------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/metis-5.1.0_8.txz Installing /packages/All/tbb-2020.1.txz Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gmp-6.2.0.txz Installing /packages/All/mpfr-4.0.2.txz Installing /packages/All/mpc-1.1.0_2.txz UNFLAVORED devel/binutils -> use devel/binutils@native Installing /packages/All/gettext-runtime-0.20.1.txz Installing /packages/All/binutils-2.33.1_2,1.txz Installing /packages/All/gcc8-8.4.0.txz ===== Message from gcc8-8.4.0: -- 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/openblas-0.3.7_2,1.txz Installing /packages/All/suitesparse-5.4.0_5.txz Installing /packages/All/expat-2.2.8.txz Installing /packages/All/libffi-3.2.1_3.txz Installing /packages/All/ncurses-6.1.20190525.txz Installing /packages/All/readline-8.0.4.txz Installing /packages/All/openssl-1.1.1d,1.txz Installing /packages/All/python27-2.7.17_1.txz ===== Message from python27-2.7.17_1: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: bsddb databases/py-bsddb gdbm databases/py-gdbm sqlite3 databases/py-sqlite3 tkinter x11-toolkits/py-tkinter Installing /packages/All/py27-setuptools-44.0.0.txz ===== Message from py27-setuptools-44.0.0: -- Only /usr/local/bin/easy_install-2.7 script has been installed since Python 2.7 is not the default Python version. Installing /packages/All/py27-numpy-1.16.5_4,1.txz Installing /packages/All/freetype2-2.10.1.txz ===== 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/fontconfig-2.12.6,1.txz 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/libfontenc-1.1.4.txz Installing /packages/All/mkfontscale-1.2.1.txz Installing /packages/All/adobe-cmaps-20051217_4.txz Installing /packages/All/jbigkit-2.1_1.txz Installing /packages/All/jpeg-turbo-2.0.4.txz Installing /packages/All/tiff-4.1.0.txz Installing /packages/All/lcms2-2.9.txz Installing /packages/All/png-1.6.37.txz Installing /packages/All/openjpeg-2.3.1.txz Installing /packages/All/giflib-5.2.1.txz Installing /packages/All/webp-1.1.0.txz Installing /packages/All/tcl86-8.6.10.txz Installing /packages/All/libXau-1.0.9.txz Installing /packages/All/libxml2-2.9.10.txz Installing /packages/All/libpthread-stubs-0.4.txz Installing /packages/All/xorgproto-2019.2.txz Installing /packages/All/libXdmcp-1.1.3.txz Installing /packages/All/libxcb-1.13.1.txz Installing /packages/All/libX11-1.6.9,1.txz Installing /packages/All/libXext-1.3.4,1.txz Installing /packages/All/libXrender-0.9.10_2.txz Installing /packages/All/libXft-2.3.3.txz Installing /packages/All/libXScrnSaver-1.2.3_2.txz Installing /packages/All/tk86-8.6.10_1.txz Installing /packages/All/py27-olefile-0.46.txz Installing /packages/All/py27-tkinter-2.7.17_6.txz Installing /packages/All/py27-pillow6-6.2.2.txz Installing /packages/All/py27-reportlab-3.5.21_1.txz Installing /packages/All/py27-biopython-1.73_1.txz Installing /packages/All/libgpg-error-1.37.txz Installing /packages/All/libgcrypt-1.8.5.txz Installing /packages/All/libxslt-1.1.34_1.txz Installing /packages/All/py27-lxml-4.5.0.txz Installing /packages/All/py27-citeproc-py-0.5.0.txz Installing /packages/All/py27-certifi-2019.11.28.txz Installing /packages/All/py27-chardet-3.0.4_3.txz Installing /packages/All/py27-idna-2.8.txz Installing /packages/All/py27-pysocks-1.7.1.txz Installing /packages/All/py27-asn1crypto-1.3.0.txz Installing /packages/All/py27-pycparser-2.19.txz Installing /packages/All/py27-cffi-1.14.0.txz Installing /packages/All/py27-enum34-1.1.6.txz Installing /packages/All/py27-ipaddress-1.0.23.txz Installing /packages/All/py27-six-1.14.0.txz Installing /packages/All/py27-cryptography-2.6.1.txz Installing /packages/All/py27-openssl-19.0.0.txz Installing /packages/All/py27-urllib3-1.25.7,1.txz ===== Message from py27-urllib3-1.25.7,1: -- Since version 1.25 HTTPS connections are now verified by default which is done via "cert_reqs = 'CERT_REQUIRED'". While certificate verification can be disabled via "cert_reqs = 'CERT_NONE'", it's highly recommended to leave it on. Various consumers of net/py-urllib3 already have implemented routines that either explicitly enable or disable HTTPS certificate verification (e.g. via configuration settings, CLI arguments, etc.). Yet it may happen that there are still some consumers which don't explicitly enable/disable certificate verification for HTTPS connections which could then lead to errors (as is often the case with self-signed certificates). In case of an error one should try first to temporarily disable certificate verification of the problematic urllib3 consumer to see if that approach will remedy the issue. Installing /packages/All/py27-requests-2.22.0.txz Installing /packages/All/py27-duecredit-0.8.0.txz Installing /packages/All/py27-GridDataFormats-0.5.0_1.txz Installing /packages/All/py27-gsd-1.10.0.txz Installing /packages/All/py27-joblib-0.13.0.txz Installing /packages/All/pcre-8.43_2.txz Installing /packages/All/libiconv-1.14_11.txz Installing /packages/All/python37-3.7.6.txz ===== Message from python37-3.7.6: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py37-gdbm databases/py-gdbm@py37 py37-sqlite3 databases/py-sqlite3@py37 py37-tkinter x11-toolkits/py-tkinter@py37 Installing /packages/All/glib-2.56.3_7,1.txz No schema files found: doing nothing. Installing /packages/All/atk-2.28.1.txz Installing /packages/All/wayland-1.16.0.txz Installing /packages/All/pciids-20200222.txz Installing /packages/All/libpciaccess-0.16.txz Installing /packages/All/libdrm-2.4.100.txz Installing /packages/All/libelf-0.8.13_3.txz Installing /packages/All/libXfixes-5.0.3_2.txz Installing /packages/All/libXdamage-1.1.5.txz Installing /packages/All/libXrandr-1.5.2.txz Installing /packages/All/libxshmfence-1.3.txz Installing /packages/All/libXxf86vm-1.1.4_3.txz Installing /packages/All/mesa-libs-18.3.2_4.txz Installing /packages/All/pixman-0.38.4.txz Installing /packages/All/cairo-1.16.0,2.txz Installing /packages/All/shared-mime-info-1.10_2.txz Installing /packages/All/gdk-pixbuf2-2.40.0.txz Installing /packages/All/libdaemon-0.14_1.txz Installing /packages/All/libICE-1.0.10,1.txz Installing /packages/All/libSM-1.2.3,1.txz Installing /packages/All/dbus-1.12.16.txz ===> Creating groups. Creating group 'messagebus' with gid '556'. ===> Creating users Creating user 'messagebus' with uid '556'. Installing /packages/All/dbus-glib-0.110.txz Installing /packages/All/gdbm-1.18.1_1.txz Installing /packages/All/gobject-introspection-1.56.1,1.txz Installing /packages/All/gnome_subr-1.0.txz Installing /packages/All/avahi-app-0.7_2.txz ===> Creating groups. Creating group 'avahi' with gid '558'. ===> Creating users Creating user 'avahi' with uid '558'. Installing /packages/All/nettle-3.5.1_1.txz Installing /packages/All/libtasn1-4.15.0.txz Installing /packages/All/libunistring-0.9.10_1.txz Installing /packages/All/libidn2-2.3.0_1.txz Installing /packages/All/ca_root_nss-3.51.txz ===== Message from ca_root_nss-3.51: -- FreeBSD does not, and can not warrant that the certification authorities whose certificates are included in this package have in any way been audited for trustworthiness or RFC 3647 compliance. Assessment and verification of trust is the complete responsibility of the system administrator. This package installs symlinks to support root certificates discovery by default for software that uses OpenSSL. This enables SSL Certificate Verification by client software without manual intervention. If you prefer to do this manually, replace the following symlinks with either an empty file or your site-local certificate bundle. * /etc/ssl/cert.pem * /usr/local/etc/ssl/cert.pem * /usr/local/openssl/cert.pem Installing /packages/All/p11-kit-0.23.18.1.txz Installing /packages/All/tpm-emulator-0.7.4_2.txz ===> Creating groups. Creating group '_tss' with gid '601'. ===> Creating users Creating user '_tss' with uid '601'. Installing /packages/All/trousers-0.3.14_2.txz ===> Creating groups. Using existing group '_tss'. ===> Creating users Using existing user '_tss'. ===== Message from trousers-0.3.14_2: -- To run tcsd automatically, add the following line to /etc/rc.conf: tcsd_enable="YES" You might want to edit /usr/local/etc/tcsd.conf to reflect your setup. If you want to use tcsd with software TPM emulator, use the following configuration in /etc/rc.conf: tcsd_enable="YES" tcsd_mode="emulator" tpmd_enable="YES" To use TPM, add your_account to '_tss' group like following: # pw groupmod _tss -m your_account Installing /packages/All/gnutls-3.6.12.txz Installing /packages/All/libpaper-1.1.24.4.txz Installing /packages/All/cups-2.2.13.txz ===> Creating groups. Creating group 'cups' with gid '193'. ===> Creating users Creating user 'cups' with uid '193'. Installing /packages/All/graphite2-1.3.13_1.txz Installing /packages/All/harfbuzz-2.6.4.txz Installing /packages/All/fribidi-0.19.7.txz Installing /packages/All/font-bh-ttf-1.0.3_4.txz Installing /packages/All/font-misc-meltho-1.0.3_4.txz Installing /packages/All/font-misc-ethiopic-1.0.3_4.txz Installing /packages/All/encodings-1.0.5,1.txz Installing /packages/All/dejavu-2.37_1.txz ===== 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.txz Installing /packages/All/pango-1.42.4_3.txz Installing /packages/All/hicolor-icon-theme-0.17.txz Installing /packages/All/libXinerama-1.1.4_2,1.txz Installing /packages/All/libXi-1.7.10,1.txz Installing /packages/All/libXcursor-1.2.0.txz Installing /packages/All/libXcomposite-0.4.5,1.txz Installing /packages/All/gtk-update-icon-cache-2.24.32.txz Installing /packages/All/gtk2-2.24.32.txz Installing /packages/All/xmlcatmgr-2.2_2.txz + Creating /usr/local/share/sgml/catalog + Registering CATALOG catalog.ports (SGML) + Creating /usr/local/share/sgml/catalog.ports + Creating /usr/local/share/xml/catalog + Registering nextCatalog catalog.ports (XML) + Creating /usr/local/share/xml/catalog.ports ===== Message from xmlcatmgr-2.2_2: -- The following catalogs are installed: 1) /usr/local/share/sgml/catalog The top level catalog for SGML stuff. It is not changed by any ports/packages except textproc/xmlcatmgr. 