=> Building science/py-MDAnalysis@py27 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/python2.7" 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/python2.7 PYTHON_LIBDIR=lib/python2.7 PYTHON_PLATFORM=dragonfly5 PYTHON_PYOEXTENSION=pyo PYTHON_SITELIBDIR=lib/python2.7/site-packages PYTHON_SUFFIX=27 PYTHON_VER=2.7 PYTHON_VERSION=python2.7 PYTHON2="" PYTHON3="@comment " 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 -------------------------------------------------------------------------------- ===> py27-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 ===> py27-MDAnalysis-0.18.0 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py27-MDAnalysis-0.18.0 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by py27-MDAnalysis-0.18.0 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by py27-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 py27-MDAnalysis-0.18.0 for building ===> Extracting for py27-MDAnalysis-0.18.0 => SHA256 Checksum OK for MDAnalysis-0.18.0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for py27-MDAnalysis-0.18.0 ===> Applying ports patches for py27-MDAnalysis-0.18.0 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> py27-MDAnalysis-0.18.0 depends on package: py27-numpy>0 - not found ===> Installing existing package /packages/All/py27-numpy-1.14.3,1.txz Installing py27-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 py27-setuptools-39.2.0... | `-- Installing python27-2.7.15... | | `-- 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 python27-2.7.15: .......... done `-- Extracting py27-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 py27-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 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 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 ===> py27-MDAnalysis-0.18.0 depends on package: py27-numpy>0 - found ===> Returning to build of py27-MDAnalysis-0.18.0 ===> py27-MDAnalysis-0.18.0 depends on package: py27-setuptools>0 - found ===> py27-MDAnalysis-0.18.0 depends on file: /usr/local/bin/python2.7 - found -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for py27-MDAnalysis-0.18.0 Attempting to autodetect OpenMP support... Compiler supports OpenMP Will not attempt to use Cython. running config -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for py27-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_64-2.7 creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis copying MDAnalysis/due.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis copying MDAnalysis/version.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis copying MDAnalysis/authors.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis copying MDAnalysis/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis copying MDAnalysis/units.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis copying MDAnalysis/exceptions.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis copying MDAnalysis/KDTree.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/tests copying MDAnalysis/tests/datafiles.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/tests copying MDAnalysis/tests/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/tests creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/core copying MDAnalysis/core/topologyobjects.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/core copying MDAnalysis/core/groups.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/core copying MDAnalysis/core/topology.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/core copying MDAnalysis/core/qcprot.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/core copying MDAnalysis/core/AtomGroup.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/core copying MDAnalysis/core/log.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/core copying MDAnalysis/core/universe.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/core copying MDAnalysis/core/parallel.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/core copying MDAnalysis/core/_get_readers.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/core copying MDAnalysis/core/topologyattrs.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/core copying MDAnalysis/core/transformations.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/core copying MDAnalysis/core/units.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/core copying MDAnalysis/core/distances.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/core copying MDAnalysis/core/selection.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/core copying MDAnalysis/core/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/core copying MDAnalysis/core/util.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/core creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRR.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/chain.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/INPCRD.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/TXYZ.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/MOL2.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/XYZ.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/DCD.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/GRO.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/DMS.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/memory.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/XDR.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/null.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/PDBQT.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/MMTF.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/XTC.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/PQR.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/PDB.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/base.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/core.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/CRD.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRJ.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/LAMMPS.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/DLPoly.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/GSD.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRZ.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/GMS.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/dummy.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib copying MDAnalysis/lib/util.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib copying MDAnalysis/lib/NeighborSearch.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib copying MDAnalysis/lib/transformations.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib copying MDAnalysis/lib/mdamath.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib copying MDAnalysis/lib/pkdtree.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib copying MDAnalysis/lib/log.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib copying MDAnalysis/lib/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib copying MDAnalysis/lib/distances.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/migration copying MDAnalysis/migration/test_dummy_torsion.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/migration copying MDAnalysis/migration/ten2eleven.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/migration copying MDAnalysis/migration/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/migration copying MDAnalysis/migration/test_dummy_old_MDA_code.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/migration creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/XVG.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/base.