------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/metis-5.1.0_8.tgz Message from metis-5.1.0_8: ===> NOTICE: The metis port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port Installing /packages/All/indexinfo-0.3.1.tgz Installing /packages/All/gmp-6.1.2_1.tgz Installing /packages/All/mpfr-4.0.2.tgz Installing /packages/All/mpc-1.1.0_2.tgz Installing /packages/All/gettext-runtime-0.20.1.tgz Installing /packages/All/binutils-2.32_1,1.tgz Installing /packages/All/gcc8-8.3.0_3.tgz Message from gcc8-8.3.0_3: To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc8 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. Installing /packages/All/blas-3.5.0_6.tgz Installing /packages/All/lapack-3.5.0_8.tgz Installing /packages/All/openblas-0.2.20_10,1.tgz Installing /packages/All/suitesparse-5.2.0_4.tgz Installing /packages/All/expat-2.2.6_1.tgz Installing /packages/All/libffi-3.2.1_3.tgz Installing /packages/All/ncurses-6.1.20190525.tgz Installing /packages/All/readline-8.0.0.tgz Installing /packages/All/openssl-1.0.2s,1.tgz Message from openssl-1.0.2s,1: Edit /usr/local/openssl/openssl.cnf to fit your needs. Installing /packages/All/python36-3.6.9.tgz Message from python36-3.6.9: =========================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py36-gdbm databases/py-gdbm@py36 py36-sqlite3 databases/py-sqlite3@py36 py36-tkinter x11-toolkits/py-tkinter@py36 =========================================================================== Installing /packages/All/py36-setuptools-41.0.1.tgz Installing /packages/All/py36-numpy-1.16.4_1,1.tgz Installing /packages/All/freetype2-2.10.1.tgz Message from freetype2-2.10.1: The 2.7.x series now uses the new subpixel hinting mode (V40 port's option) as the default, emulating a modern version of ClearType. This change inevitably leads to different rendering results, and you might change port's options to adapt it to your taste (or use the new "FREETYPE_PROPERTIES" environment variable). The environment variable "FREETYPE_PROPERTIES" can be used to control the driver properties. Example: FREETYPE_PROPERTIES=truetype:interpreter-version=35 \ cff:no-stem-darkening=1 \ autofitter:warping=1 This allows to select, say, the subpixel hinting mode at runtime for a given application. If LONG_PCF_NAMES port's option was enabled, the PCF family names may include the foundry and information whether they contain wide characters. For example, "Sony Fixed" or "Misc Fixed Wide", instead of "Fixed". This can be disabled at run time with using pcf:no-long-family-names property, if needed. Example: FREETYPE_PROPERTIES=pcf:no-long-family-names=1 How to recreate fontconfig cache with using such environment variable, if needed: # env FREETYPE_PROPERTIES=pcf:no-long-family-names=1 fc-cache -fsv The controllable properties are listed in the section "Controlling FreeType Modules" in the reference's table of contents (/usr/local/share/doc/freetype2/reference/site/index.html, if documentation was installed). Installing /packages/All/jbigkit-2.1_1.tgz Installing /packages/All/jpeg-turbo-2.0.2.tgz Installing /packages/All/tiff-4.0.10_1.tgz Installing /packages/All/lcms2-2.9.tgz Installing /packages/All/png-1.6.37.tgz Installing /packages/All/openjpeg-2.3.1.tgz Installing /packages/All/giflib-5.1.9.tgz Installing /packages/All/webp-1.0.3_1.tgz Installing /packages/All/fontconfig-2.12.6,1.tgz Running fc-cache to build fontconfig cache... /usr/local/share/fonts: skipping, no such directory /usr/local/lib/X11/fonts: skipping, no such directory /var/db/fontconfig: cleaning cache directory fc-cache: succeeded Installing /packages/All/tcl86-8.6.9_1.tgz Installing /packages/All/libXau-1.0.9.tgz Installing /packages/All/xorgproto-2019.1.tgz Installing /packages/All/libXdmcp-1.1.3.tgz Installing /packages/All/libxml2-2.9.9.tgz Installing /packages/All/libpthread-stubs-0.4.tgz Installing /packages/All/libxcb-1.13.1.tgz Installing /packages/All/libX11-1.6.8,1.tgz Installing /packages/All/libXext-1.3.4,1.tgz Installing /packages/All/libXrender-0.9.10_2.tgz Installing /packages/All/libXft-2.3.2_3.tgz Installing /packages/All/libXScrnSaver-1.2.3_2.tgz Installing /packages/All/tk86-8.6.9_1.tgz Installing /packages/All/py36-olefile-0.46.tgz Installing /packages/All/py36-tkinter-3.6.9_6.tgz Installing /packages/All/py36-pillow-6.0.0_2.tgz Installing /packages/All/libfontenc-1.1.4.tgz Installing /packages/All/mkfontscale-1.2.1.tgz Installing /packages/All/adobe-cmaps-20051217_4.tgz Installing /packages/All/py36-reportlab-3.5.21.tgz Installing /packages/All/py36-biopython-1.73_1.tgz Installing /packages/All/libgpg-error-1.36.tgz Installing /packages/All/libgcrypt-1.8.4_1.tgz Installing /packages/All/libxslt-1.1.33.tgz Installing /packages/All/py36-lxml-4.3.4_1.tgz Installing /packages/All/py36-citeproc-py-0.4.0_1.tgz Installing /packages/All/py36-chardet-3.0.4_1.tgz Installing /packages/All/py36-idna-2.8.tgz Installing /packages/All/py36-asn1crypto-0.24.0.tgz Installing /packages/All/py36-pycparser-2.19.tgz Installing /packages/All/py36-cffi-1.12.3.tgz Installing /packages/All/py36-six-1.12.0.tgz Installing /packages/All/py36-cryptography-2.6.1.tgz Installing /packages/All/py36-openssl-19.0.0.tgz Installing /packages/All/py36-pysocks-1.7.0.tgz Installing /packages/All/py36-urllib3-1.22,1.tgz Message from py36-urllib3-1.22,1: Be careful, support of IPv6 is broken with PySocks 1.5.7. Installing /packages/All/py36-certifi-2019.6.16.tgz Installing /packages/All/py36-requests-2.21.0.tgz Installing /packages/All/py36-duecredit-0.7.0_1.tgz Installing /packages/All/py36-GridDataFormats-0.5.0_1.tgz Installing /packages/All/py36-gsd-1.7.0.tgz Installing /packages/All/py36-joblib-0.13.0.tgz Installing /packages/All/py36-cycler-0.10.0.tgz Installing /packages/All/py36-dateutil-2.8.0.tgz Installing /packages/All/py36-pytz-2019.1,1.tgz Installing /packages/All/py36-pyparsing-2.4.1.1.tgz Installing /packages/All/py36-tornado-5.1.1.tgz Installing /packages/All/py36-kiwisolver-1.1.0.tgz Installing /packages/All/py36-matplotlib-2.2.4_1.tgz Installing /packages/All/py36-msgpack-0.6.1.tgz Installing /packages/All/py36-mmtf-python-1.1.2.tgz Installing /packages/All/py36-pip-19.1.1.tgz Message from py36-pip-19.1.1: ============================== !!!! WARNING !!!! ========================== pip MUST ONLY be used: * With the --user flag, OR * To install or manage Python packages in virtual environments Failure to follow this warning can and will result in an inconsistent system-wide Python environment (LOCALBASE/lib/pythonX.Y/site-packages) and cause errors. Avoid using pip as root unless you know what you're doing. ============================== !!!! WARNING !!!! ========================== Installing /packages/All/py36-pbr-3.1.1_1.tgz Installing /packages/All/py36-mock-2.0.0.tgz Installing /packages/All/py36-decorator-4.3.0.tgz Installing /packages/All/libltdl-2.4.6.tgz Installing /packages/All/libgd-2.2.5_1,1.tgz Installing /packages/All/pcre-8.43_2.tgz Installing /packages/All/libiconv-1.14_11.tgz Installing /packages/All/glib-2.56.3_6,1.tgz No schema files found: doing nothing. Installing /packages/All/wayland-1.16.0.tgz Installing /packages/All/pciids-20190725.tgz Installing /packages/All/libpciaccess-0.16.tgz Installing /packages/All/libdrm-2.4.99.tgz Installing /packages/All/libelf-0.8.13_3.tgz Installing /packages/All/libXfixes-5.0.3_2.tgz Installing /packages/All/libXdamage-1.1.5.tgz Installing /packages/All/libXrandr-1.5.2.tgz Installing /packages/All/libxshmfence-1.3.tgz Installing /packages/All/libXxf86vm-1.1.4_3.tgz Installing /packages/All/mesa-libs-18.3.2_1.tgz Installing /packages/All/pixman-0.38.4.tgz Installing /packages/All/cairo-1.16.0,2.tgz Installing /packages/All/graphite2-1.3.13_1.tgz Installing /packages/All/harfbuzz-2.5.3_1.tgz Installing /packages/All/fribidi-0.19.7.tgz Installing /packages/All/font-bh-ttf-1.0.3_4.tgz Installing /packages/All/font-misc-meltho-1.0.3_4.tgz Installing /packages/All/font-misc-ethiopic-1.0.3_4.tgz Installing /packages/All/font-util-1.3.1.tgz Installing /packages/All/encodings-1.0.5,1.tgz Installing /packages/All/dejavu-2.37_1.tgz Message from dejavu-2.37_1: 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. Installing /packages/All/xorg-fonts-truetype-7.7_1.tgz Installing /packages/All/pango-1.42.4_3.tgz Installing /packages/All/libICE-1.0.9_3,1.tgz Installing /packages/All/libSM-1.2.3,1.tgz Installing /packages/All/libXt-1.2.0,1.tgz Installing /packages/All/libXmu-1.1.3,1.tgz Installing /packages/All/libXp-1.0.3_2,1.tgz Installing /packages/All/libXpm-3.5.12_2.tgz Installing /packages/All/libXaw-1.0.13_2,2.tgz Installing /packages/All/graphviz-2.40.1_11.tgz Installing /packages/All/py36-pygraphviz-1.5.tgz Installing /packages/All/py36-scipy-1.2.2_1.tgz Installing /packages/All/py36-scikit-sparse-0.4.4_3.tgz