2) /usr/local/share/sgml/catalog.ports This catalog is for handling SGML stuff installed under /usr/local/share/sgml. It is changed by ports/packages. 3) /usr/local/share/xml/catalog The top level catalog for XML stuff. It is not changed by any ports/packages except textproc/xmlcatmgr. 4) /usr/local/share/xml/catalog.ports This catalog is for handling XML stuff installed under /usr/local/share/xml. It is changed by ports/packages. Installing /packages/All/libglade2-2.6.4_10.txz Installing /packages/All/py27-cycler-0.10.0.txz Installing /packages/All/py27-dateutil-2.8.0.txz Installing /packages/All/py27-pytz-2019.3,1.txz Installing /packages/All/py27-pyparsing-2.4.6.txz Installing /packages/All/py27-futures-3.3.0.txz Installing /packages/All/py27-singledispatch-3.4.0.3_1.txz Installing /packages/All/py27-backports_abc-0.5.txz Installing /packages/All/py27-tornado-5.1.1.txz Installing /packages/All/py27-kiwisolver-1.1.0.txz UNFLAVORED devel/py-gobject -> use devel/py-gobject@py27 Installing /packages/All/py27-cairo-1.18.1_1.txz Installing /packages/All/py27-gobject-2.28.6_8.txz UNFLAVORED x11-toolkits/py-gtk2 -> use x11-toolkits/py-gtk2@py27 UNFLAVORED devel/py-gobject -> use devel/py-gobject@py27 Installing /packages/All/py27-gtk2-2.24.0_5.txz Installing /packages/All/py27-backports-1.txz Installing /packages/All/py27-backports.functools_lru_cache-1.5.txz Installing /packages/All/py27-matplotlib-2.2.4_1.txz Installing /packages/All/py27-msgpack-0.6.2.txz Installing /packages/All/py27-mmtf-python-1.1.2.txz Installing /packages/All/py27-funcsigs-1.0.2.txz Installing /packages/All/py27-mock-3.0.5.txz Installing /packages/All/py27-decorator-4.3.0.txz Installing /packages/All/libltdl-2.4.6.txz Installing /packages/All/libgd-2.2.5_2,1.txz Installing /packages/All/libXt-1.2.0,1.txz Installing /packages/All/libXmu-1.1.3,1.txz Installing /packages/All/libXpm-3.5.13.txz Installing /packages/All/libXaw-1.0.13_3,2.txz Installing /packages/All/graphviz-2.42.3.txz Installing /packages/All/py27-pygraphviz-1.5.txz Installing /packages/All/py27-scipy-1.2.2_1.txz Installing /packages/All/py27-scikit-sparse-0.4.4_3.txz Installing /packages/All/py27-yaml-5.2.txz Installing /packages/All/py27-networkx-2.1,1.txz UNFLAVORED devel/binutils -> use devel/binutils@native UNFLAVORED devel/py-gobject -> use devel/py-gobject@py27 UNFLAVORED x11-toolkits/py-gtk2 -> use x11-toolkits/py-gtk2@py27 UNFLAVORED devel/py-gobject -> use devel/py-gobject@py27 SUCCEEDED 00:01:11 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> py27-MDAnalysis-0.19.2_2 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> py27-MDAnalysis-0.19.2_2 depends on file: /usr/local/sbin/pkg - found => MDAnalysis-0.19.2.tar.gz doesn't seem to exist in /distfiles/. => Attempting to fetch https://files.pythonhosted.org/packages/source/M/MDAnalysis/MDAnalysis-0.19.2.tar.gz MDAnalysis-0.19.2.tar.gz 0% of 15 MB 0 Bps MDAnalysis-0.19.2.tar.gz 93% of 15 MB 70 MBps MDAnalysis-0.19.2.tar.gz 15 MB 71 MBps 01s ===> Fetching all distfiles required by py27-MDAnalysis-0.19.2_2 for building SUCCEEDED 00:00:02 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> py27-MDAnalysis-0.19.2_2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py27-MDAnalysis-0.19.2_2 for building => SHA256 Checksum OK for MDAnalysis-0.19.2.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> py27-MDAnalysis-0.19.2_2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py27-MDAnalysis-0.19.2_2 for building ===> Extracting for py27-MDAnalysis-0.19.2_2 => SHA256 Checksum OK for MDAnalysis-0.19.2.tar.gz. Extracted Memory Use: 91.43M SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for py27-MDAnalysis-0.19.2_2 ===> Applying ports patches for py27-MDAnalysis-0.19.2_2 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> py27-MDAnalysis-0.19.2_2 depends on package: py27-numpy>=1.15,1<1.19,1 - found ===> py27-MDAnalysis-0.19.2_2 depends on package: py27-setuptools>0 - found ===> py27-MDAnalysis-0.19.2_2 depends on file: /usr/local/bin/python2.7 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> py27-MDAnalysis-0.19.2_2 depends on package: py27-numpy>=1.15,1<1.19,1 - found ===> py27-MDAnalysis-0.19.2_2 depends on package: py27-setuptools>0 - found ===> py27-MDAnalysis-0.19.2_2 depends on file: /usr/local/bin/python2.7 - found ===> Configuring for py27-MDAnalysis-0.19.2_2 Attempting to autodetect OpenMP support... Compiler supports OpenMP Will not attempt to use Cython. running config SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for py27-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-5.9-x86_64-2.7 creating build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis copying MDAnalysis/exceptions.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis copying MDAnalysis/units.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis copying MDAnalysis/authors.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis copying MDAnalysis/KDTree.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis copying MDAnalysis/version.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis copying MDAnalysis/due.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis copying MDAnalysis/__init__.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis creating build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis copying MDAnalysis/analysis/leaflet.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis copying MDAnalysis/analysis/pca.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis copying MDAnalysis/analysis/rdf.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis copying MDAnalysis/analysis/__init__.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis copying MDAnalysis/analysis/base.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis copying MDAnalysis/analysis/waterdynamics.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis copying MDAnalysis/analysis/contacts.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis copying MDAnalysis/analysis/align.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis copying MDAnalysis/analysis/polymer.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis copying MDAnalysis/analysis/rms.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis copying MDAnalysis/analysis/gnm.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis copying MDAnalysis/analysis/helanal.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis copying MDAnalysis/analysis/hole.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis copying MDAnalysis/analysis/x3dna.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis copying MDAnalysis/analysis/distances.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis copying MDAnalysis/analysis/dihedrals.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis copying MDAnalysis/analysis/lineardensity.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis copying MDAnalysis/analysis/nuclinfo.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis copying MDAnalysis/analysis/density.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis copying MDAnalysis/analysis/psa.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis copying MDAnalysis/analysis/diffusionmap.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis creating build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/core copying MDAnalysis/core/log.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/core copying MDAnalysis/core/distances.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/core copying MDAnalysis/core/groups.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/core copying MDAnalysis/core/_get_readers.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/core copying MDAnalysis/core/qcprot.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/core copying MDAnalysis/core/__init__.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/core copying MDAnalysis/core/topologyobjects.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/core copying MDAnalysis/core/AtomGroup.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/core copying MDAnalysis/core/parallel.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/core copying MDAnalysis/core/universe.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/core copying MDAnalysis/core/transformations.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/core copying MDAnalysis/core/topology.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/core copying MDAnalysis/core/util.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/core copying MDAnalysis/core/units.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/core copying MDAnalysis/core/topologyattrs.