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/core.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/auxiliary creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/selections copying MDAnalysis/selections/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/selections copying MDAnalysis/selections/pymol.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/selections copying MDAnalysis/selections/charmm.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/selections copying MDAnalysis/selections/base.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/selections copying MDAnalysis/selections/jmol.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/selections copying MDAnalysis/selections/vmd.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/selections copying MDAnalysis/selections/gromacs.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/selections creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis copying MDAnalysis/analysis/gnm.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis copying MDAnalysis/analysis/contacts.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis copying MDAnalysis/analysis/base.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis copying MDAnalysis/analysis/leaflet.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis copying MDAnalysis/analysis/lineardensity.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis copying MDAnalysis/analysis/polymer.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis copying MDAnalysis/analysis/rms.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis copying MDAnalysis/analysis/align.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis copying MDAnalysis/analysis/x3dna.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis copying MDAnalysis/analysis/density.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis copying MDAnalysis/analysis/waterdynamics.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis copying MDAnalysis/analysis/psa.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis copying MDAnalysis/analysis/pca.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis copying MDAnalysis/analysis/rdf.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis copying MDAnalysis/analysis/diffusionmap.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis copying MDAnalysis/analysis/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis copying MDAnalysis/analysis/helanal.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis copying MDAnalysis/analysis/nuclinfo.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis copying MDAnalysis/analysis/distances.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis copying MDAnalysis/analysis/hole.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/guessers.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/GMSParser.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/MinimalParser.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/TXYZParser.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/GSDParser.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/PQRParser.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/_elements.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/ExtendedPDBParser.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/HoomdXMLParser.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/PDBParser.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/DMSParser.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/LAMMPSParser.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/tables.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/GROParser.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/core.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/CRDParser.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/TPRParser.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/MOL2Parser.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/base.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/PSFParser.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/XYZParser.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/PDBQTParser.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/DLPolyParser.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/TOPParser.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/MMTFParser.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/visualization copying MDAnalysis/visualization/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/visualization copying MDAnalysis/visualization/streamlines_3D.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/visualization copying MDAnalysis/visualization/streamlines.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/visualization creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib/formats creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_framenumberingzerobased2.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_calctorsions.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_agsetterpluralization.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_mdaimports.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_camelcase.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_torsions.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_framenumberingzerobased.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_torsionclasses.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_writer.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_selectatoms.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_numframes.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_agmethods.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_agmethods2.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_agcountmethods.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/migration/fixes creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/legacy copying MDAnalysis/analysis/legacy/x3dna.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/legacy copying MDAnalysis/analysis/legacy/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/legacy creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/similarity.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/confdistmatrix.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/bootstrap.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/covariance.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/utils.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/encore creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/hbonds copying MDAnalysis/analysis/hbonds/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/hbonds copying MDAnalysis/analysis/hbonds/hbond_analysis.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/hbonds copying MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/hbonds copying MDAnalysis/analysis/hbonds/wbridge_analysis.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/hbonds creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/encore/dimensionality_reduction creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/cluster.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/encore/clustering creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/setting.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/utils.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/obj.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology/tpr running build_ext building 'MDAnalysis.lib.formats.libdcd' extension creating build/temp.dragonfly-5.2-SYNTH-x86_64-2.7 creating build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis creating build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib creating build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib/formats cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python2.7/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -I/usr/local/include/python2.7 -c MDAnalysis/lib/formats/libdcd.