Installing /packages/All/py36-yaml-5.1.tgz Installing /packages/All/py36-networkx-2.1_2.tgz SUCCEEDED 00:00:56 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- x SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- x SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- x SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- x===> Fetching all distfiles required by py36-MDAnalysis-0.19.2_2 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- x===> Fetching all distfiles required by py36-MDAnalysis-0.19.2_2 for building => SHA256 Checksum OK for MDAnalysis-0.19.2.tar.gz. SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- x SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- x===> Fetching all distfiles required by py36-MDAnalysis-0.19.2_2 for building ===> Extracting for py36-MDAnalysis-0.19.2_2 => SHA256 Checksum OK for MDAnalysis-0.19.2.tar.gz. Extracted Memory Use: 91.43M SUCCEEDED 00:00:02 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- x SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- x===> Patching for py36-MDAnalysis-0.19.2_2 ===> Applying ports patches for py36-MDAnalysis-0.19.2_2 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- x SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- x SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- x===> Configuring for py36-MDAnalysis-0.19.2_2 Attempting to autodetect OpenMP support... Compiler supports OpenMP Will not attempt to use Cython. running config SUCCEEDED 00:00:03 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- x===> Building for py36-MDAnalysis-0.19.2_2 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-5.7-x86_64-3.6 creating build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis copying MDAnalysis/version.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis copying MDAnalysis/due.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis copying MDAnalysis/KDTree.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis copying MDAnalysis/exceptions.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis copying MDAnalysis/units.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis copying MDAnalysis/__init__.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis copying MDAnalysis/authors.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis creating build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/transformations copying MDAnalysis/transformations/rotate.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/transformations copying MDAnalysis/transformations/__init__.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/transformations copying MDAnalysis/transformations/translate.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/transformations creating build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib copying MDAnalysis/lib/log.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib copying MDAnalysis/lib/distances.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib copying MDAnalysis/lib/__init__.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib copying MDAnalysis/lib/pkdtree.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib copying MDAnalysis/lib/mdamath.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib copying MDAnalysis/lib/NeighborSearch.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib copying MDAnalysis/lib/util.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib copying MDAnalysis/lib/transformations.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib creating build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/base.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/core.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/XVG.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/__init__.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/auxiliary creating build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/TOPParser.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/GMSParser.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/LAMMPSParser.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/DLPolyParser.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/__init__.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/CRDParser.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/HoomdXMLParser.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/PQRParser.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/PSFParser.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/TPRParser.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/TXYZParser.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/GSDParser.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/tables.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/MOL2Parser.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/DMSParser.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/GROParser.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/MinimalParser.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/PDBQTParser.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/guessers.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/MMTFParser.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/XYZParser.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/core.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/ExtendedPDBParser.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/PDBParser.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/base.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology copying MDAnalysis/topology/_elements.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology creating build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis copying MDAnalysis/analysis/gnm.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis copying MDAnalysis/analysis/density.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis copying MDAnalysis/analysis/lineardensity.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis copying MDAnalysis/analysis/leaflet.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis copying MDAnalysis/analysis/helanal.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis copying MDAnalysis/analysis/x3dna.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis copying MDAnalysis/analysis/pca.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis copying MDAnalysis/analysis/dihedrals.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis copying MDAnalysis/analysis/polymer.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis copying MDAnalysis/analysis/base.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis copying MDAnalysis/analysis/align.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis copying MDAnalysis/analysis/nuclinfo.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis copying MDAnalysis/analysis/psa.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis copying MDAnalysis/analysis/distances.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis copying MDAnalysis/analysis/contacts.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis copying MDAnalysis/analysis/__init__.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis copying MDAnalysis/analysis/rdf.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis copying MDAnalysis/analysis/diffusionmap.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis copying MDAnalysis/analysis/rms.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis copying MDAnalysis/analysis/hole.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis copying MDAnalysis/analysis/waterdynamics.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis creating build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/migration copying MDAnalysis/migration/test_dummy_old_MDA_code.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/migration copying MDAnalysis/migration/ten2eleven.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/migration copying MDAnalysis/migration/test_dummy_torsion.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/migration copying MDAnalysis/migration/__init__.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/migration creating build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/core copying MDAnalysis/core/parallel.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/core copying MDAnalysis/core/AtomGroup.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/core copying MDAnalysis/core/groups.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/core copying MDAnalysis/core/universe.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/core copying MDAnalysis/core/topologyobjects.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/core copying MDAnalysis/core/util.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/core copying MDAnalysis/core/topologyattrs.