Open FranklinBetten opened 5 years ago
vivek-bala
commented
5 years ago Hey Franklin, I am not sure about the latest version on BW. I believe we installed a specific commit (e91e37d), which you were using previously. That is the one that I have in the instructions as well. Is that not installable any more? or do you need to use the latest coco version?
If it is the latter, it might be useful to drop Charlie and Chris a note regarding installation issues.
CharlieLaughton
commented
5 years ago Woah all!
Gromacs_coco.git is way, way obsolete – once upon a time this provided a way of running the CoCo-MD workflow in a way completely independent of Ensemble Toolkit, Radical Pilot, whatever – surely Franklin this has no relation to the CoCo version etc. that you have been using up to now?
The most up-to-date version of pyCoCo, as required for an Ensemble Toolkit, etc, is available here:
pip install extasycoco
note “extasycoco” all one word, and no “.” In the middle.
If you type “pyCoCo -V” you should then get version 0.3.6
Keep me posted as you try this out.
Charlie
From: FranklinBetten notifications@github.com Reply-To: radical-collaboration/extasy-bpti reply@reply.github.com Date: Saturday, 15 December 2018 at 18:27 To: radical-collaboration/extasy-bpti extasy-bpti@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [radical-collaboration/extasy-bpti] Latest version of pyCoCo doesnt Install on BW looks like an MDAnalysis issue? (#14)
I could not used the exact commands listed in the instructions.md file of this git. I need to run that issue by Vivek so I will make a ticket for that as well. For now though the bitbucket I was using is listed below in the installation commands.
I think this is a different error than Vivek and I got when we were trying to install pyCoCo before.
The installation commands I used were
module load bwpy/0.3.0
virtualenv ve-coco
source ve-coco/bin/activate
pip install numpy scipy cython
pip install scikit-image
pip install pypcazip mdtraj
git clone https://bitbucket.org/extasy-project/gromacs_coco.git
cd gromacs_coco
python setup.py install
...
byte-compiling build/bdist.linux-x86_64/egg/gmxcoco_wkflw/_version.py to _version.pyc
byte-compiling build/bdist.linux-x86_64/egg/gmxcoco_wkflw/init.py to init.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
installing scripts to build/bdist.linux-x86_64/egg/EGG-INFO/scripts
running install_scripts
running build_scripts
creating build/scripts-2.7
copying and adjusting src/gmxcoco -> build/scripts-2.7
changing mode of build/scripts-2.7/gmxcoco from 644 to 755
creating build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/gmxcoco -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/gmxcoco to 755
copying src/extasy.gromacs_coco.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying src/extasy.gromacs_coco.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying src/extasy.gromacs_coco.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying src/extasy.gromacs_coco.egg-info/not-zip-safe -> build/bdist.linux-x86_64/egg/EGG-INFO
copying src/extasy.gromacs_coco.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying src/extasy.gromacs_coco.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
creating dist
creating 'dist/extasy.gromacs_coco-0.1-py2.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing extasy.gromacs_coco-0.1-py2.7.egg
creating /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/extasy.gromacs_coco-0.1-py2.7.egg
Extracting extasy.gromacs_coco-0.1-py2.7.egg to /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages
Adding extasy.gromacs-coco 0.1 to easy-install.pth file
Installing gmxcoco script to /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/bin
Installed /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/extasy.gromacs_coco-0.1-py2.7.egg
Processing dependencies for extasy.gromacs-coco==0.1
Searching for MDAnalysis==0.9.0
Reading https://pypi.org/simple/MDAnalysis/
Download error on https://pypi.org/simple/MDAnalysis/: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:590) -- Some packages may not be found!
Couldn't find index page for 'MDAnalysis' (maybe misspelled?)
Scanning index of all packages (this may take a while)
Reading https://pypi.org/simple/
Download error on https://pypi.org/simple/: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:590) -- Some packages may not be found!
