-1.1.2.txz Installing py36-mmtf-python-1.1.2... `-- Installing py36-msgpack-0.5.6... `-- Extracting py36-msgpack-0.5.6: .......... done Extracting py36-mmtf-python-1.1.2: .......... done ===> py36-MDAnalysis-0.18.0 depends on package: py36-mmtf-python>=1.0.0 - found ===> Returning to build of py36-MDAnalysis-0.18.0 ===> py36-MDAnalysis-0.18.0 depends on package: py36-networkx>=1.0 - not found ===> Installing existing package /packages/All/py36-networkx-1.10_4.txz Installing py36-networkx-1.10_4... `-- Installing py36-decorator-4.3.0... `-- Extracting py36-decorator-4.3.0: .......... done `-- Installing py36-pygraphviz-1.3.1... | `-- Installing graphviz-2.40.1_5... | | `-- Installing cairo-1.14.8_1,2... | | `-- Installing dri2proto-2.8... | | `-- Extracting dri2proto-2.8: .... done | | `-- Installing glib-2.50.3_4,1... | | | `-- Installing libiconv-1.14_11... | | | `-- Extracting libiconv-1.14_11: .......... done | | | `-- Installing pcre-8.42... | | | `-- Extracting pcre-8.42: .......... done | | | `-- Installing perl5-5.26.2... | | | `-- Extracting perl5-5.26.2: .......... done | | | `-- Installing python27-2.7.15... | | | `-- Extracting python27-2.7.15: .......... done | | `-- Extracting glib-2.50.3_4,1: .......... done No schema files found: doing nothing. | | `-- Installing glproto-1.4.17... | | `-- Extracting glproto-1.4.17: ...... done | | `-- Installing mesa-libs-18.1.2... | | | `-- Installing libXdamage-1.1.4_3... | | | `-- Installing damageproto-1.2.1... | | | `-- Extracting damageproto-1.2.1: .... done | | | `-- Installing libXfixes-5.0.3... | | | | `-- Installing fixesproto-5.0... | | | | `-- Extracting fixesproto-5.0: .... done | | | `-- Extracting libXfixes-5.0.3: .......... done | | | `-- Extracting libXdamage-1.1.4_3: ...... done | | | `-- Installing libXxf86vm-1.1.4_1... | | | `-- Installing xf86vidmodeproto-2.3.1... | | | `-- Extracting xf86vidmodeproto-2.3.1: .... done | | | `-- Extracting libXxf86vm-1.1.4_1: .......... done | | | `-- Installing libdrm-2.4.92,1... | | | `-- Installing libpciaccess-0.13.5... | | | | `-- Installing pciids-20180428... | | | | `-- Extracting pciids-20180428: ..... done | | | `-- Extracting libpciaccess-0.13.5: ......... done | | | `-- Extracting libdrm-2.4.92,1: .......... done | | | `-- Installing libelf-0.8.13_3... | | | `-- Extracting libelf-0.8.13_3: .......... done | | | `-- Installing libxshmfence-1.2_2... | | | `-- Extracting libxshmfence-1.2_2: ......... done | | `-- Extracting mesa-libs-18.1.2: .......... done | | `-- Installing pixman-0.34.0... | | `-- Extracting pixman-0.34.0: .......... done | | `-- Installing xcb-util-renderutil-0.3.9_1... | | | `-- Installing xcb-util-0.4.0_2,1... | | | `-- Extracting xcb-util-0.4.0_2,1: .......... done | | `-- Extracting xcb-util-renderutil-0.3.9_1: ...... done | | `-- Extracting cairo-1.14.8_1,2: .......... done | | `-- Installing libICE-1.0.9_1,1... | | `-- Extracting libICE-1.0.9_1,1: .......... done | | `-- Installing libSM-1.2.2_3,1... | | `-- Extracting libSM-1.2.2_3,1: .......... done | | `-- Installing libXaw-1.0.13,2... | | `-- Installing libXmu-1.1.2_3,1... | | | `-- Installing libXt-1.1.5,1... | | | `-- Extracting libXt-1.1.5,1: .......... done | | `-- Extracting libXmu-1.1.2_3,1: .......... done | | `-- Installing libXp-1.0.3,1... | | | `-- Installing printproto-1.0.5... | | | `-- Extracting printproto-1.0.5: .... done | | `-- Extracting libXp-1.0.3,1: .......... done | | `-- Installing libXpm-3.5.12... | | `-- Extracting libXpm-3.5.12: .......... done | | `-- Extracting libXaw-1.0.13,2: .......... done | | `-- Installing libgd-2.2.4_1,1... | | `-- Extracting libgd-2.2.4_1,1: .......... done | | `-- Installing libltdl-2.4.6... | | `-- Extracting libltdl-2.4.6: .......... done | | `-- Installing pango-1.42.0... | | `-- Installing encodings-1.0.4_4,1... | | | `-- Installing font-util-1.3.1... | | | `-- Extracting font-util-1.3.1: .......... done | | `-- Extracting encodings-1.0.4_4,1: .......... done | | `-- Installing fribidi-0.19.7... | | `-- Extracting fribidi-0.19.7: .......... done | | `-- Installing harfbuzz-1.8.2... | | | `-- Installing graphite2-1.3.11... | | | `-- Extracting graphite2-1.3.11: .......... done | | `-- Extracting harfbuzz-1.8.2: .......... done | | `-- Installing xorg-fonts-truetype-7.7_1... | | | `-- Installing dejavu-2.37... | | | `-- Extracting dejavu-2.37: .......... done | | | `-- Installing font-bh-ttf-1.0.3_3... | | | `-- Extracting font-bh-ttf-1.0.3_3: .......... done | | | `-- Installing font-misc-ethiopic-1.0.3_3... | | | `-- Extracting font-misc-ethiopic-1.0.3_3: ... done | | | `-- Installing font-misc-meltho-1.0.3_3... | | | `-- Extracting font-misc-meltho-1.0.3_3: .......... done | | `-- Extracting pango-1.42.0: .......... done | `-- Extracting graphviz-2.40.1_5: .......... done `-- Extracting py36-pygraphviz-1.3.1: .......... done `-- Installing py36-scikit-sparse-0.4.3_1... | `-- Installing py36-scipy-1.1.0... | `-- Extracting py36-scipy-1.1.0: .......... done `-- Extracting py36-scikit-sparse-0.4.3_1: .......... done `-- Installing py36-yaml-3.12... `-- Extracting py36-yaml-3.12: .......... done Extracting py36-networkx-1.10_4: .......... done Message from perl5-5.26.2: The /usr/bin/perl symlink has been removed starting with Perl 5.20. For shebangs, you should either use: #!/usr/local/bin/perl or #!/usr/bin/env perl The first one will only work if you have a /usr/local/bin/perl, the second will work as long as perl is in PATH. Message from python27-2.7.15: =========================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: bsddb databases/py-bsddb gdbm databases/py-gdbm sqlite3 databases/py-sqlite3 tkinter x11-toolkits/py-tkinter =========================================================================== Message from dejavu-2.37: Make sure that the freetype module is loaded. If it is not, add the following line to the "Modules" section of your X Windows configuration file: Load "freetype" Add the following line to the "Files" section of X Windows configuration file: FontPath "/usr/local/share/fonts/dejavu/" Note: your X Windows configuration file is typically /etc/X11/XF86Config if you are using XFree86, and /etc/X11/xorg.conf if you are using X.Org. ===> py36-MDAnalysis-0.18.0 depends on package: py36-networkx>=1.0 - found ===> Returning to build of py36-MDAnalysis-0.18.0 ===> py36-MDAnalysis-0.18.0 depends on package: py36-scipy>0 - found ===> py36-MDAnalysis-0.18.0 depends on package: py36-six>=1.4.0 - found ===> py36-MDAnalysis-0.18.0 depends on package: py36-setuptools>0 - found ===> py36-MDAnalysis-0.18.0 depends on file: /usr/local/bin/python3.6 - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for py36-MDAnalysis-0.18.0 ===> Generating temporary packing list Attempting to autodetect OpenMP support... Compiler supports OpenMP Will not attempt to use Cython. running install running build running build_py copying MDAnalysis/authors.