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/core copying MDAnalysis/core/units.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/core copying MDAnalysis/core/transformations.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/core copying MDAnalysis/core/topology.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/core copying MDAnalysis/core/__init__.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/core copying MDAnalysis/core/qcprot.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/core copying MDAnalysis/core/selection.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/core copying MDAnalysis/core/distances.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/core copying MDAnalysis/core/_get_readers.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/core copying MDAnalysis/core/log.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/core creating build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/XTC.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/core.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/memory.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/DLPoly.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/DMS.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/chain.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/null.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/INPCRD.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/MMTF.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/XYZ.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/PDB.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/XDR.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRR.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRJ.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/PQR.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/__init__.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/MOL2.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/PDBQT.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/GRO.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/TXYZ.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/GMS.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/CRD.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/DCD.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/GSD.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/LAMMPS.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRZ.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates copying MDAnalysis/coordinates/base.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates creating build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/tests copying MDAnalysis/tests/__init__.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/tests copying MDAnalysis/tests/datafiles.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/tests creating build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/selections copying MDAnalysis/selections/pymol.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/selections copying MDAnalysis/selections/charmm.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/selections copying MDAnalysis/selections/vmd.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/selections copying MDAnalysis/selections/base.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/selections copying MDAnalysis/selections/__init__.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/selections copying MDAnalysis/selections/jmol.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/selections copying MDAnalysis/selections/gromacs.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/selections creating build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/visualization copying MDAnalysis/visualization/__init__.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/visualization copying MDAnalysis/visualization/streamlines_3D.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/visualization copying MDAnalysis/visualization/streamlines.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/visualization creating build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/__init__.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/formats creating build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/obj.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/utils.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/__init__.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/setting.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology/tpr creating build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/legacy copying MDAnalysis/analysis/legacy/__init__.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/legacy copying MDAnalysis/analysis/legacy/x3dna.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/legacy creating build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/data copying MDAnalysis/analysis/data/filenames.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/data copying MDAnalysis/analysis/data/__init__.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/data creating build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/hbonds copying MDAnalysis/analysis/hbonds/hbond_analysis.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/hbonds copying MDAnalysis/analysis/hbonds/wbridge_analysis.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/hbonds copying MDAnalysis/analysis/hbonds/__init__.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/hbonds copying MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/hbonds creating build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/covariance.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/__init__.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/similarity.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/confdistmatrix.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/bootstrap.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/utils.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore creating build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore/dimensionality_reduction creating build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/cluster.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/__init__.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore/clustering creating build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_numframes.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_framenumberingzerobased.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_calctorsions.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_mdaimports.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_agmethods.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_writer.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_selectatoms.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_framenumberingzerobased2.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_agmethods2.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_agcountmethods.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_torsionclasses.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_agsetterpluralization.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_camelcase.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/__init__.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_torsions.py -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/migration/fixes copying MDAnalysis/analysis/data/rama_ref_data.npy -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/data copying MDAnalysis/analysis/data/janin_ref_data.npy -> build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/data running build_ext building 'MDAnalysis.lib.formats.libdcd' extension creating build/temp.dragonfly-5.7-x86_64-3.6 creating build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis creating build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib creating build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/formats cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.6/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -I/usr/local/include/python3.6m -c MDAnalysis/lib/formats/libdcd.c -o build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/formats/libdcd.o -std=c99 -ffast-math -funroll-loops In file included from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/lib/formats/libdcd.c:596: /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/formats/libdcd.o -L/usr/local/lib -lpython3.6m -o build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/formats/libdcd.so building 'MDAnalysis.lib.c_distances' extension cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.6/site-packages/numpy/core/include -IMDAnalysis/lib/include -I/usr/local/include/python3.6m -c MDAnalysis/lib/c_distances.c -o build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/c_distances.o -std=c99 -ffast-math -funroll-loops In file included from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/lib/c_distances.c:597: /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ MDAnalysis/lib/c_distances.c: In function '__pyx_pf_10MDAnalysis_3lib_11c_distances_12coord_transform': MDAnalysis/lib/c_distances.c:3572:23: warning: passing argument 1 of '_coord_transform' from incompatible pointer type [-Wincompatible-pointer-types] _coord_transform((&(*((float *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_coords.data + __pyx_t_5 * __pyx_v_coords.strides[0]) ) + __pyx_t_6 * __pyx_v_coords.strides[1]) )))), __pyx_v_numcoords, (&(*((float *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_box.data + __pyx_t_7 * __pyx_v_box.strides[0]) ) + __pyx_t_8 * __pyx_v_box.strides[1]) ))))); ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from MDAnalysis/lib/c_distances.c:600: MDAnalysis/lib/include/calc_distances.h:310:29: note: expected 'float (*)[3]' but argument is of type 'float *' void _coord_transform(float coords[][3], int numCoords, float box[][3]) ~~~~~~^~~~~~~~~~~ MDAnalysis/lib/c_distances.c:3572:197: warning: passing argument 3 of '_coord_transform' from incompatible pointer type [-Wincompatible-pointer-types] _coord_transform((&(*((float *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_coords.data + __pyx_t_5 * __pyx_v_coords.strides[0]) ) + __pyx_t_6 * __pyx_v_coords.strides[1]) )))), __pyx_v_numcoords, (&(*((float *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_box.data + __pyx_t_7 * __pyx_v_box.strides[0]) ) + __pyx_t_8 * __pyx_v_box.strides[1]) ))))); ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from MDAnalysis/lib/c_distances.c:600: MDAnalysis/lib/include/calc_distances.h:310:63: note: expected 'float (*)[3]' but argument is of type 'float *' void _coord_transform(float coords[][3], int numCoords, float box[][3]) ~~~~~~^~~~~~~~ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/c_distances.o -L/usr/local/lib -lm -lpython3.6m -o build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/c_distances.so building 'MDAnalysis.lib.c_distances_openmp' extension cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -DPARALLEL -I/usr/local/lib/python3.6/site-packages/numpy/core/include -IMDAnalysis/lib/include -I/usr/local/include/python3.6m -c MDAnalysis/lib/c_distances_openmp.c -o build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/c_distances_openmp.o -fopenmp -std=c99 -ffast-math -funroll-loops In file included from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/lib/c_distances_openmp.c:597: /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/c_distances_openmp.o -L/usr/local/lib -lm -lgomp -lpython3.6m -o build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/c_distances_openmp.so -fopenmp building 'MDAnalysis.lib.qcprot' extension cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/usr/local/include/python3.6m -c MDAnalysis/lib/qcprot.c -o build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/qcprot.o -std=c99 -ffast-math -funroll-loops In file included from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/lib/qcprot.c:592: /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/qcprot.o -L/usr/local/lib -lpython3.6m -o build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/qcprot.so building 'MDAnalysis.lib._transformations' extension creating build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/src creating build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/src/transformations cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/usr/local/include/python3.6m -c MDAnalysis/lib/src/transformations/transformations.c -o build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/src/transformations/transformations.o -std=c99 -ffast-math -funroll-loops In file included from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/lib/src/transformations/transformations.c:73: /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/src/transformations/transformations.o -L/usr/local/lib -lm -lpython3.6m -o build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/_transformations.so building 'MDAnalysis.lib.formats.libmdaxdr' extension creating build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/formats/src cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/local/lib/python3.6/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/local/include/python3.6m -c MDAnalysis/lib/formats/libmdaxdr.c -o build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/formats/libmdaxdr.o -std=c99 -ffast-math -funroll-loops In file included from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/lib/formats/libmdaxdr.c:618: /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/local/lib/python3.6/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/local/include/python3.6m -c MDAnalysis/lib/formats/src/xdrfile.c -o build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/formats/src/xdrfile.o -std=c99 -ffast-math -funroll-loops MDAnalysis/lib/formats/src/xdrfile.c:2535:3: warning: initialization of 'unsigned int (*)(XDR *)' {aka 'unsigned int (*)(struct XDR *)'} from incompatible pointer type 'int64_t (*)(XDR *)' {aka 'long int (*)(struct XDR *)'} [-Wincompatible-pointer-types] xdrstdio_getpos, /* get offset in the stream */ ^~~~~~~~~~~~~~~ MDAnalysis/lib/formats/src/xdrfile.c:2535:3: note: (near initialization for 'xdrstdio_ops.x_getpostn') MDAnalysis/lib/formats/src/xdrfile.c:2536:3: warning: initialization of 'int (*)(XDR *, unsigned int)' {aka 'int (*)(struct XDR *, unsigned int)'} from incompatible pointer type 'int (*)(XDR *, int64_t, int)' {aka 'int (*)(struct XDR *, long int, int)'} [-Wincompatible-pointer-types] xdrstdio_setpos, /* set offset in the stream */ ^~~~~~~~~~~~~~~ MDAnalysis/lib/formats/src/xdrfile.c:2536:3: note: (near initialization for 'xdrstdio_ops.x_setpostn') cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/local/lib/python3.6/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/local/include/python3.6m -c MDAnalysis/lib/formats/src/xdrfile_xtc.c -o build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/formats/src/xdrfile_xtc.o -std=c99 -ffast-math -funroll-loops cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/local/lib/python3.6/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/local/include/python3.6m -c MDAnalysis/lib/formats/src/xdrfile_trr.c -o build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/formats/src/xdrfile_trr.o -std=c99 -ffast-math -funroll-loops cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/local/lib/python3.6/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/local/include/python3.6m -c MDAnalysis/lib/formats/src/trr_seek.c -o build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/formats/src/trr_seek.o -std=c99 -ffast-math -funroll-loops cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/local/lib/python3.6/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/local/include/python3.6m -c MDAnalysis/lib/formats/src/xtc_seek.c -o build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/formats/src/xtc_seek.o -std=c99 -ffast-math -funroll-loops cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/formats/libmdaxdr.o build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/formats/src/xdrfile.o build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/formats/src/xdrfile_xtc.o build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/formats/src/xdrfile_trr.o build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/formats/src/trr_seek.o build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/formats/src/xtc_seek.o -L/usr/local/lib -lpython3.6m -o build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/formats/libmdaxdr.so building 'MDAnalysis.lib.formats.cython_util' extension cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/usr/local/include/python3.6m -c MDAnalysis/lib/formats/cython_util.c -o build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/formats/cython_util.o -std=c99 -ffast-math -funroll-loops In file included from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/lib/formats/cython_util.c:592: /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/formats/cython_util.o -L/usr/local/lib -lpython3.6m -o build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/formats/cython_util.so building 'MDAnalysis.analysis.encore.cutils' extension creating build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis creating build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/usr/local/include/python3.6m -c MDAnalysis/analysis/encore/cutils.c -o build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore/cutils.o -std=c99 -ffast-math -funroll-loops In file included from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/analysis/encore/cutils.c:592: /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore/cutils.o -L/usr/local/lib -lpython3.6m -o build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore/cutils.so building 'MDAnalysis.analysis.encore.clustering.affinityprop' extension creating build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore/clustering creating build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore/clustering/src cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.6/site-packages/numpy/core/include -IMDAnalysis/analysis/encore/clustering/include -I/usr/local/include/python3.6m -c MDAnalysis/analysis/encore/clustering/affinityprop.c -o build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore/clustering/affinityprop.o -std=c99 -ffast-math -funroll-loops In file included from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/analysis/encore/clustering/affinityprop.c:598: /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.6/site-packages/numpy/core/include -IMDAnalysis/analysis/encore/clustering/include -I/usr/local/include/python3.6m -c MDAnalysis/analysis/encore/clustering/src/ap.c -o build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore/clustering/src/ap.o -std=c99 -ffast-math -funroll-loops cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore/clustering/affinityprop.o build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore/clustering/src/ap.o -L/usr/local/lib -lm -lpython3.6m -o build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore/clustering/affinityprop.so building 'MDAnalysis.analysis.encore.dimensionality_reduction.stochasticproxembed' extension creating build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore/dimensionality_reduction creating build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore/dimensionality_reduction/src cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.6/site-packages/numpy/core/include -IMDAnalysis/analysis/encore/dimensionality_reduction/include -I/usr/local/include/python3.6m -c MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -o build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.o -std=c99 -ffast-math -funroll-loops In file included from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c:598: /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.6/site-packages/numpy/core/include -IMDAnalysis/analysis/encore/dimensionality_reduction/include -I/usr/local/include/python3.6m -c MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -o build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.o -std=c99 -ffast-math -funroll-loops cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.o build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.o -L/usr/local/lib -lm -lpython3.6m -o build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.so building 'MDAnalysis.lib._cutil' extension cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.6/site-packages/numpy/core/include -IMDAnalysis/lib/include -I/usr/local/include/python3.6m -c MDAnalysis/lib/_cutil.cpp -o build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/_cutil.o -ffast-math -funroll-loops -std=c++11 In file included from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/lib/_cutil.cpp:613: /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ c++ -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/_cutil.o -L/usr/local/lib -lm -lpython3.6m -o build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/_cutil.so building 'MDAnalysis.lib._augment' extension cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/usr/local/include/python3.6m -c MDAnalysis/lib/_augment.cpp -o build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/_augment.o -ffast-math -funroll-loops -std=c++11 In file included from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/lib/_augment.cpp:608: /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ c++ -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/_augment.o -L/usr/local/lib -lpython3.6m -o build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/_augment.so building 'MDAnalysis.lib.nsgrid' extension cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.6/site-packages/numpy/core/include -I/usr/local/include/python3.6m -c MDAnalysis/lib/nsgrid.cpp -o build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/nsgrid.o -ffast-math -funroll-loops -std=c++11 In file included from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/lib/nsgrid.cpp:614: /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ c++ -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/nsgrid.o -L/usr/local/lib -lpython3.6m -o build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/nsgrid.so SUCCEEDED 00:04:04 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- x SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- x===> Staging for py36-MDAnalysis-0.19.2_2 ===> 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-5.7-x86_64-3.6/MDAnalysis running build_ext running install_lib creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6 creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/migration/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/migration/test_dummy_torsion.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/migration/ten2eleven.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/migration/fixes/fix_agmethods.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/migration/fixes/fix_writer.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/migration/fixes/fix_agcountmethods.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/migration/fixes/fix_torsions.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/migration/fixes/fix_agsetterpluralization.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/migration/fixes/fix_mdaimports.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/migration/fixes/fix_calctorsions.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/migration/fixes/fix_selectatoms.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/migration/fixes/fix_numframes.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/migration/fixes/fix_camelcase.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/migration/fixes/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/migration/fixes/fix_torsionclasses.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/migration/fixes/fix_framenumberingzerobased2.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/migration/fixes/fix_framenumberingzerobased.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/migration/fixes/fix_agmethods2.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/migration/test_dummy_old_MDA_code.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates/TRJ.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates/XTC.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates/XDR.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates/memory.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates/INPCRD.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates/LAMMPS.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates/PDB.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates/TRR.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates/CRD.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates/MOL2.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates/DLPoly.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates/GMS.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates/DMS.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates/base.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates/null.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates/PDBQT.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates/GRO.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates/DCD.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates/TXYZ.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates/TRZ.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates/MMTF.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates/GSD.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates/PQR.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates/core.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates/XYZ.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/coordinates/chain.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/exceptions.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/units.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/leaflet.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/distances.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/legacy copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/legacy/x3dna.