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib/formats/libdcd.o -std=c99 -ffast-math -funroll-loops In file included from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1816:0, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/lib/formats/libdcd.c:595: /usr/local/lib/python2.7/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_64-2.7/MDAnalysis/lib/formats/libdcd.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib/formats/libdcd.so building 'MDAnalysis.lib.c_distances' extension cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python2.7/site-packages/numpy/core/include -IMDAnalysis/lib/include -I/usr/local/include/python2.7 -c MDAnalysis/lib/c_distances.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib/c_distances.o -std=c99 -ffast-math -funroll-loops In file included from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1816:0, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/lib/c_distances.c:596: /usr/local/lib/python2.7/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_64-2.7/MDAnalysis/lib/c_distances.o -L/usr/local/lib -lm -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/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/python2.7/site-packages/numpy/core/include -IMDAnalysis/lib/include -I/usr/local/include/python2.7 -c MDAnalysis/lib/c_distances_openmp.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib/c_distances_openmp.o -fopenmp -std=c99 -ffast-math -funroll-loops In file included from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1816:0, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/lib/c_distances_openmp.c:607: /usr/local/lib/python2.7/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_64-2.7/MDAnalysis/lib/c_distances_openmp.o -L/usr/local/lib -lm -lgomp -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib/c_distances_openmp.so -fopenmp building 'MDAnalysis.lib.qcprot' extension cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python2.7/site-packages/numpy/core/include -I/usr/local/include/python2.7 -c MDAnalysis/lib/qcprot.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib/qcprot.o -std=c99 -ffast-math -funroll-loops In file included from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1816:0, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/lib/qcprot.c:591: /usr/local/lib/python2.7/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_64-2.7/MDAnalysis/lib/qcprot.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib/qcprot.so building 'MDAnalysis.lib._transformations' extension creating build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib/src creating build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib/src/transformations cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python2.7/site-packages/numpy/core/include -I/usr/local/include/python2.7 -c MDAnalysis/lib/src/transformations/transformations.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib/src/transformations/transformations.o -std=c99 -ffast-math -funroll-loops In file included from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1816:0, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/lib/src/transformations/transformations.c:73: /usr/local/lib/python2.7/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_64-2.7/MDAnalysis/lib/src/transformations/transformations.o -L/usr/local/lib -lm -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib/_transformations.so building 'MDAnalysis.lib.formats.libmdaxdr' extension creating build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/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/python2.7/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/local/include/python2.7 -c MDAnalysis/lib/formats/libmdaxdr.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib/formats/libmdaxdr.o -std=c99 -ffast-math -funroll-loops In file included from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1816:0, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/lib/formats/libmdaxdr.c:617: /usr/local/lib/python2.7/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/python2.7/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/local/include/python2.7 -c MDAnalysis/lib/formats/src/xdrfile.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/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/python2.7/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/local/include/python2.7 -c MDAnalysis/lib/formats/src/xdrfile_xtc.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/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/python2.7/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/local/include/python2.7 -c MDAnalysis/lib/formats/src/xdrfile_trr.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/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/python2.7/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/local/include/python2.7 -c MDAnalysis/lib/formats/src/trr_seek.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/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/python2.7/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/local/include/python2.7 -c MDAnalysis/lib/formats/src/xtc_seek.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/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_64-2.7/MDAnalysis/lib/formats/libmdaxdr.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib/formats/src/xdrfile.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib/formats/src/xdrfile_xtc.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib/formats/src/xdrfile_trr.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib/formats/src/trr_seek.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib/formats/src/xtc_seek.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib/formats/libmdaxdr.so building 'MDAnalysis.lib.formats.cython_util' extension cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python2.7/site-packages/numpy/core/include -I/usr/local/include/python2.7 -c MDAnalysis/lib/formats/cython_util.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib/formats/cython_util.o -std=c99 -ffast-math -funroll-loops In file included from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1816:0, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/lib/formats/cython_util.c:591: /usr/local/lib/python2.7/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_64-2.7/MDAnalysis/lib/formats/cython_util.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib/formats/cython_util.so building 'MDAnalysis.analysis.encore.cutils' extension creating build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis creating build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/encore cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python2.7/site-packages/numpy/core/include -I/usr/local/include/python2.7 -c MDAnalysis/analysis/encore/cutils.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/encore/cutils.o -std=c99 -ffast-math -funroll-loops In file included from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1816:0, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/analysis/encore/cutils.c:591: /usr/local/lib/python2.7/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_64-2.7/MDAnalysis/analysis/encore/cutils.