No local packages or working download links found for MDAnalysis==0.9.0
error: Could not find suitable distribution for Requirement.parse('MDAnalysis==0.9.0')
(ve-coco) bettenco@h2ologin3:~/coco_test_build_15_12_2018/gromacs_coco> pip install MDAnalysis
Collecting MDAnalysis
Downloading https://files.pythonhosted.org/packages/be/72/6c2f9fcd842c9a50315ac93c4079b3f70735c6125fe903d04fb68a6e616a/MDAnalysis-0.19.2.tar.gz (16.5MB)
100% |████████████████████████████████| 16.5MB 921kB/sRequirement already satisfied: numpy>=1.10.4 in /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages (from MDAnalysis) (1.15.4)
Collecting biopython>=1.71 (from MDAnalysis)
Downloading https://files.pythonhosted.org/packages/e5/3c/1aae19dc685dab77ccd0adfded6bba93821619ad6c57766b349d61cbe61b/biopython-1.72-cp27-cp27mu-manylinux1_x86_64.whl (2.1MB)
100% |████████████████████████████████| 2.1MB 4.3MB/sRequirement already satisfied: networkx>=1.0 in /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages (from MDAnalysis) (2.2)
Collecting GridDataFormats>=0.4.0 (from MDAnalysis)
Requirement already satisfied: six>=1.4.0 in /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages (from MDAnalysis) (1.12.0)
Collecting mmtf-python>=1.0.0 (from MDAnalysis)
Collecting joblib (from MDAnalysis)
Downloading https://files.pythonhosted.org/packages/0d/1b/995167f6c66848d4eb7eabc386aebe07a1571b397629b2eac3b7bebdc343/joblib-0.13.0-py2.py3-none-any.whl (276kB)
100% |████████████████████████████████| 276kB 9.7MB/sRequirement already satisfied: scipy>=1.0.0 in /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages (from MDAnalysis) (1.1.0)
Requirement already satisfied: matplotlib>=1.5.1 in /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages (from MDAnalysis) (2.2.3)
Collecting mock (from MDAnalysis)
Downloading https://files.pythonhosted.org/packages/e6/35/f187bdf23be87092bd0f1200d43d23076cee4d0dec109f195173fd3ebc79/mock-2.0.0-py2.py3-none-any.whl (56kB)
100% |████████████████████████████████| 61kB 6.6MB/sCollecting gsd>=1.4.0 (from MDAnalysis)
Downloading https://files.pythonhosted.org/packages/0c/51/ba1bfa4c6520e9797eeaaafdf53339074522e03a04158b5a79987504dfa3/gsd-1.5.5-cp27-cp27mu-manylinux1_x86_64.whl (269kB)
100% |████████████████████████████████| 276kB 9.5MB/sRequirement already satisfied: decorator>=4.3.0 in /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages (from networkx>=1.0->MDAnalysis) (4.3.0)
Collecting msgpack>=0.5.6 (from mmtf-python>=1.0.0->MDAnalysis)
Downloading https://files.pythonhosted.org/packages/49/15/1857b4d250ca780c1ee3238ba7cd7ded5aeb1df27ed5d039a2034cd69a96/msgpack-0.6.0-cp27-cp27mu-manylinux1_x86_64.whl (230kB)
100% |████████████████████████████████| 235kB 9.9MB/sRequirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages (from matplotlib>=1.5.1->MDAnalysis) (2.3.0)
Requirement already satisfied: backports.functools-lru-cache in /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages (from matplotlib>=1.5.1->MDAnalysis) (1.5)
Requirement already satisfied: subprocess32 in /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages (from matplotlib>=1.5.1->MDAnalysis) (3.5.3)
Requirement already satisfied: pytz in /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages (from matplotlib>=1.5.1->MDAnalysis) (2018.7)
Requirement already satisfied: python-dateutil>=2.1 in /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages (from matplotlib>=1.5.1->MDAnalysis) (2.7.5)
Requirement already satisfied: kiwisolver>=1.0.1 in /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages (from matplotlib>=1.5.1->MDAnalysis) (1.0.1)
Requirement already satisfied: cycler>=0.10 in /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages (from matplotlib>=1.5.1->MDAnalysis) (0.10.0)
Collecting pbr>=0.11 (from mock->MDAnalysis)
Downloading https://files.pythonhosted.org/packages/f3/04/fddc1c2dd75b256eda4d360024692231a2c19a0c61ad7f4a162407c1ab58/pbr-5.1.1-py2.py3-none-any.whl (106kB)
100% |████████████████████████████████| 112kB 10.6MB/sCollecting funcsigs>=1; python_version < "3.3" (from mock->MDAnalysis)
Requirement already satisfied: setuptools in /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages (from kiwisolver>=1.0.1->matplotlib>=1.5.1->MDAnalysis) (40.6.3)
Building wheels for collected packages: MDAnalysis