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/legacy copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/legacy/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/legacy copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/base.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/data copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/data/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/data copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/data/rama_ref_data.npy -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/data copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/data/filenames.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/data copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/data/janin_ref_data.npy -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/data copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/lineardensity.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/hbonds copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/hbonds/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/hbonds copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/hbonds/hbond_analysis.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/hbonds copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/hbonds copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/hbonds/wbridge_analysis.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/hbonds copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/waterdynamics.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/dihedrals.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore/cutils.so -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore/similarity.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore/covariance.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.so -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore/confdistmatrix.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore/bootstrap.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/clustering copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore/clustering/affinityprop.so -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/clustering copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore/clustering/cluster.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/clustering copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore/clustering/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/clustering copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/clustering copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/clustering copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/encore/utils.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/psa.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/gnm.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/pca.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/helanal.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/hole.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/polymer.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/nuclinfo.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/rms.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/contacts.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/density.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/diffusionmap.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/rdf.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/align.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/analysis/x3dna.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/transformations copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/transformations/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/transformations copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/transformations/rotate.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/transformations copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/transformations/translate.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/transformations creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/selections copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/selections/charmm.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/selections copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/selections/pymol.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/selections copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/selections/gromacs.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/selections copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/selections/jmol.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/selections copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/selections/base.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/selections copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/selections/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/selections copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/selections/vmd.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/selections copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/KDTree.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/version.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology/MMTFParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology/base.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology/TPRParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/tpr copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology/tpr/utils.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/tpr copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology/tpr/setting.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/tpr copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology/tpr/obj.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/tpr copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology/tpr/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/tpr copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology/PSFParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology/_elements.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology/DLPolyParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology/ExtendedPDBParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology/XYZParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology/PDBQTParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology/core.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology/TOPParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology/CRDParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology/HoomdXMLParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology/tables.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology/LAMMPSParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology/guessers.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology/GROParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology/PQRParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology/MinimalParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology/DMSParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology/MOL2Parser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology/GSDParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology/GMSParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology/PDBParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/topology/TXYZParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/auxiliary copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/auxiliary/core.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/auxiliary copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/auxiliary/XVG.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/auxiliary copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/auxiliary/base.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/auxiliary copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/auxiliary/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/auxiliary copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/due.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/authors.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/visualization copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/visualization/streamlines_3D.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/visualization copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/visualization/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/visualization copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/visualization/streamlines.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/visualization creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/c_distances_openmp.so -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/qcprot.so -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/_transformations.so -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/_cutil.so -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/_augment.so -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/c_distances.so -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/util.