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis running build_ext running install_lib creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6 creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates/CRD.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates/GRO.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates/TRZ.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates/PQR.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates/LAMMPS.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates/dummy.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates/core.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates/GMS.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates/TXYZ.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates/TRJ.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates/PDB.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates/PDBQT.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates/GSD.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates/XDR.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates/MMTF.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates/memory.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates/null.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates/MOL2.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates/base.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates/XYZ.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates/DMS.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates/chain.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates/XTC.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates/INPCRD.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates/TRR.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates/DCD.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/coordinates/DLPoly.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/tests copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/tests/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/tests copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/tests/datafiles.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/tests copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/version.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/migration/test_dummy_old_MDA_code.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/migration/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/migration/test_dummy_torsion.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/migration/ten2eleven.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/migration/fixes/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/migration/fixes/fix_agcountmethods.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/migration/fixes/fix_agsetterpluralization.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/migration/fixes/fix_framenumberingzerobased2.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/migration/fixes/fix_numframes.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/migration/fixes/fix_camelcase.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/migration/fixes/fix_agmethods.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/migration/fixes/fix_torsions.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/migration/fixes/fix_torsionclasses.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/migration/fixes/fix_framenumberingzerobased.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/migration/fixes/fix_agmethods2.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/migration/fixes/fix_mdaimports.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/migration/fixes/fix_writer.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/migration/fixes/fix_selectatoms.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/migration/fixes/fix_calctorsions.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/units.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/due.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/KDTree.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/auxiliary copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/auxiliary/XVG.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/auxiliary copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/auxiliary/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/auxiliary copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/auxiliary/base.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/auxiliary copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/auxiliary/core.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/auxiliary copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/authors.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/core/topologyattrs.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/core/transformations.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/core/selection.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/core/log.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/core/distances.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/core/units.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/core/qcprot.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/core/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/core/topology.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/core/topologyobjects.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/core/universe.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/core/groups.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/core/AtomGroup.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/core/util.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/core/parallel.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/core/_get_readers.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/exceptions.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/visualization copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/visualization/streamlines_3D.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/visualization copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/visualization/streamlines.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/visualization copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/visualization/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/visualization creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/selections copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/selections/gromacs.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/selections copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/selections/vmd.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/selections copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/selections/pymol.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/selections copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/selections/base.