Running setup.py bdist_wheel for MDAnalysis ... error
Complete output from command /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/bin/python2.7 -u -c "import setuptools, tokenize;file='/tmp/pip-install-ZVYZEf/MDAnalysis/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" bdist_wheel -d /tmp/pip-wheel-jG6cmn --python-tag cp27:
Attempting to autodetect OpenMP support... Did not detect OpenMP support.
No openmp compatible compiler found default to serial build.
Will not attempt to use Cython.
running bdist_wheel
The [wheel] section is deprecated. Use [bdist_wheel] instead.
running build
running build_py
creating build
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/MDAnalysis
copying MDAnalysis/exceptions.py -> build/lib.linux-x86_64-2.7/MDAnalysis
copying MDAnalysis/units.py -> build/lib.linux-x86_64-2.7/MDAnalysis
copying MDAnalysis/version.py -> build/lib.linux-x86_64-2.7/MDAnalysis
copying MDAnalysis/KDTree.py -> build/lib.linux-x86_64-2.7/MDAnalysis
copying MDAnalysis/due.py -> build/lib.linux-x86_64-2.7/MDAnalysis
copying MDAnalysis/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis
copying MDAnalysis/authors.py -> build/lib.linux-x86_64-2.7/MDAnalysis
creating build/lib.linux-x86_64-2.7/MDAnalysis/transformations
copying MDAnalysis/transformations/rotate.py -> build/lib.linux-x86_64-2.7/MDAnalysis/transformations
copying MDAnalysis/transformations/translate.py -> build/lib.linux-x86_64-2.7/MDAnalysis/transformations
copying MDAnalysis/transformations/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis/transformations
creating build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/DCD.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/GSD.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/null.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/XYZ.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/TXYZ.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/DLPoly.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/TRJ.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/MOL2.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/LAMMPS.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/chain.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/MMTF.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/PDBQT.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/base.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/PQR.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/DMS.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/PDB.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/CRD.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/INPCRD.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/memory.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/XTC.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/GRO.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/GMS.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/TRZ.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/core.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/TRR.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/XDR.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
creating build/lib.linux-x86_64-2.7/MDAnalysis/tests
copying MDAnalysis/tests/datafiles.py -> build/lib.linux-x86_64-2.7/MDAnalysis/tests
copying MDAnalysis/tests/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis/tests
creating build/lib.linux-x86_64-2.7/MDAnalysis/lib
copying MDAnalysis/lib/NeighborSearch.py -> build/lib.linux-x86_64-2.7/MDAnalysis/lib
copying MDAnalysis/lib/util.py -> build/lib.linux-x86_64-2.7/MDAnalysis/lib
copying MDAnalysis/lib/transformations.py -> build/lib.linux-x86_64-2.7/MDAnalysis/lib
copying MDAnalysis/lib/log.py -> build/lib.linux-x86_64-2.7/MDAnalysis/lib
copying MDAnalysis/lib/pkdtree.py -> build/lib.linux-x86_64-2.7/MDAnalysis/lib
copying MDAnalysis/lib/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis/lib
copying MDAnalysis/lib/distances.py -> build/lib.linux-x86_64-2.7/MDAnalysis/lib
copying MDAnalysis/lib/mdamath.py -> build/lib.linux-x86_64-2.7/MDAnalysis/lib