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/NeighborSearch.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/transformations.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib/formats copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/formats/libdcd.so -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib/formats copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/formats/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib/formats copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/formats/cython_util.so -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib/formats copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/formats/libmdaxdr.so -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib/formats copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/log.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/pkdtree.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/distances.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/mdamath.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/lib/nsgrid.so -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/tests copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/tests/datafiles.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/tests copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/tests/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/tests creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/core/units.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/core/transformations.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/core/universe.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/core/qcprot.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/core/log.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/core/distances.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/core/topologyobjects.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/core/_get_readers.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/core/topology.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/core/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/core/topologyattrs.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/core/groups.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/core/selection.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/core/util.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/core/parallel.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.7-x86_64-3.6/MDAnalysis/core/AtomGroup.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/test_dummy_torsion.py to test_dummy_torsion.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/ten2eleven.py to ten2eleven.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes/fix_agmethods.py to fix_agmethods.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes/fix_writer.py to fix_writer.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes/fix_agcountmethods.py to fix_agcountmethods.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes/fix_torsions.py to fix_torsions.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes/fix_agsetterpluralization.py to fix_agsetterpluralization.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes/fix_mdaimports.py to fix_mdaimports.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes/fix_calctorsions.py to fix_calctorsions.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes/fix_selectatoms.py to fix_selectatoms.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes/fix_numframes.py to fix_numframes.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes/fix_camelcase.py to fix_camelcase.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes/fix_torsionclasses.py to fix_torsionclasses.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes/fix_framenumberingzerobased2.py to fix_framenumberingzerobased2.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes/fix_framenumberingzerobased.py to fix_framenumberingzerobased.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/fixes/fix_agmethods2.py to fix_agmethods2.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/migration/test_dummy_old_MDA_code.py to test_dummy_old_MDA_code.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/TRJ.py to TRJ.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/XTC.py to XTC.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/XDR.py to XDR.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/memory.py to memory.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/INPCRD.py to INPCRD.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/LAMMPS.py to LAMMPS.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/PDB.py to PDB.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/TRR.py to TRR.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/CRD.py to CRD.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/MOL2.py to MOL2.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/DLPoly.py to DLPoly.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/GMS.py to GMS.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/DMS.py to DMS.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/base.py to base.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/null.py to null.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/PDBQT.py to PDBQT.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/GRO.py to GRO.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/DCD.py to DCD.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/TXYZ.py to TXYZ.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/TRZ.py to TRZ.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/MMTF.py to MMTF.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/GSD.py to GSD.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/PQR.py to PQR.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/core.py to core.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/XYZ.py to XYZ.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/coordinates/chain.py to chain.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/exceptions.py to exceptions.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/units.py to units.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/leaflet.py to leaflet.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/distances.py to distances.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/legacy/x3dna.py to x3dna.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/legacy/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/base.py to base.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/data/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/data/filenames.py to filenames.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/lineardensity.py to lineardensity.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/hbonds/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/hbonds/hbond_analysis.py to hbond_analysis.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/hbonds/hbond_autocorrel.py to hbond_autocorrel.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/hbonds/wbridge_analysis.py to wbridge_analysis.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/waterdynamics.py to waterdynamics.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/dihedrals.py to dihedrals.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/similarity.py to similarity.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/covariance.py to covariance.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py to DimensionalityReductionMethod.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py to reduce_dimensionality.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py to confdistmatrix.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/bootstrap.py to bootstrap.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/clustering/cluster.py to cluster.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/clustering/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py to ClusteringMethod.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/clustering/ClusterCollection.py to ClusterCollection.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/utils.py to utils.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/psa.py to psa.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/gnm.py to gnm.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/pca.py to pca.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/helanal.py to helanal.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/hole.py to hole.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/polymer.py to polymer.