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/selections copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/selections/jmol.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/selections copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/selections/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/selections copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/selections/charmm.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/selections creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/lineardensity.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/rdf.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/diffusionmap.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/base.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/clustering copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore/clustering/cluster.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/clustering copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/clustering copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore/clustering/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/clustering copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/clustering copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore/clustering/affinityprop.so -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/clustering copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore/utils.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.so -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore/covariance.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore/bootstrap.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore/similarity.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore/confdistmatrix.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/encore/cutils.so -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/polymer.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/density.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/x3dna.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/helanal.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/gnm.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/distances.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/contacts.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/nuclinfo.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/psa.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/hole.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/hbonds copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/hbonds/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/hbonds copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/hbonds/hbond_analysis.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/hbonds copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/hbonds/wbridge_analysis.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/hbonds copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/hbonds copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/leaflet.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/rms.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/align.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/legacy copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/legacy/x3dna.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/legacy copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/legacy/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/legacy copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/waterdynamics.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/analysis/pca.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/mdamath.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib/formats copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/formats/libdcd.so -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib/formats copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/formats/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib/formats copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/formats/cython_util.so -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib/formats copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/formats/libmdaxdr.so -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib/formats copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/distances.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/util.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/pkdtree.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/NeighborSearch.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/transformations.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/log.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/_transformations.so -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/qcprot.so -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/c_distances.so -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/lib/c_distances_openmp.so -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology/TPRParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology/TXYZParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology/XYZParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology/PSFParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology/MMTFParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology/HoomdXMLParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology/MOL2Parser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology/GSDParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology/tables.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology/guessers.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology/PDBParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology/DMSParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology/TOPParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology/ExtendedPDBParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/tpr copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology/tpr/utils.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/tpr copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology/tpr/setting.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/tpr copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology/tpr/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/tpr copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology/tpr/obj.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/tpr copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology/PDBQTParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology/LAMMPSParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology/PQRParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology/base.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology/CRDParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology/GROParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology/DLPolyParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology/MinimalParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology/core.