creating build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/PDBParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/HoomdXMLParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/DMSParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/TOPParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/GSDParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/MOL2Parser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/ExtendedPDBParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/GROParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/PSFParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/tables.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/PQRParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/_elements.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/TXYZParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/XYZParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/base.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/MMTFParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/GMSParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/TPRParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/guessers.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/LAMMPSParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/PDBQTParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/CRDParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/DLPolyParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/core.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/MinimalParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
creating build/lib.linux-x86_64-2.7/MDAnalysis/migration
copying MDAnalysis/migration/test_dummy_old_MDA_code.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration
copying MDAnalysis/migration/ten2eleven.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration
copying MDAnalysis/migration/test_dummy_torsion.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration
copying MDAnalysis/migration/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration
creating build/lib.linux-x86_64-2.7/MDAnalysis/selections
copying MDAnalysis/selections/base.py -> build/lib.linux-x86_64-2.7/MDAnalysis/selections
copying MDAnalysis/selections/charmm.py -> build/lib.linux-x86_64-2.7/MDAnalysis/selections
copying MDAnalysis/selections/vmd.py -> build/lib.linux-x86_64-2.7/MDAnalysis/selections
copying MDAnalysis/selections/gromacs.py -> build/lib.linux-x86_64-2.7/MDAnalysis/selections
copying MDAnalysis/selections/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis/selections
copying MDAnalysis/selections/pymol.py -> build/lib.linux-x86_64-2.7/MDAnalysis/selections
copying MDAnalysis/selections/jmol.py -> build/lib.linux-x86_64-2.7/MDAnalysis/selections
creating build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/topologyattrs.py -> build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/AtomGroup.py -> build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/parallel.py -> build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/topologyobjects.py -> build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/universe.py -> build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/util.py -> build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/units.py -> build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/qcprot.py -> build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/selection.py -> build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/transformations.py -> build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/groups.py -> build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/_get_readers.py -> build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/log.py -> build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/topology.py -> build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/distances.py -> build/lib.linux-x86_64-2.7/MDAnalysis/core
creating build/lib.linux-x86_64-2.7/MDAnalysis/visualization
copying MDAnalysis/visualization/streamlines.py -> build/lib.linux-x86_64-2.7/MDAnalysis/visualization
copying MDAnalysis/visualization/streamlines_3D.py -> build/lib.linux-x86_64-2.7/MDAnalysis/visualization
copying MDAnalysis/visualization/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis/visualization