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/core copying MDAnalysis/core/selection.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/core creating build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/tests copying MDAnalysis/tests/__init__.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/tests copying MDAnalysis/tests/datafiles.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/tests creating build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/visualization copying MDAnalysis/visualization/streamlines_3D.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/visualization copying MDAnalysis/visualization/streamlines.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/visualization copying MDAnalysis/visualization/__init__.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/visualization creating build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/core.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/DMSParser.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/base.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/TXYZParser.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/XYZParser.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/GROParser.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/PSFParser.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/TOPParser.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/guessers.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/PDBParser.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/TPRParser.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/tables.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/MMTFParser.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/ExtendedPDBParser.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/GSDParser.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/CRDParser.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/GMSParser.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/DLPolyParser.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/PDBQTParser.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/PQRParser.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/LAMMPSParser.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/_elements.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/HoomdXMLParser.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/__init__.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/MOL2Parser.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology copying MDAnalysis/topology/MinimalParser.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology creating build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/migration copying MDAnalysis/migration/__init__.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/migration copying MDAnalysis/migration/test_dummy_old_MDA_code.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/migration copying MDAnalysis/migration/ten2eleven.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/migration copying MDAnalysis/migration/test_dummy_torsion.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/migration creating build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/core.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/__init__.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/XVG.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/base.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/auxiliary creating build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/transformations copying MDAnalysis/transformations/translate.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/transformations copying MDAnalysis/transformations/__init__.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/transformations copying MDAnalysis/transformations/rotate.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/transformations creating build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/selections copying MDAnalysis/selections/vmd.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/selections copying MDAnalysis/selections/pymol.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/selections copying MDAnalysis/selections/gromacs.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/selections copying MDAnalysis/selections/charmm.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/selections copying MDAnalysis/selections/base.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/selections copying MDAnalysis/selections/jmol.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/selections copying MDAnalysis/selections/__init__.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/selections creating build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/GRO.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/MOL2.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/GMS.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/XTC.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/PDBQT.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/DLPoly.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/PQR.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRJ.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/null.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRZ.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/MMTF.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/memory.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/XDR.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/base.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/chain.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/PDB.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/XYZ.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/CRD.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/LAMMPS.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRR.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/GSD.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/__init__.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/DMS.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/TXYZ.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/core.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/INPCRD.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates copying MDAnalysis/coordinates/DCD.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates creating build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib copying MDAnalysis/lib/pkdtree.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib copying MDAnalysis/lib/mdamath.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib copying MDAnalysis/lib/log.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib copying MDAnalysis/lib/transformations.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib copying MDAnalysis/lib/NeighborSearch.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib copying MDAnalysis/lib/distances.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib copying MDAnalysis/lib/util.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib copying MDAnalysis/lib/__init__.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib creating build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/confdistmatrix.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/__init__.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/similarity.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/utils.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/bootstrap.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/covariance.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore creating build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/hbonds copying MDAnalysis/analysis/hbonds/hbond_analysis.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/hbonds copying MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/hbonds copying MDAnalysis/analysis/hbonds/__init__.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/hbonds copying MDAnalysis/analysis/hbonds/wbridge_analysis.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/hbonds creating build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/legacy copying MDAnalysis/analysis/legacy/__init__.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/legacy copying MDAnalysis/analysis/legacy/x3dna.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/legacy creating build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/data copying MDAnalysis/analysis/data/__init__.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/data copying MDAnalysis/analysis/data/filenames.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/data creating build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/__init__.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/cluster.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore/clustering creating build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore/dimensionality_reduction creating build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/setting.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/obj.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/utils.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/__init__.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology/tpr creating build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_agcountmethods.