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology/GMSParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-3.6/MDAnalysis/topology/_elements.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/CRD.py to CRD.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/GRO.py to GRO.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/TRZ.py to TRZ.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/PQR.py to PQR.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/LAMMPS.py to LAMMPS.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/dummy.py to dummy.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/core.py to core.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/GMS.py to GMS.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/TXYZ.py to TXYZ.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/TRJ.py to TRJ.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/PDB.py to PDB.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/PDBQT.py to PDBQT.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/GSD.py to GSD.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/XDR.py to XDR.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/MMTF.py to MMTF.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/memory.py to memory.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/null.py to null.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/MOL2.py to MOL2.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/base.py to base.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/XYZ.py to XYZ.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/DMS.py to DMS.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/chain.py to chain.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/XTC.py to XTC.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/INPCRD.py to INPCRD.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/TRR.py to TRR.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/DCD.py to DCD.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/DLPoly.py to DLPoly.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/tests/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/tests/datafiles.py to datafiles.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/version.py to version.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/test_dummy_old_MDA_code.py to test_dummy_old_MDA_code.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/test_dummy_torsion.py to test_dummy_torsion.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/ten2eleven.py to ten2eleven.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes/fix_agcountmethods.py to fix_agcountmethods.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes/fix_agsetterpluralization.py to fix_agsetterpluralization.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes/fix_framenumberingzerobased2.py to fix_framenumberingzerobased2.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes/fix_numframes.py to fix_numframes.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes/fix_camelcase.py to fix_camelcase.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes/fix_agmethods.py to fix_agmethods.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes/fix_torsions.py to fix_torsions.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes/fix_torsionclasses.py to fix_torsionclasses.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes/fix_framenumberingzerobased.py to fix_framenumberingzerobased.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes/fix_agmethods2.py to fix_agmethods2.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes/fix_mdaimports.py to fix_mdaimports.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes/fix_writer.py to fix_writer.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes/fix_selectatoms.py to fix_selectatoms.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes/fix_calctorsions.py to fix_calctorsions.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/units.py to units.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/due.py to due.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/KDTree.py to KDTree.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/auxiliary/XVG.py to XVG.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/auxiliary/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/auxiliary/base.py to base.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/auxiliary/core.py to core.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/authors.py to authors.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core/topologyattrs.py to topologyattrs.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core/transformations.py to transformations.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core/selection.py to selection.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core/log.py to log.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core/distances.py to distances.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core/units.py to units.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core/qcprot.py to qcprot.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core/topology.py to topology.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core/topologyobjects.py to topologyobjects.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core/universe.py to universe.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core/groups.py to groups.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core/AtomGroup.py to AtomGroup.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core/util.py to util.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core/parallel.py to parallel.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core/_get_readers.py to _get_readers.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/exceptions.py to exceptions.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/visualization/streamlines_3D.py to streamlines_3D.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/visualization/streamlines.py to streamlines.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/visualization/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/selections/gromacs.py to gromacs.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/selections/vmd.py to vmd.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/selections/pymol.py to pymol.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/selections/base.py to base.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/selections/jmol.py to jmol.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/selections/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/selections/charmm.py to charmm.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/lineardensity.py to lineardensity.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/rdf.py to rdf.