creating build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/hole.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/diffusionmap.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/dihedrals.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/polymer.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/rdf.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/helanal.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/pca.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/align.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/waterdynamics.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/x3dna.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/base.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/rms.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/density.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/contacts.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/distances.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/lineardensity.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/nuclinfo.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/leaflet.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/gnm.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/psa.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
creating build/lib.linux-x86_64-2.7/MDAnalysis/auxiliary
copying MDAnalysis/auxiliary/XVG.py -> build/lib.linux-x86_64-2.7/MDAnalysis/auxiliary
copying MDAnalysis/auxiliary/base.py -> build/lib.linux-x86_64-2.7/MDAnalysis/auxiliary
copying MDAnalysis/auxiliary/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis/auxiliary
copying MDAnalysis/auxiliary/core.py -> build/lib.linux-x86_64-2.7/MDAnalysis/auxiliary
creating build/lib.linux-x86_64-2.7/MDAnalysis/lib/formats
copying MDAnalysis/lib/formats/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis/lib/formats
creating build/lib.linux-x86_64-2.7/MDAnalysis/topology/tpr
copying MDAnalysis/topology/tpr/obj.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology/tpr
copying MDAnalysis/topology/tpr/utils.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology/tpr
copying MDAnalysis/topology/tpr/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology/tpr
copying MDAnalysis/topology/tpr/setting.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology/tpr
creating build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_numframes.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_mdaimports.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_agmethods.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_writer.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_calctorsions.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_selectatoms.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_torsions.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_agcountmethods.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_agsetterpluralization.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_framenumberingzerobased.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_camelcase.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_framenumberingzerobased2.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_agmethods2.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_torsionclasses.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
creating build/lib.linux-x86_64-2.7/MDAnalysis/analysis/hbonds
copying MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis/hbonds
copying MDAnalysis/analysis/hbonds/hbond_analysis.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis/hbonds
copying MDAnalysis/analysis/hbonds/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis/hbonds
copying MDAnalysis/analysis/hbonds/wbridge_analysis.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis/hbonds
creating build/lib.linux-x86_64-2.7/MDAnalysis/analysis/data
copying MDAnalysis/analysis/data/filenames.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis/data
copying MDAnalysis/analysis/data/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis/data
creating build/lib.linux-x86_64-2.7/MDAnalysis/analysis/encore
copying MDAnalysis/analysis/encore/utils.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis/encore
copying MDAnalysis/analysis/encore/covariance.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis/encore
copying MDAnalysis/analysis/encore/similarity.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis/encore
copying MDAnalysis/analysis/encore/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis/encore