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_torsionclasses.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_mdaimports.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_selectatoms.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_framenumberingzerobased2.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_calctorsions.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_agmethods2.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/__init__.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_camelcase.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_agsetterpluralization.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_framenumberingzerobased.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_writer.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_agmethods.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_numframes.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/migration/fixes copying MDAnalysis/migration/fixes/fix_torsions.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/migration/fixes creating build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/__init__.py -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/formats copying MDAnalysis/analysis/data/janin_ref_data.npy -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/data copying MDAnalysis/analysis/data/rama_ref_data.npy -> build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/data running build_ext building 'MDAnalysis.lib.formats.libdcd' extension creating build/temp.dragonfly-5.9-x86_64-2.7 creating build/temp.dragonfly-5.9-x86_64-2.7/MDAnalysis creating build/temp.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib creating build/temp.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/formats cc -fno-strict-aliasing -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python2.7/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -I/usr/local/include/python2.7 -c MDAnalysis/lib/formats/libdcd.c -o build/temp.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/formats/libdcd.o -std=c99 -ffast-math -funroll-loops In file included from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/lib/formats/libdcd.c:596: /usr/local/lib/python2.7/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-5.9-x86_64-2.7/MDAnalysis/lib/formats/libdcd.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/formats/libdcd.so building 'MDAnalysis.lib.c_distances' extension cc -fno-strict-aliasing -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python2.7/site-packages/numpy/core/include -IMDAnalysis/lib/include -I/usr/local/include/python2.7 -c MDAnalysis/lib/c_distances.c -o build/temp.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/c_distances.o -std=c99 -ffast-math -funroll-loops In file included from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/lib/c_distances.c:597: /usr/local/lib/python2.7/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-5.9-x86_64-2.7/MDAnalysis/lib/c_distances.o -L/usr/local/lib -lm -lpython2.7 -o build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/c_distances.so building 'MDAnalysis.lib.c_distances_openmp' extension cc -fno-strict-aliasing -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -DPARALLEL -I/usr/local/lib/python2.7/site-packages/numpy/core/include -IMDAnalysis/lib/include -I/usr/local/include/python2.7 -c MDAnalysis/lib/c_distances_openmp.c -o build/temp.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/c_distances_openmp.o -fopenmp -std=c99 -ffast-math -funroll-loops In file included from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/lib/c_distances_openmp.c:597: /usr/local/lib/python2.7/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-5.9-x86_64-2.7/MDAnalysis/lib/c_distances_openmp.o -L/usr/local/lib -lm -lgomp -lpython2.7 -o build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/c_distances_openmp.so -fopenmp building 'MDAnalysis.lib.qcprot' extension cc -fno-strict-aliasing -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python2.7/site-packages/numpy/core/include -I/usr/local/include/python2.7 -c MDAnalysis/lib/qcprot.c -o build/temp.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/qcprot.o -std=c99 -ffast-math -funroll-loops In file included from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/lib/qcprot.c:592: /usr/local/lib/python2.7/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-5.9-x86_64-2.7/MDAnalysis/lib/qcprot.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/qcprot.so building 'MDAnalysis.lib._transformations' extension creating build/temp.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/src creating build/temp.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/src/transformations cc -fno-strict-aliasing -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python2.7/site-packages/numpy/core/include -I/usr/local/include/python2.7 -c MDAnalysis/lib/src/transformations/transformations.c -o build/temp.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/src/transformations/transformations.o -std=c99 -ffast-math -funroll-loops In file included from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/lib/src/transformations/transformations.c:73: /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h: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-5.9-x86_64-2.7/MDAnalysis/lib/src/transformations/transformations.o -L/usr/local/lib -lm -lpython2.7 -o build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/_transformations.so building 'MDAnalysis.lib.formats.libmdaxdr' extension creating build/temp.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/formats/src cc -fno-strict-aliasing -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/local/lib/python2.7/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/local/include/python2.7 -c MDAnalysis/lib/formats/libmdaxdr.c -o build/temp.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/formats/libmdaxdr.o -std=c99 -ffast-math -funroll-loops In file included from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/lib/formats/libmdaxdr.c:618: /usr/local/lib/python2.7/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 -fno-strict-aliasing -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/local/lib/python2.7/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/local/include/python2.7 -c MDAnalysis/lib/formats/src/xdrfile.c -o build/temp.dragonfly-5.9-x86_64-2.7/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 -fno-strict-aliasing -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/local/lib/python2.7/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/local/include/python2.7 -c MDAnalysis/lib/formats/src/xdrfile_xtc.c -o build/temp.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/formats/src/xdrfile_xtc.o -std=c99 -ffast-math -funroll-loops cc -fno-strict-aliasing -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/local/lib/python2.7/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/local/include/python2.7 -c MDAnalysis/lib/formats/src/xdrfile_trr.c -o build/temp.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/formats/src/xdrfile_trr.o -std=c99 -ffast-math -funroll-loops cc -fno-strict-aliasing -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/local/lib/python2.7/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/local/include/python2.7 -c MDAnalysis/lib/formats/src/trr_seek.c -o build/temp.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/formats/src/trr_seek.o -std=c99 -ffast-math -funroll-loops cc -fno-strict-aliasing -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/local/lib/python2.7/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/local/include/python2.7 -c MDAnalysis/lib/formats/src/xtc_seek.c -o build/temp.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/formats/src/xtc_seek.o -std=c99 -ffast-math -funroll-loops cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/formats/libmdaxdr.o build/temp.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/formats/src/xdrfile.o build/temp.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/formats/src/xdrfile_xtc.o build/temp.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/formats/src/xdrfile_trr.o build/temp.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/formats/src/trr_seek.o build/temp.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/formats/src/xtc_seek.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/formats/libmdaxdr.so building 'MDAnalysis.lib.formats.cython_util' extension cc -fno-strict-aliasing -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python2.7/site-packages/numpy/core/include -I/usr/local/include/python2.7 -c MDAnalysis/lib/formats/cython_util.c -o build/temp.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/formats/cython_util.o -std=c99 -ffast-math -funroll-loops In file included from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/lib/formats/cython_util.c:592: /usr/local/lib/python2.7/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-5.9-x86_64-2.7/MDAnalysis/lib/formats/cython_util.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/formats/cython_util.so building 'MDAnalysis.analysis.encore.cutils' extension creating build/temp.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis creating build/temp.