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/encore/cutils.so building 'MDAnalysis.analysis.encore.clustering.affinityprop' extension creating build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/encore/clustering creating build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/encore/clustering/src cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python2.7/site-packages/numpy/core/include -IMDAnalysis/analysis/encore/clustering/include -I/usr/local/include/python2.7 -c MDAnalysis/analysis/encore/clustering/affinityprop.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/encore/clustering/affinityprop.o -std=c99 -ffast-math -funroll-loops In file included from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1816:0, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/analysis/encore/clustering/affinityprop.c:597: /usr/local/lib/python2.7/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/python2.7/site-packages/numpy/core/include -IMDAnalysis/analysis/encore/clustering/include -I/usr/local/include/python2.7 -c MDAnalysis/analysis/encore/clustering/src/ap.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/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_64-2.7/MDAnalysis/analysis/encore/clustering/affinityprop.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/encore/clustering/src/ap.o -L/usr/local/lib -lm -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/encore/clustering/affinityprop.so building 'MDAnalysis.analysis.encore.dimensionality_reduction.stochasticproxembed' extension creating build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/encore/dimensionality_reduction creating build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/encore/dimensionality_reduction/src cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python2.7/site-packages/numpy/core/include -IMDAnalysis/analysis/encore/dimensionality_reduction/include -I/usr/local/include/python2.7 -c MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.o -std=c99 -ffast-math -funroll-loops In file included from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1816:0, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c:597: /usr/local/lib/python2.7/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/python2.7/site-packages/numpy/core/include -IMDAnalysis/analysis/encore/dimensionality_reduction/include -I/usr/local/include/python2.7 -c MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/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_64-2.7/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.o -L/usr/local/lib -lm -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.so -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> 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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). ===> py27-MDAnalysis-0.18.0 depends on package: py27-biopython>=1.59 - found ===> Returning to build of py27-MDAnalysis-0.18.0 ===> py27-MDAnalysis-0.18.0 depends on package: py27-duecredit>0 - not found ===> Installing existing package /packages/All/py27-duecredit-0.6.4.txz Installing py27-duecredit-0.6.4... `-- Installing py27-citeproc-py-0.4.0... | `-- Installing py27-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 py27-lxml-4.1.1: .......... done `-- Extracting py27-citeproc-py-0.4.0: .......... done `-- Installing py27-requests-2.18.4... | `-- Installing py27-certifi-2018.4.16... | `-- Extracting py27-certifi-2018.4.16: .......... done | `-- Installing py27-chardet-3.0.4... | `-- Extracting py27-chardet-3.0.4: .......... done | `-- Installing py27-idna-2.6... | `-- Extracting py27-idna-2.6: .......... done | `-- Installing py27-urllib3-1.22,1... | | `-- Installing py27-cryptography-2.1.4... | | `-- Installing py27-asn1crypto-0.22.0... | | `-- Extracting py27-asn1crypto-0.22.0: .......... done | | `-- Installing py27-cffi-1.11.5... | | | `-- Installing py27-pycparser-2.18... | | | `-- Extracting py27-pycparser-2.18: .......... done | | `-- Extracting py27-cffi-1.11.5: .......... done | | `-- Installing py27-enum34-1.1.6... | | `-- Extracting py27-enum34-1.1.6: .......... done | | `-- Installing py27-ipaddress-1.0.22... | | `-- Extracting py27-ipaddress-1.0.22: .......... done | | `-- Installing py27-six-1.11.0... | | `-- Extracting py27-six-1.11.0: .......... done | | `-- Extracting py27-cryptography-2.1.4: .......... done | | `-- Installing py27-openssl-17.5.0_1... | | `-- Extracting py27-openssl-17.5.0_1: .......... done | | `-- Installing py27-pysocks-1.6.8... | | `-- Extracting py27-pysocks-1.6.8: .......... done | `-- Extracting py27-urllib3-1.22,1: .......... done `-- Extracting py27-requests-2.18.4: .......... done Extracting py27-duecredit-0.6.4: .......... done Message from py27-urllib3-1.22,1: Be careful, support of IPv6 is broken with PySocks 1.5.7. ===> py27-MDAnalysis-0.18.0 depends on package: py27-duecredit>0 - found ===> Returning to build of py27-MDAnalysis-0.18.0 ===> py27-MDAnalysis-0.18.0 depends on package: py27-GridDataFormats>=0.4.0 - not found ===> Installing existing package /packages/All/py27-GridDataFormats-0.4.0.txz Installing py27-GridDataFormats-0.4.0... 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Extracting py27-joblib-0.9.4: .......... done ===> py27-MDAnalysis-0.18.0 depends on package: py27-joblib>0 - found ===> Returning to build of py27-MDAnalysis-0.18.0 ===> py27-MDAnalysis-0.18.0 depends on package: py27-matplotlib>=1.5.1 - not found ===> Installing existing package /packages/All/py27-matplotlib-2.1.2_2.txz Installing py27-matplotlib-2.1.2_2... `-- Installing atk-2.24.0... | `-- 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 | `-- Extracting glib-2.50.3_4,1: .......... done No schema files found: doing nothing. `-- Extracting atk-2.24.0: .......... done `-- Installing cairo-1.14.8_1,2... | `-- Installing dri2proto-2.8... | `-- Extracting dri2proto-2.8: .... done | `-- 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 gdk-pixbuf2-2.36.11... | `-- Installing jasper-1.900.1_17... | `-- Extracting jasper-1.900.1_17: .......... done | `-- Installing libXi-1.7.9,1... | | `-- Installing inputproto-2.3.2... | | `-- Extracting inputproto-2.3.2: ........ done | `-- Extracting libXi-1.7.9,1: .......... done | `-- Installing libXt-1.1.5,1... | | `-- 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 | `-- Extracting libXt-1.1.5,1: .......... done | `-- Installing shared-mime-info-1.8... | `-- Extracting shared-mime-info-1.8: .......... done `-- Extracting gdk-pixbuf2-2.36.11: .......... done `-- Installing gtk2-2.24.32... | `-- Installing cups-2.2.8_1... | | `-- Installing avahi-app-0.6.31_6... | | `-- Installing dbus-glib-0.108... | | | `-- Installing dbus-1.10.16_1... ===> Creating groups. 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Creating group 'avahi' with gid '558'. ===> Creating users Creating user 'avahi' with uid '558'. | | `-- Extracting avahi-app-0.6.31_6: .......... done | | `-- Installing gnutls-3.5.18... | | `-- Installing ca_root_nss-3.38... | | `-- Extracting ca_root_nss-3.38: ........ done | | `-- Installing libidn2-2.0.5... | | | `-- Installing libunistring-0.9.10... | | | `-- Extracting libunistring-0.9.10: .......... done | | `-- Extracting libidn2-2.0.5: .......... done | | `-- Installing libtasn1-4.13... | | `-- Extracting libtasn1-4.13: .......... done | | `-- Installing nettle-3.4... | | `-- Extracting nettle-3.4: .......... done | | `-- Installing p11-kit-0.23.12... | | `-- Extracting p11-kit-0.23.12: .......... done | | `-- Installing trousers-0.3.14_2... | | | `-- Installing tpm-emulator-0.7.4_2... ===> Creating groups. Using existing group '_tss'. ===> Creating users Using existing user '_tss'. | | | `-- Extracting tpm-emulator-0.7.4_2: ......... done ===> Creating groups. Using existing group '_tss'. ===> Creating users Using existing user '_tss'. | | `-- Extracting trousers-0.3.14_2: .......... done | | `-- Extracting gnutls-3.5.18: .......... done | | `-- Installing libpaper-1.1.24.4... | | `-- Extracting libpaper-1.1.24.4: .......... done ===> Creating groups. Creating group 'cups' with gid '193'. ===> Creating users Creating user 'cups' with uid '193'. | `-- Extracting cups-2.2.8_1: .......... done | `-- Installing gtk-update-icon-cache-2.24.32... | | `-- Installing hicolor-icon-theme-0.15... | | `-- Extracting hicolor-icon-theme-0.15: . done | | `-- Installing libXcomposite-0.4.4_3,1... | | `-- Installing compositeproto-0.4.2... | | `-- Extracting compositeproto-0.4.2: ....... done | | `-- Extracting libXcomposite-0.4.4_3,1: .......... done | | `-- Installing libXcursor-1.1.15... | | `-- Extracting libXcursor-1.1.15: .......... done | | `-- Installing libXinerama-1.1.3_3,1... | | `-- Installing xineramaproto-1.2.1... | | `-- Extracting xineramaproto-1.2.1: .. done | | `-- Extracting libXinerama-1.1.3_3,1: .......... done | | `-- Installing libXrandr-1.5.1... | | `-- Installing randrproto-1.5.0... | | `-- Extracting randrproto-1.5.0: ....... done | | `-- Extracting libXrandr-1.5.1: .......... 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 gtk-update-icon-cache-2.24.32: .... done `-- Extracting gtk2-2.24.32: .......... done `-- Installing libglade2-2.6.4_9... | `-- Installing xmlcatmgr-2.2_2... | `-- Extracting xmlcatmgr-2.2_2: ......... done + Creating /usr/local/share/sgml/catalog + Registering CATALOG catalog.ports (SGML) + Creating /usr/local/share/sgml/catalog.ports + Creating /usr/local/share/xml/catalog + Registering nextCatalog catalog.ports (XML) + Creating /usr/local/share/xml/catalog.ports `-- Extracting libglade2-2.6.4_9: .......... done `-- Installing py27-backports.functools_lru_cache-1.5... | `-- Installing py27-backports-1... | `-- Extracting py27-backports-1: ...... done `-- Extracting py27-backports.functools_lru_cache-1.5: .......... done `-- Installing py27-cycler-0.10.0... `-- Extracting py27-cycler-0.10.0: .......... done `-- Installing py27-dateutil-2.6.1... `-- Extracting py27-dateutil-2.6.1: .......... done `-- Installing py27-gobject-2.28.6_8... | `-- Installing py27-cairo-1.14.1... | `-- Extracting py27-cairo-1.14.1: .......... done `-- Extracting py27-gobject-2.28.6_8: .......... done `-- Installing py27-gtk2-2.24.0_5... `-- Extracting py27-gtk2-2.24.0_5: .......... done `-- Installing py27-pyparsing-2.2.0... `-- Extracting py27-pyparsing-2.2.0: .......... done `-- Installing py27-pytz-2018.5,1... `-- Extracting py27-pytz-2018.5,1: .......... done `-- Installing py27-tornado-5.0.2... | `-- Installing py27-backports_abc-0.5... | `-- Extracting py27-backports_abc-0.5: .......... done | `-- Installing py27-singledispatch-3.4.0.3_1... | `-- Extracting py27-singledispatch-3.4.0.3_1: .......... done `-- Extracting py27-tornado-5.0.2: .......... done Extracting py27-matplotlib-2.1.2_2: .......... 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 ca_root_nss-3.38: ********************************* WARNING ********************************* FreeBSD does not, and can not warrant that the certification authorities whose certificates are included in this package have in any way been audited for trustworthiness or RFC 3647 compliance. Assessment and verification of trust is the complete responsibility of the system administrator. *********************************** NOTE ********************************** This package installs symlinks to support root certificates discovery by default for software that uses OpenSSL. This enables SSL Certificate Verification by client software without manual intervention. If you prefer to do this manually, replace the following symlinks with either an empty file or your site-local certificate bundle. * /etc/ssl/cert.pem * /usr/local/etc/ssl/cert.pem * /usr/local/openssl/cert.pem *************************************************************************** Message from trousers-0.3.14_2: To run tcsd automatically, add the following line to /etc/rc.conf: tcsd_enable="YES" You might want to edit /usr/local/etc/tcsd.conf to reflect your setup. If you want to use tcsd with software TPM emulator, use the following configuration in /etc/rc.conf: tcsd_enable="YES" tcsd_mode="emulator" tpmd_enable="YES" To use TPM, add your_account to '_tss' group like following: # pw groupmod _tss -m your_account 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. Message from xmlcatmgr-2.2_2: The following catalogs are installed: 1) /usr/local/share/sgml/catalog The top level catalog for SGML stuff. It is not changed by any ports/packages except textproc/xmlcatmgr. 2) /usr/local/share/sgml/catalog.ports This catalog is for handling SGML stuff installed under /usr/local/share/sgml. It is changed by ports/packages. 3) /usr/local/share/xml/catalog The top level catalog for XML stuff. It is not changed by any ports/packages except textproc/xmlcatmgr. 4) /usr/local/share/xml/catalog.ports This catalog is for handling XML stuff installed under /usr/local/share/xml. It is changed by ports/packages. ===> py27-MDAnalysis-0.18.0 depends on package: py27-matplotlib>=1.5.1 - found ===> Returning to build of py27-MDAnalysis-0.18.0 ===> py27-MDAnalysis-0.18.0 depends on package: py27-mmtf-python>=1.0.0 - not found ===> Installing existing package /packages/All/py27-mmtf-python-1.1.2.txz Installing py27-mmtf-python-1.1.2... `-- Installing py27-msgpack-0.5.6... `-- Extracting py27-msgpack-0.5.6: .......... done Extracting py27-mmtf-python-1.1.2: .......... done ===> py27-MDAnalysis-0.18.0 depends on package: py27-mmtf-python>=1.0.0 - found ===> Returning to build of py27-MDAnalysis-0.18.0 ===> py27-MDAnalysis-0.18.0 depends on package: py27-networkx>=1.0 - not found ===> Installing existing package /packages/All/py27-networkx-1.10_4.txz Installing py27-networkx-1.10_4... `-- Installing py27-decorator-4.3.0... `-- Extracting py27-decorator-4.3.0: .......... done `-- Installing py27-pygraphviz-1.3.1... | `-- Installing graphviz-2.40.1_5... | | `-- Installing libXaw-1.0.13,2... | | `-- Installing libXmu-1.1.2_3,1... | | `-- 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 | `-- Extracting graphviz-2.40.1_5: .......... done `-- Extracting py27-pygraphviz-1.3.1: .......... done `-- Installing py27-scikit-sparse-0.4.3_1... | `-- Installing py27-scipy-1.1.0... | `-- Extracting py27-scipy-1.1.0: .......... done `-- Extracting py27-scikit-sparse-0.4.3_1: .......... done `-- Installing py27-yaml-3.12... `-- Extracting py27-yaml-3.12: .......... done Extracting py27-networkx-1.10_4: .......... done ===> py27-MDAnalysis-0.18.0 depends on package: py27-networkx>=1.0 - found ===> Returning to build of py27-MDAnalysis-0.18.0 ===> py27-MDAnalysis-0.18.0 depends on package: py27-scipy>0 - found ===> py27-MDAnalysis-0.18.0 depends on package: py27-six>=1.4.0 - found ===> py27-MDAnalysis-0.18.0 depends on package: py27-setuptools>0 - found ===> py27-MDAnalysis-0.18.0 depends on file: /usr/local/bin/python2.7 - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for py27-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_64-2.7/MDAnalysis running build_ext running install_lib creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7 creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/migration/test_dummy_torsion.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/migration/ten2eleven.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/migration/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/migration/test_dummy_old_MDA_code.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/migration/fixes/fix_framenumberingzerobased2.