copying MDAnalysis/analysis/encore/bootstrap.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis/encore
copying MDAnalysis/analysis/encore/confdistmatrix.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis/encore
creating build/lib.linux-x86_64-2.7/MDAnalysis/analysis/legacy
copying MDAnalysis/analysis/legacy/x3dna.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis/legacy
copying MDAnalysis/analysis/legacy/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis/legacy
creating build/lib.linux-x86_64-2.7/MDAnalysis/analysis/encore/clustering
copying MDAnalysis/analysis/encore/clustering/cluster.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis/encore/clustering
copying MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis/encore/clustering
copying MDAnalysis/analysis/encore/clustering/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis/encore/clustering
copying MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis/encore/clustering
creating build/lib.linux-x86_64-2.7/MDAnalysis/analysis/encore/dimensionality_reduction
copying MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis/encore/dimensionality_reduction
copying MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis/encore/dimensionality_reduction
copying MDAnalysis/analysis/encore/dimensionality_reduction/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis/encore/dimensionality_reduction
copying MDAnalysis/analysis/data/janin_ref_data.npy -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis/data
copying MDAnalysis/analysis/data/rama_ref_data.npy -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis/data
running build_ext
building 'MDAnalysis.lib.formats.libdcd' extension
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/MDAnalysis
creating build/temp.linux-x86_64-2.7/MDAnalysis/lib
creating build/temp.linux-x86_64-2.7/MDAnalysis/lib/formats
gcc -fPIC -I/mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -I/sw/bw/bwpy/0.3.0/python-single/usr/include/python2.7 -c MDAnalysis/lib/formats/libdcd.c -o build/temp.linux-x86_64-2.7/MDAnalysis/lib/formats/libdcd.o -std=c99 -ffast-math -O3 -funroll-loops
In file included from /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1821,
from /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
from /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from MDAnalysis/lib/formats/libdcd.c:596:/mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION"
gcc -shared -Wl,--rpath=/sw/bw/bwpy/0.3.0/python-single/usr/lib -Wl,--rpath=/sw/bw/bwpy/0.3.0/python-single/lib -Wl,-O1 -Wl,--enable-new-dtags -I/usr/include/ncures -lncurses -lrt -Wl,--rpath=/opt/gcc/4.9.3/snos/lib64 -L. -L/sw/bw/bwpy/0.3.0/python-single/lib -L/sw/bw/bwpy/0.3.0/python-single/usr/lib -L/usr/lib64 -L/usr/lib -L/lib64 build/temp.linux-x86_64-2.7/MDAnalysis/lib/formats/libdcd.o -L/sw/bw/bwpy/0.3.0/python-single/usr/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/MDAnalysis/lib/formats/libdcd.so
building 'MDAnalysis.lib.c_distances' extension
gcc -fPIC -I/mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include -IMDAnalysis/lib/include -I/sw/bw/bwpy/0.3.0/python-single/usr/include/python2.7 -c MDAnalysis/lib/c_distances.c -o build/temp.linux-x86_64-2.7/MDAnalysis/lib/c_distances.o -std=c99 -ffast-math -O3 -funroll-loops
In file included from /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1821,
from /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
from /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from MDAnalysis/lib/c_distances.c:597:/mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION"
MDAnalysis/lib/c_distances.c: In function ‘__pyx_pf_10MDAnalysis_3lib_11c_distances_12coord_transform’:
MDAnalysis/lib/c_distances.c:3572: warning: passing argument 1 of ‘_coord_transform’ from incompatible pointer type
MDAnalysis/lib/c_distances.c:3572: warning: passing argument 3 of ‘_coord_transform’ from incompatible pointer type
gcc -shared -Wl,--rpath=/sw/bw/bwpy/0.3.0/python-single/usr/lib -Wl,--rpath=/sw/bw/bwpy/0.3.0/python-single/lib -Wl,-O1 -Wl,--enable-new-dtags -I/usr/include/ncures -lncurses -lrt -Wl,--rpath=/opt/gcc/4.9.3/snos/lib64 -L. -L/sw/bw/bwpy/0.3.0/python-single/lib -L/sw/bw/bwpy/0.3.0/python-single/usr/lib -L/usr/lib64 -L/usr/lib -L/lib64 build/temp.linux-x86_64-2.7/MDAnalysis/lib/c_distances.o -L/sw/bw/bwpy/0.3.0/python-single/usr/lib -lm -lpython2.7 -o build/lib.linux-x86_64-2.7/MDAnalysis/lib/c_distances.so