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore cc -fno-strict-aliasing -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python2.7/site-packages/numpy/core/include -I/usr/local/include/python2.7 -c MDAnalysis/analysis/encore/cutils.c -o build/temp.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore/cutils.o -std=c99 -ffast-math -funroll-loops In file included from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/analysis/encore/cutils.c:592: /usr/local/lib/python2.7/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-5.9-x86_64-2.7/MDAnalysis/analysis/encore/cutils.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore/cutils.so building 'MDAnalysis.analysis.encore.clustering.affinityprop' extension creating build/temp.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore/clustering creating build/temp.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore/clustering/src cc -fno-strict-aliasing -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python2.7/site-packages/numpy/core/include -IMDAnalysis/analysis/encore/clustering/include -I/usr/local/include/python2.7 -c MDAnalysis/analysis/encore/clustering/affinityprop.c -o build/temp.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore/clustering/affinityprop.o -std=c99 -ffast-math -funroll-loops In file included from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/analysis/encore/clustering/affinityprop.c:598: /usr/local/lib/python2.7/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 -fno-strict-aliasing -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python2.7/site-packages/numpy/core/include -IMDAnalysis/analysis/encore/clustering/include -I/usr/local/include/python2.7 -c MDAnalysis/analysis/encore/clustering/src/ap.c -o build/temp.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore/clustering/src/ap.o -std=c99 -ffast-math -funroll-loops cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore/clustering/affinityprop.o build/temp.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore/clustering/src/ap.o -L/usr/local/lib -lm -lpython2.7 -o build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore/clustering/affinityprop.so building 'MDAnalysis.analysis.encore.dimensionality_reduction.stochasticproxembed' extension creating build/temp.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore/dimensionality_reduction creating build/temp.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore/dimensionality_reduction/src cc -fno-strict-aliasing -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python2.7/site-packages/numpy/core/include -IMDAnalysis/analysis/encore/dimensionality_reduction/include -I/usr/local/include/python2.7 -c MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -o build/temp.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.o -std=c99 -ffast-math -funroll-loops In file included from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c:598: /usr/local/lib/python2.7/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 -fno-strict-aliasing -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python2.7/site-packages/numpy/core/include -IMDAnalysis/analysis/encore/dimensionality_reduction/include -I/usr/local/include/python2.7 -c MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -o build/temp.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.o -std=c99 -ffast-math -funroll-loops cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.o build/temp.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.o -L/usr/local/lib -lm -lpython2.7 -o build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.so building 'MDAnalysis.lib._cutil' extension cc -fno-strict-aliasing -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python2.7/site-packages/numpy/core/include -IMDAnalysis/lib/include -I/usr/local/include/python2.7 -c MDAnalysis/lib/_cutil.cpp -o build/temp.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/_cutil.o -ffast-math -funroll-loops -std=c++11 In file included from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/lib/_cutil.cpp:613: /usr/local/lib/python2.7/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-5.9-x86_64-2.7/MDAnalysis/lib/_cutil.o -L/usr/local/lib -lm -lpython2.7 -o build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/_cutil.so building 'MDAnalysis.lib._augment' extension cc -fno-strict-aliasing -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python2.7/site-packages/numpy/core/include -I/usr/local/include/python2.7 -c MDAnalysis/lib/_augment.cpp -o build/temp.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/_augment.o -ffast-math -funroll-loops -std=c++11 In file included from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/lib/_augment.cpp:608: /usr/local/lib/python2.7/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-5.9-x86_64-2.7/MDAnalysis/lib/_augment.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/_augment.so building 'MDAnalysis.lib.nsgrid' extension cc -fno-strict-aliasing -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python2.7/site-packages/numpy/core/include -I/usr/local/include/python2.7 -c MDAnalysis/lib/nsgrid.cpp -o build/temp.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/nsgrid.o -ffast-math -funroll-loops -std=c++11 In file included from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/lib/nsgrid.cpp:614: /usr/local/lib/python2.7/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-5.9-x86_64-2.7/MDAnalysis/lib/nsgrid.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/nsgrid.so SUCCEEDED 00:01:47 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- ===> py27-MDAnalysis-0.19.2_2 depends on package: py27-numpy>=1.15,1<1.19,1 - found ===> py27-MDAnalysis-0.19.2_2 depends on package: py27-biopython>=1.71 - found ===> py27-MDAnalysis-0.19.2_2 depends on package: py27-duecredit>0 - found ===> py27-MDAnalysis-0.19.2_2 depends on package: py27-GridDataFormats>=0.4.0 - found ===> py27-MDAnalysis-0.19.2_2 depends on package: py27-gsd>=1.4.0 - found ===> py27-MDAnalysis-0.19.2_2 depends on package: py27-joblib>0 - found ===> py27-MDAnalysis-0.19.2_2 depends on package: py27-matplotlib>=1.5.1 - found ===> py27-MDAnalysis-0.19.2_2 depends on package: py27-mmtf-python>=1.0.0 - found ===> py27-MDAnalysis-0.19.2_2 depends on package: py27-mock>0 - found ===> py27-MDAnalysis-0.19.2_2 depends on package: py27-networkx>=1.0 - found ===> py27-MDAnalysis-0.19.2_2 depends on package: py27-scipy>=1.0.0 - found ===> py27-MDAnalysis-0.19.2_2 depends on package: py27-six>=1.4.0 - found ===> py27-MDAnalysis-0.19.2_2 depends on package: py27-setuptools>0 - found ===> py27-MDAnalysis-0.19.2_2 depends on file: /usr/local/bin/python2.7 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for py27-MDAnalysis-0.19.2_2 ===> py27-MDAnalysis-0.19.2_2 depends on package: py27-numpy>=1.15,1<1.19,1 - found ===> py27-MDAnalysis-0.19.2_2 depends on package: py27-biopython>=1.71 - found ===> py27-MDAnalysis-0.19.2_2 depends on package: py27-duecredit>0 - found ===> py27-MDAnalysis-0.19.2_2 depends on package: py27-GridDataFormats>=0.4.0 - found ===> py27-MDAnalysis-0.19.2_2 depends on package: py27-gsd>=1.4.0 - found ===> py27-MDAnalysis-0.19.2_2 depends on package: py27-joblib>0 - found ===> py27-MDAnalysis-0.19.2_2 depends on package: py27-matplotlib>=1.5.1 - found ===> py27-MDAnalysis-0.19.2_2 depends on package: py27-mmtf-python>=1.0.0 - found ===> py27-MDAnalysis-0.19.2_2 depends on package: py27-mock>0 - found ===> py27-MDAnalysis-0.19.2_2 depends on package: py27-networkx>=1.0 - found ===> py27-MDAnalysis-0.19.2_2 depends on package: py27-scipy>=1.0.0 - found ===> py27-MDAnalysis-0.19.2_2 depends on package: py27-six>=1.4.0 - found ===> py27-MDAnalysis-0.19.2_2 depends on package: py27-setuptools>0 - found ===> py27-MDAnalysis-0.19.2_2 depends on file: /usr/local/bin/python2.7 - found ===> 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-5.9-x86_64-2.7/MDAnalysis running build_ext running install_lib creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7 creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/selections copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/selections/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/selections copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/selections/base.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/selections copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/selections/jmol.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/selections copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/selections/pymol.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/selections copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/selections/gromacs.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/selections copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/selections/charmm.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/selections copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/selections/vmd.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/selections creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/core/_get_readers.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/core/units.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/core/log.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/core/universe.