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/migration/fixes/fix_calctorsions.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/migration/fixes/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/migration/fixes/fix_agsetterpluralization.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/migration/fixes/fix_mdaimports.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/migration/fixes/fix_camelcase.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/migration/fixes/fix_torsions.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/migration/fixes/fix_framenumberingzerobased.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/migration/fixes/fix_torsionclasses.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/migration/fixes/fix_writer.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/migration/fixes/fix_selectatoms.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/migration/fixes/fix_numframes.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/migration/fixes/fix_agmethods.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/migration/fixes/fix_agmethods2.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/migration/fixes/fix_agcountmethods.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/auxiliary copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/auxiliary/XVG.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/auxiliary copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/auxiliary/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/auxiliary copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/auxiliary/base.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/auxiliary copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/auxiliary/core.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/auxiliary creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/selections copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/selections/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/selections copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/selections/pymol.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/selections copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/selections/charmm.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/selections copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/selections/base.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/selections copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/selections/jmol.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/selections copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/selections/vmd.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/selections copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/selections/gromacs.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/selections creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/gnm.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/contacts.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/base.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/leaflet.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/lineardensity.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/polymer.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/rms.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/align.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/x3dna.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/density.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/waterdynamics.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/psa.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/pca.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/rdf.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/diffusionmap.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/helanal.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/nuclinfo.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/distances.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/hole.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/legacy copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/legacy/x3dna.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/legacy copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/legacy/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/legacy creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/encore/similarity.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/encore/confdistmatrix.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/encore/bootstrap.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/encore/covariance.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/encore/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/encore/utils.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.so -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/clustering copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/encore/clustering/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/clustering copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/encore/clustering/cluster.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/clustering copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/clustering copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/clustering copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/encore/clustering/affinityprop.so -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/clustering copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/encore/cutils.so -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/hbonds copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/hbonds/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/hbonds copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/hbonds/hbond_analysis.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/hbonds copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/hbonds copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/analysis/hbonds/wbridge_analysis.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/hbonds creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology/guessers.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology/GMSParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology/MinimalParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology/TXYZParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology/GSDParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology/PQRParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology/_elements.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology/ExtendedPDBParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology/HoomdXMLParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology/PDBParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology/DMSParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology/LAMMPSParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology/tables.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology/GROParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology/core.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology/CRDParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology/TPRParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology/MOL2Parser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology/base.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology/PSFParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology/XYZParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology/PDBQTParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology/DLPolyParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology/TOPParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology/MMTFParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/tpr copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology/tpr/setting.