building 'MDAnalysis.lib.c_distances_openmp' extension
gcc -fPIC -I/mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include -IMDAnalysis/lib/include -I/sw/bw/bwpy/0.3.0/python-single/usr/include/python2.7 -c MDAnalysis/lib/c_distances_openmp.c -o build/temp.linux-x86_64-2.7/MDAnalysis/lib/c_distances_openmp.o -std=c99 -ffast-math -O3 -funroll-loops
In file included from /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1821,
from /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
from /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from MDAnalysis/lib/c_distances_openmp.c:597:/mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION"
gcc -shared -Wl,--rpath=/sw/bw/bwpy/0.3.0/python-single/usr/lib -Wl,--rpath=/sw/bw/bwpy/0.3.0/python-single/lib -Wl,-O1 -Wl,--enable-new-dtags -I/usr/include/ncures -lncurses -lrt -Wl,--rpath=/opt/gcc/4.9.3/snos/lib64 -L. -L/sw/bw/bwpy/0.3.0/python-single/lib -L/sw/bw/bwpy/0.3.0/python-single/usr/lib -L/usr/lib64 -L/usr/lib -L/lib64 build/temp.linux-x86_64-2.7/MDAnalysis/lib/c_distances_openmp.o -L/sw/bw/bwpy/0.3.0/python-single/usr/lib -lm -lpython2.7 -o build/lib.linux-x86_64-2.7/MDAnalysis/lib/c_distances_openmp.so
building 'MDAnalysis.lib.qcprot' extension
gcc -fPIC -I/mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include -I/sw/bw/bwpy/0.3.0/python-single/usr/include/python2.7 -c MDAnalysis/lib/qcprot.c -o build/temp.linux-x86_64-2.7/MDAnalysis/lib/qcprot.o -std=c99 -ffast-math -O3 -funroll-loops
In file included from /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1821,
from /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
from /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from MDAnalysis/lib/qcprot.c:592:/mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION"
gcc -shared -Wl,--rpath=/sw/bw/bwpy/0.3.0/python-single/usr/lib -Wl,--rpath=/sw/bw/bwpy/0.3.0/python-single/lib -Wl,-O1 -Wl,--enable-new-dtags -I/usr/include/ncures -lncurses -lrt -Wl,--rpath=/opt/gcc/4.9.3/snos/lib64 -L. -L/sw/bw/bwpy/0.3.0/python-single/lib -L/sw/bw/bwpy/0.3.0/python-single/usr/lib -L/usr/lib64 -L/usr/lib -L/lib64 build/temp.linux-x86_64-2.7/MDAnalysis/lib/qcprot.o -L/sw/bw/bwpy/0.3.0/python-single/usr/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/MDAnalysis/lib/qcprot.so
building 'MDAnalysis.lib._transformations' extension
creating build/temp.linux-x86_64-2.7/MDAnalysis/lib/src
creating build/temp.linux-x86_64-2.7/MDAnalysis/lib/src/transformations
gcc -fPIC -I/mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include -I/sw/bw/bwpy/0.3.0/python-single/usr/include/python2.7 -c MDAnalysis/lib/src/transformations/transformations.c -o build/temp.linux-x86_64-2.7/MDAnalysis/lib/src/transformations/transformations.o -std=c99 -ffast-math -O3 -funroll-loops
In file included from /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1821,
from /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
from /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from MDAnalysis/lib/src/transformations/transformations.c:73:/mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION"
gcc -shared -Wl,--rpath=/sw/bw/bwpy/0.3.0/python-single/usr/lib -Wl,--rpath=/sw/bw/bwpy/0.3.0/python-single/lib -Wl,-O1 -Wl,--enable-new-dtags -I/usr/include/ncures -lncurses -lrt -Wl,--rpath=/opt/gcc/4.9.3/snos/lib64 -L. -L/sw/bw/bwpy/0.3.0/python-single/lib -L/sw/bw/bwpy/0.3.0/python-single/usr/lib -L/usr/lib64 -L/usr/lib -L/lib64 build/temp.linux-x86_64-2.7/MDAnalysis/lib/src/transformations/transformations.o -L/sw/bw/bwpy/0.3.0/python-single/usr/lib -lm -lpython2.7 -o build/lib.linux-x86_64-2.7/MDAnalysis/lib/_transformations.so
building 'MDAnalysis.lib.formats.libmdaxdr' extension
creating build/temp.linux-x86_64-2.7/MDAnalysis/lib/formats/src
gcc -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/sw/bw/bwpy/0.3.0/python-single/usr/include/python2.7 -c MDAnalysis/lib/formats/libmdaxdr.c -o build/temp.linux-x86_64-2.7/MDAnalysis/lib/formats/libmdaxdr.o -std=c99 -ffast-math -O3 -funroll-loops
In file included from /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1821,
from /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