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/core/AtomGroup.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/core/parallel.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/core/qcprot.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/core/distances.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/core/groups.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/core/selection.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/core/topologyattrs.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/core/topology.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/core/topologyobjects.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/core/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/core/util.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/core/transformations.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/visualization copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/visualization/streamlines.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/visualization copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/visualization/streamlines_3D.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/visualization copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/visualization/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/visualization creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/c_distances_openmp.so -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/c_distances.so -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/distances.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/mdamath.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib/formats copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/formats/libmdaxdr.so -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib/formats copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/formats/cython_util.so -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib/formats copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/formats/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib/formats copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/formats/libdcd.so -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib/formats copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/transformations.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/log.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/util.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/pkdtree.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/NeighborSearch.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/qcprot.so -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/_transformations.so -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/_augment.so -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/_cutil.so -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/lib/nsgrid.so -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates/PDBQT.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates/GSD.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates/GMS.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates/DMS.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates/TXYZ.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates/LAMMPS.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates/base.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates/DCD.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates/DLPoly.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates/GRO.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates/chain.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates/null.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates/PQR.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates/PDB.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates/MMTF.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates/TRZ.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates/core.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates/CRD.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates/memory.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates/XTC.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates/XYZ.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates/INPCRD.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates/TRJ.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates/XDR.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates/MOL2.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates/TRR.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/coordinates/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/authors.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/auxiliary copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/auxiliary/XVG.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/auxiliary copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/auxiliary/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/auxiliary copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/auxiliary/core.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/auxiliary copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/auxiliary/base.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/auxiliary creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/transformations copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/transformations/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/transformations copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/transformations/translate.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/transformations copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/transformations/rotate.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/transformations copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/version.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/base.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/hole.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/x3dna.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/contacts.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/data copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/data/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/data copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/data/filenames.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/data copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/data/janin_ref_data.npy -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/data copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/data/rama_ref_data.npy -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/data creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/hbonds copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/hbonds copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/hbonds/wbridge_analysis.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/hbonds copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/hbonds/hbond_analysis.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/hbonds copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/hbonds/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/hbonds copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/polymer.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/psa.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/distances.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/density.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore/cutils.so -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore/utils.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore/bootstrap.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore/similarity.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.so -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore/confdistmatrix.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/clustering copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore/clustering/affinityprop.so -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/clustering copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/clustering copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore/clustering/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/clustering copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/clustering copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore/clustering/cluster.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/clustering copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/encore/covariance.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/rdf.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/pca.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/helanal.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/waterdynamics.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/rms.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/lineardensity.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/leaflet.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/gnm.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/nuclinfo.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/align.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/diffusionmap.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/dihedrals.