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/tpr copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology/tpr/utils.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/tpr copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology/tpr/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/tpr copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/topology/tpr/obj.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/tpr creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/visualization copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/visualization/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/visualization copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/visualization/streamlines_3D.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/visualization copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/visualization/streamlines.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/visualization copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/due.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/version.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/authors.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/units.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/exceptions.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/KDTree.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/tests copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/tests/datafiles.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/tests copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/tests/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/tests creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/core/topologyobjects.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/core/groups.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/core/topology.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/core/qcprot.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/core/AtomGroup.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/core/log.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/core/universe.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/core/parallel.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/core/_get_readers.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/core/topologyattrs.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/core/transformations.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/core/units.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/core/distances.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/core/selection.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/core/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/core/util.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates/TRR.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates/chain.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates/INPCRD.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates/TXYZ.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates/MOL2.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates/XYZ.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates/DCD.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates/GRO.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates/DMS.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates/memory.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates/XDR.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates/null.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates/PDBQT.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates/MMTF.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates/XTC.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates/PQR.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates/PDB.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates/base.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates/core.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates/CRD.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates/TRJ.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates/LAMMPS.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates/DLPoly.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates/GSD.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates/TRZ.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates/GMS.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/coordinates/dummy.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib/qcprot.so -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib/_transformations.so -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib/distances.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib/formats copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib/formats/libdcd.so -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib/formats copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib/formats/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib/formats copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib/formats/libmdaxdr.so -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib/formats copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib/formats/cython_util.so -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib/formats copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib/util.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib/NeighborSearch.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib/transformations.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib/mdamath.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib/pkdtree.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib/log.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib/c_distances_openmp.so -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/MDAnalysis/lib/c_distances.so -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/test_dummy_torsion.py to test_dummy_torsion.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/ten2eleven.py to ten2eleven.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/__init__.py to __init__.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/test_dummy_old_MDA_code.py to test_dummy_old_MDA_code.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes/fix_framenumberingzerobased2.py to fix_framenumberingzerobased2.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes/fix_calctorsions.py to fix_calctorsions.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes/__init__.py to __init__.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes/fix_agsetterpluralization.py to fix_agsetterpluralization.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes/fix_mdaimports.py to fix_mdaimports.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes/fix_camelcase.py to fix_camelcase.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes/fix_torsions.py to fix_torsions.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes/fix_framenumberingzerobased.py to fix_framenumberingzerobased.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes/fix_torsionclasses.py to fix_torsionclasses.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes/fix_writer.py to fix_writer.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes/fix_selectatoms.py to fix_selectatoms.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes/fix_numframes.py to fix_numframes.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes/fix_agmethods.py to fix_agmethods.