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/diffusionmap.py to diffusionmap.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/base.py to base.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/clustering/cluster.py to cluster.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py to ClusteringMethod.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/clustering/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/clustering/ClusterCollection.py to ClusterCollection.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/utils.py to utils.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py to reduce_dimensionality.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py to DimensionalityReductionMethod.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/covariance.py to covariance.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/bootstrap.py to bootstrap.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/similarity.py to similarity.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py to confdistmatrix.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/polymer.py to polymer.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/density.py to density.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/x3dna.py to x3dna.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/helanal.py to helanal.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/gnm.py to gnm.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/distances.py to distances.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/contacts.py to contacts.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/nuclinfo.py to nuclinfo.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/psa.py to psa.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/hole.py to hole.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/hbonds/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/hbonds/hbond_analysis.py to hbond_analysis.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/hbonds/wbridge_analysis.py to wbridge_analysis.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/hbonds/hbond_autocorrel.py to hbond_autocorrel.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/leaflet.py to leaflet.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/rms.py to rms.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/align.py to align.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/legacy/x3dna.py to x3dna.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/legacy/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/waterdynamics.py to waterdynamics.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/pca.py to pca.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib/mdamath.py to mdamath.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib/formats/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib/distances.py to distances.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib/util.py to util.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib/pkdtree.py to pkdtree.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib/NeighborSearch.py to NeighborSearch.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib/transformations.py to transformations.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib/log.py to log.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/TPRParser.py to TPRParser.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/TXYZParser.py to TXYZParser.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/XYZParser.py to XYZParser.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/PSFParser.py to PSFParser.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/MMTFParser.py to MMTFParser.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/HoomdXMLParser.py to HoomdXMLParser.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/MOL2Parser.py to MOL2Parser.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/GSDParser.py to GSDParser.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/tables.py to tables.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/guessers.py to guessers.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/PDBParser.py to PDBParser.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/DMSParser.py to DMSParser.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/TOPParser.py to TOPParser.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/ExtendedPDBParser.py to ExtendedPDBParser.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/tpr/utils.py to utils.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/tpr/setting.py to setting.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/tpr/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/tpr/obj.py to obj.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/PDBQTParser.py to PDBQTParser.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/LAMMPSParser.py to LAMMPSParser.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/PQRParser.py to PQRParser.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/base.py to base.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/CRDParser.py to CRDParser.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/GROParser.py to GROParser.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/DLPolyParser.py to DLPolyParser.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/MinimalParser.py to MinimalParser.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/core.py to core.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/GMSParser.py to GMSParser.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/_elements.py to _elements.cpython-36.pyc writing byte-compilation script '/tmp/tmpp98xvw0_.py' /usr/local/bin/python3.6 /tmp/tmpp98xvw0_.py removing /tmp/tmpp98xvw0_.py running install_egg_info running egg_info writing MDAnalysis.egg-info/PKG-INFO writing dependency_links to MDAnalysis.egg-info/dependency_links.txt writing requirements to MDAnalysis.egg-info/requires.txt writing top-level names to MDAnalysis.egg-info/top_level.txt reading manifest file 'MDAnalysis.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'MDAnalysis/coordinates/xdrfile/src/*' warning: no files found matching 'MDAnalysis/lib/src/pyqcprot/*' warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution warning: no previously-included files matching '*.pyd' found anywhere in distribution warning: no previously-included files matching '*~' found anywhere in distribution writing manifest file 'MDAnalysis.egg-info/SOURCES.txt' Copying MDAnalysis.egg-info to /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis-0.18.0-py3.6.egg-info running install_scripts writing list of installed files to '/construction/science/py-MDAnalysis/.PLIST.pymodtmp' ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for py36-MDAnalysis-0.18.0 file sizes/checksums [511]: ...... done packing files [511]: ...... done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Friday, 20 JUL 2018 at 20:13:35 UTC Duration: 00:01:42