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/legacy copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/legacy/x3dna.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/legacy copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/analysis/legacy/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/legacy copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/units.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/KDTree.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology/TXYZParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology/guessers.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology/PDBParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/tpr copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology/tpr/utils.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/tpr copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology/tpr/setting.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/tpr copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology/tpr/obj.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/tpr copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology/tpr/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/tpr copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology/GMSParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology/PQRParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology/LAMMPSParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology/MMTFParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology/DMSParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology/CRDParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology/DLPolyParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology/PDBQTParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology/tables.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology/MOL2Parser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology/ExtendedPDBParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology/MinimalParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology/GROParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology/PSFParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology/HoomdXMLParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology/TOPParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology/core.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology/GSDParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology/XYZParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology/TPRParser.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology/base.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/topology/_elements.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/due.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/migration/test_dummy_torsion.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/migration/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/migration/fixes/fix_agmethods2.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/migration/fixes/fix_numframes.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/migration/fixes/fix_torsions.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/migration/fixes/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/migration/fixes/fix_camelcase.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/migration/fixes/fix_calctorsions.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/migration/fixes/fix_selectatoms.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/migration/fixes/fix_writer.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/migration/fixes/fix_agcountmethods.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/migration/fixes/fix_agsetterpluralization.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/migration/fixes/fix_torsionclasses.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/migration/fixes/fix_mdaimports.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/migration/fixes/fix_framenumberingzerobased.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/migration/fixes/fix_framenumberingzerobased2.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/migration/fixes/fix_agmethods.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/migration/test_dummy_old_MDA_code.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/migration/ten2eleven.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration creating /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/tests copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/tests/datafiles.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/tests copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/tests/__init__.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/tests copying build/lib.dragonfly-5.9-x86_64-2.7/MDAnalysis/exceptions.py -> /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/selections/__init__.py to __init__.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/selections/base.py to base.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/selections/jmol.py to jmol.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/selections/pymol.py to pymol.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/selections/gromacs.py to gromacs.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/selections/charmm.py to charmm.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/selections/vmd.py to vmd.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core/_get_readers.py to _get_readers.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core/units.py to units.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core/log.py to log.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core/universe.py to universe.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core/AtomGroup.py to AtomGroup.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core/parallel.py to parallel.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core/qcprot.py to qcprot.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core/distances.py to distances.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core/groups.py to groups.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core/selection.py to selection.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core/topologyattrs.py to topologyattrs.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core/topology.py to topology.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core/topologyobjects.py to topologyobjects.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core/__init__.py to __init__.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core/util.py to util.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/core/transformations.py to transformations.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/visualization/streamlines.py to streamlines.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/visualization/streamlines_3D.py to streamlines_3D.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/visualization/__init__.py to __init__.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib/distances.py to distances.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib/mdamath.py to mdamath.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib/formats/__init__.py to __init__.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib/transformations.py to transformations.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib/log.py to log.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib/util.py to util.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib/__init__.py to __init__.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib/pkdtree.py to pkdtree.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/lib/NeighborSearch.py to NeighborSearch.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates/PDBQT.py to PDBQT.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates/GSD.py to GSD.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates/GMS.py to GMS.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates/DMS.py to DMS.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates/TXYZ.py to TXYZ.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates/LAMMPS.py to LAMMPS.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates/base.py to base.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates/DCD.py to DCD.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates/DLPoly.py to DLPoly.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates/GRO.py to GRO.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates/chain.py to chain.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates/null.py to null.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates/PQR.py to PQR.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates/PDB.py to PDB.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates/MMTF.py to MMTF.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates/TRZ.py to TRZ.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates/core.py to core.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates/CRD.py to CRD.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates/memory.py to memory.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates/XTC.py to XTC.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates/XYZ.py to XYZ.