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes/fix_agmethods2.py to fix_agmethods2.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes/fix_agcountmethods.py to fix_agcountmethods.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/auxiliary/XVG.py to XVG.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/auxiliary/__init__.py to __init__.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/auxiliary/base.py to base.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/auxiliary/core.py to core.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/selections/__init__.py to __init__.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/selections/pymol.py to pymol.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/selections/charmm.py to charmm.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/selections/base.py to base.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/selections/jmol.py to jmol.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/selections/vmd.py to vmd.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/selections/gromacs.py to gromacs.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/gnm.py to gnm.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/contacts.py to contacts.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/base.py to base.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/leaflet.py to leaflet.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/lineardensity.py to lineardensity.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/polymer.py to polymer.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/rms.py to rms.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/align.py to align.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/x3dna.py to x3dna.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/density.py to density.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/waterdynamics.py to waterdynamics.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/psa.py to psa.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/pca.py to pca.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/rdf.py to rdf.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/diffusionmap.py to diffusionmap.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/__init__.py to __init__.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/helanal.py to helanal.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/nuclinfo.py to nuclinfo.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/distances.py to distances.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/hole.py to hole.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/legacy/x3dna.py to x3dna.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/legacy/__init__.py to __init__.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/similarity.py to similarity.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py to confdistmatrix.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/bootstrap.py to bootstrap.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/covariance.py to covariance.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/__init__.py to __init__.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/utils.py to utils.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py to reduce_dimensionality.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py to __init__.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py to DimensionalityReductionMethod.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/clustering/__init__.py to __init__.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/clustering/cluster.py to cluster.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py to ClusteringMethod.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/clustering/ClusterCollection.py to ClusterCollection.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/hbonds/__init__.py to __init__.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/hbonds/hbond_analysis.py to hbond_analysis.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/hbonds/hbond_autocorrel.py to hbond_autocorrel.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/hbonds/wbridge_analysis.py to wbridge_analysis.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/guessers.py to guessers.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/GMSParser.py to GMSParser.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/MinimalParser.py to MinimalParser.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/TXYZParser.py to TXYZParser.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/GSDParser.py to GSDParser.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/__init__.py to __init__.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/PQRParser.py to PQRParser.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/_elements.py to _elements.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/ExtendedPDBParser.py to ExtendedPDBParser.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/HoomdXMLParser.py to HoomdXMLParser.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/PDBParser.py to PDBParser.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/DMSParser.py to DMSParser.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/LAMMPSParser.py to LAMMPSParser.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/tables.py to tables.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/GROParser.py to GROParser.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/core.py to core.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/CRDParser.py to CRDParser.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/TPRParser.py to TPRParser.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/MOL2Parser.py to MOL2Parser.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/base.py to base.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/PSFParser.py to PSFParser.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/XYZParser.py to XYZParser.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/PDBQTParser.py to PDBQTParser.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/DLPolyParser.py to DLPolyParser.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/TOPParser.py to TOPParser.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/MMTFParser.py to MMTFParser.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/tpr/setting.py to setting.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/tpr/utils.py to utils.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/tpr/__init__.py to __init__.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/tpr/obj.py to obj.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/visualization/__init__.py to __init__.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/visualization/streamlines_3D.py to streamlines_3D.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/visualization/streamlines.py to streamlines.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/due.py to due.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/version.py to version.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/authors.py to authors.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/__init__.py to __init__.pyc byte-compiling 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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/python2.7/site-packages/MDAnalysis-0.18.0-py2.7.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 py27-MDAnalysis-0.18.0 file sizes/checksums [511]: ...... done packing files [511]: ...... done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Friday, 20 JUL 2018 at 20:13:37 UTC Duration: 00:01:44