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/nuclinfo.py to nuclinfo.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/rms.py to rms.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/contacts.py to contacts.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/density.py to density.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/diffusionmap.py to diffusionmap.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/rdf.py to rdf.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/align.py to align.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/x3dna.py to x3dna.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/transformations/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/transformations/rotate.py to rotate.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/transformations/translate.py to translate.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/selections/charmm.py to charmm.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/selections/pymol.py to pymol.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/selections/gromacs.py to gromacs.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/selections/jmol.py to jmol.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/selections/base.py to base.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/selections/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/selections/vmd.py to vmd.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/KDTree.py to KDTree.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/version.py to version.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/MMTFParser.py to MMTFParser.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/base.py to base.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/TPRParser.py to TPRParser.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/tpr/utils.py to utils.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/tpr/setting.py to setting.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/tpr/obj.py to obj.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/tpr/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/PSFParser.py to PSFParser.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/_elements.py to _elements.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/DLPolyParser.py to DLPolyParser.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/ExtendedPDBParser.py to ExtendedPDBParser.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/XYZParser.py to XYZParser.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/PDBQTParser.py to PDBQTParser.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/core.py to core.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/TOPParser.py to TOPParser.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/CRDParser.py to CRDParser.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/HoomdXMLParser.py to HoomdXMLParser.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/tables.py to tables.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/LAMMPSParser.py to LAMMPSParser.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/guessers.py to guessers.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/GROParser.py to GROParser.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/PQRParser.py to PQRParser.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/MinimalParser.py to MinimalParser.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/DMSParser.py to DMSParser.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/MOL2Parser.py to MOL2Parser.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/GSDParser.py to GSDParser.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/GMSParser.py to GMSParser.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/PDBParser.py to PDBParser.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/topology/TXYZParser.py to TXYZParser.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/auxiliary/core.py to core.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/auxiliary/XVG.py to XVG.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/auxiliary/base.py to base.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/auxiliary/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/due.py to due.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/authors.py to authors.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/visualization/streamlines_3D.py to streamlines_3D.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/visualization/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/visualization/streamlines.py to streamlines.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib/util.py to util.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib/NeighborSearch.py to NeighborSearch.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib/transformations.py to transformations.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib/formats/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib/log.py to log.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib/pkdtree.py to pkdtree.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib/distances.py to distances.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/lib/mdamath.py to mdamath.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/tests/datafiles.py to datafiles.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/tests/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core/units.py to units.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core/transformations.py to transformations.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core/universe.py to universe.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core/qcprot.py to qcprot.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core/log.py to log.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core/distances.py to distances.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core/topologyobjects.py to topologyobjects.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core/_get_readers.py to _get_readers.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core/topology.py to topology.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core/topologyattrs.py to topologyattrs.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core/groups.py to groups.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core/selection.py to selection.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core/util.py to util.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core/parallel.py to parallel.cpython-36.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis/core/AtomGroup.py to AtomGroup.cpython-36.pyc writing byte-compilation script '/tmp/tmprlwhbrj3.py' /usr/local/bin/python3.6 /tmp/tmprlwhbrj3.py removing /tmp/tmprlwhbrj3.py running install_egg_info running egg_info writing MDAnalysis.egg-info/PKG-INFO writing dependency_links to MDAnalysis.egg-info/dependency_links.txt writing requirements to MDAnalysis.egg-info/requires.txt writing top-level names to MDAnalysis.egg-info/top_level.txt reading manifest file 'MDAnalysis.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'MDAnalysis/coordinates/xdrfile/src/*' warning: no files found matching 'MDAnalysis/lib/src/pyqcprot/*' warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution warning: no previously-included files matching '*.pyd' found anywhere in distribution warning: no previously-included files matching '*~' found anywhere in distribution writing manifest file 'MDAnalysis.egg-info/SOURCES.txt' Copying MDAnalysis.egg-info to /construction/science/py-MDAnalysis/stage/usr/local/lib/python3.6/site-packages/MDAnalysis-0.19.2-py3.6.egg-info running install_scripts writing list of installed files to '/construction/science/py-MDAnalysis/.PLIST.pymodtmp' ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Error: /usr/local/lib/python3.6/site-packages/MDAnalysis/analysis/encore/clustering/affinityprop.so is linked to /usr/local/lib/libintl.so.8 from devel/gettext-runtime but it is not declared as a dependency Warning: you need USES+=gettext-runtime Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:09 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- x====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- x===> Building package for py36-MDAnalysis-0.19.2_2 file sizes/checksums [528]: 0% file sizes/checksums [528]: 18% file sizes/checksums [528]: 37% file sizes/checksums [528]: 56% file sizes/checksums [528]: 75% file sizes/checksums [528]: 94% file sizes/checksums [528]: 100% packing files [528]: 0% packing files [528]: 18% packing files [528]: 37% packing files [528]: 56% packing files [528]: 75% packing files [528]: 94% packing files [528]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:02 TOTAL TIME 00:05:18