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates/INPCRD.py to INPCRD.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates/TRJ.py to TRJ.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates/XDR.py to XDR.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates/MOL2.py to MOL2.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates/TRR.py to TRR.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/coordinates/__init__.py to __init__.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/authors.py to authors.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/auxiliary/XVG.py to XVG.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/auxiliary/__init__.py to __init__.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/auxiliary/core.py to core.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/auxiliary/base.py to base.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/transformations/__init__.py to __init__.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/transformations/translate.py to translate.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/transformations/rotate.py to rotate.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/version.py to version.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/base.py to base.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/hole.py to hole.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/x3dna.py to x3dna.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/contacts.py to contacts.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/data/__init__.py to __init__.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/data/filenames.py to filenames.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/hbonds/hbond_autocorrel.py to hbond_autocorrel.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/hbonds/wbridge_analysis.py to wbridge_analysis.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/hbonds/hbond_analysis.py to hbond_analysis.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/hbonds/__init__.py to __init__.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/polymer.py to polymer.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/psa.py to psa.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/__init__.py to __init__.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/distances.py to distances.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/density.py to density.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/utils.py to utils.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/bootstrap.py to bootstrap.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/similarity.py to similarity.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py to __init__.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py to reduce_dimensionality.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py to DimensionalityReductionMethod.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/__init__.py to __init__.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py to confdistmatrix.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py to ClusteringMethod.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/clustering/__init__.py to __init__.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/clustering/ClusterCollection.py to ClusterCollection.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/clustering/cluster.py to cluster.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/encore/covariance.py to covariance.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/rdf.py to rdf.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/pca.py to pca.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/helanal.py to helanal.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/waterdynamics.py to waterdynamics.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/rms.py to rms.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/lineardensity.py to lineardensity.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/leaflet.py to leaflet.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/gnm.py to gnm.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/nuclinfo.py to nuclinfo.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/align.py to align.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/diffusionmap.py to diffusionmap.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/dihedrals.py to dihedrals.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/legacy/x3dna.py to x3dna.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/analysis/legacy/__init__.py to __init__.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/__init__.py to __init__.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/units.py to units.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/KDTree.py to KDTree.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/TXYZParser.py to TXYZParser.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/guessers.py to guessers.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/PDBParser.py to PDBParser.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/__init__.py to __init__.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/tpr/utils.py to utils.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/tpr/setting.py to setting.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/tpr/obj.py to obj.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/tpr/__init__.py to __init__.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/GMSParser.py to GMSParser.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/PQRParser.py to PQRParser.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/LAMMPSParser.py to LAMMPSParser.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/topology/MMTFParser.py to 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/construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes/fix_torsionclasses.py to fix_torsionclasses.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes/fix_mdaimports.py to fix_mdaimports.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes/fix_framenumberingzerobased.py to fix_framenumberingzerobased.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes/fix_framenumberingzerobased2.py to fix_framenumberingzerobased2.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/fixes/fix_agmethods.py to fix_agmethods.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/test_dummy_old_MDA_code.py to test_dummy_old_MDA_code.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/migration/ten2eleven.py to ten2eleven.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/tests/datafiles.py to datafiles.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/tests/__init__.py to __init__.pyc byte-compiling /construction/science/py-MDAnalysis/stage/usr/local/lib/python2.7/site-packages/MDAnalysis/exceptions.py to exceptions.pyc writing byte-compilation script '/tmp/tmpmju0AL.py' /usr/local/bin/python2.7 -O /tmp/tmpmju0AL.py removing /tmp/tmpmju0AL.py running install_egg_info running egg_info writing requirements to MDAnalysis.egg-info/requires.txt writing MDAnalysis.egg-info/PKG-INFO writing top-level names to MDAnalysis.egg-info/top_level.txt writing dependency_links to MDAnalysis.egg-info/dependency_links.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/python2.7/site-packages/MDAnalysis-0.19.2-py2.7.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) Warning: 'lib/python2.7/site-packages/MDAnalysis/lib/nsgrid.so' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD} Warning: 'lib/python2.7/site-packages/MDAnalysis/lib/_augment.so' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD} Warning: 'lib/python2.7/site-packages/MDAnalysis/lib/_transformations.so' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD} Warning: 'lib/python2.7/site-packages/MDAnalysis/lib/c_distances_openmp.so' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD} Warning: 'lib/python2.7/site-packages/MDAnalysis/lib/c_distances.so' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD} Warning: 'lib/python2.7/site-packages/MDAnalysis/lib/formats/libdcd.so' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD} Warning: 'lib/python2.7/site-packages/MDAnalysis/lib/formats/cython_util.so' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD} Warning: 'lib/python2.7/site-packages/MDAnalysis/lib/formats/libmdaxdr.so' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD} Warning: 'lib/python2.7/site-packages/MDAnalysis/lib/_cutil.so' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD} Warning: 'lib/python2.7/site-packages/MDAnalysis/lib/qcprot.so' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD} Warning: 'lib/python2.7/site-packages/MDAnalysis/analysis/encore/clustering/affinityprop.so' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD} Warning: 'lib/python2.7/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.so' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD} Warning: 'lib/python2.7/site-packages/MDAnalysis/analysis/encore/cutils.so' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD} Error: /usr/local/lib/python2.7/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 00:00:04 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for py27-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 00:00:05 TOTAL TIME 00:03:11