from /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from MDAnalysis/lib/formats/libmdaxdr.c:618:/mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION"
gcc -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/sw/bw/bwpy/0.3.0/python-single/usr/include/python2.7 -c MDAnalysis/lib/formats/src/xdrfile.c -o build/temp.linux-x86_64-2.7/MDAnalysis/lib/formats/src/xdrfile.o -std=c99 -ffast-math -O3 -funroll-loops
MDAnalysis/lib/formats/src/xdrfile.c:2535: warning: initialization from incompatible pointer type
MDAnalysis/lib/formats/src/xdrfile.c:2536: warning: initialization from incompatible pointer type
gcc -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/sw/bw/bwpy/0.3.0/python-single/usr/include/python2.7 -c MDAnalysis/lib/formats/src/xdrfile_xtc.c -o build/temp.linux-x86_64-2.7/MDAnalysis/lib/formats/src/xdrfile_xtc.o -std=c99 -ffast-math -O3 -funroll-loops
gcc -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/sw/bw/bwpy/0.3.0/python-single/usr/include/python2.7 -c MDAnalysis/lib/formats/src/xdrfile_trr.c -o build/temp.linux-x86_64-2.7/MDAnalysis/lib/formats/src/xdrfile_trr.o -std=c99 -ffast-math -O3 -funroll-loops
gcc -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/sw/bw/bwpy/0.3.0/python-single/usr/include/python2.7 -c MDAnalysis/lib/formats/src/trr_seek.c -o build/temp.linux-x86_64-2.7/MDAnalysis/lib/formats/src/trr_seek.o -std=c99 -ffast-math -O3 -funroll-loops
gcc -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/sw/bw/bwpy/0.3.0/python-single/usr/include/python2.7 -c MDAnalysis/lib/formats/src/xtc_seek.c -o build/temp.linux-x86_64-2.7/MDAnalysis/lib/formats/src/xtc_seek.o -std=c99 -ffast-math -O3 -funroll-loops
gcc -shared -Wl,--rpath=/sw/bw/bwpy/0.3.0/python-single/usr/lib -Wl,--rpath=/sw/bw/bwpy/0.3.0/python-single/lib -Wl,-O1 -Wl,--enable-new-dtags -I/usr/include/ncures -lncurses -lrt -Wl,--rpath=/opt/gcc/4.9.3/snos/lib64 -L. -L/sw/bw/bwpy/0.3.0/python-single/lib -L/sw/bw/bwpy/0.3.0/python-single/usr/lib -L/usr/lib64 -L/usr/lib -L/lib64 build/temp.linux-x86_64-2.7/MDAnalysis/lib/formats/libmdaxdr.o build/temp.linux-x86_64-2.7/MDAnalysis/lib/formats/src/xdrfile.o build/temp.linux-x86_64-2.7/MDAnalysis/lib/formats/src/xdrfile_xtc.o build/temp.linux-x86_64-2.7/MDAnalysis/lib/formats/src/xdrfile_trr.o build/temp.linux-x86_64-2.7/MDAnalysis/lib/formats/src/trr_seek.o build/temp.linux-x86_64-2.7/MDAnalysis/lib/formats/src/xtc_seek.o -L/sw/bw/bwpy/0.3.0/python-single/usr/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/MDAnalysis/lib/formats/libmdaxdr.so
building 'MDAnalysis.lib.formats.cython_util' extension
gcc -fPIC -I/mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include -I/sw/bw/bwpy/0.3.0/python-single/usr/include/python2.7 -c MDAnalysis/lib/formats/cython_util.c -o build/temp.linux-x86_64-2.7/MDAnalysis/lib/formats/cython_util.o -std=c99 -ffast-math -O3 -funroll-loops
In file included from /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1821,
from /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
from /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from MDAnalysis/lib/formats/cython_util.c:592:/mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION"
gcc -shared -Wl,--rpath=/sw/bw/bwpy/0.3.0/python-single/usr/lib -Wl,--rpath=/sw/bw/bwpy/0.3.0/python-single/lib -Wl,-O1 -Wl,--enable-new-dtags -I/usr/include/ncures -lncurses -lrt -Wl,--rpath=/opt/gcc/4.9.3/snos/lib64 -L. -L/sw/bw/bwpy/0.3.0/python-single/lib -L/sw/bw/bwpy/0.3.0/python-single/usr/lib -L/usr/lib64 -L/usr/lib -L/lib64 build/temp.linux-x86_64-2.7/MDAnalysis/lib/formats/cython_util.o -L/sw/bw/bwpy/0.3.0/python-single/usr/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/MDAnalysis/lib/formats/cython_util.so
building 'MDAnalysis.analysis.encore.cutils' extension
creating build/temp.linux-x86_64-2.7/MDAnalysis/analysis
creating build/temp.linux-x86_64-2.7/MDAnalysis/analysis/encore
gcc -fPIC -I/mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include -I/sw/bw/bwpy/0.3.0/python-single/usr/include/python2.7 -c MDAnalysis/analysis/encore/cutils.c -o build/temp.linux-x86_64-2.7/MDAnalysis/analysis/encore/cutils.o -std=c99 -ffast-math -O3 -funroll-loops
In file included from /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1821,
from /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
from /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from MDAnalysis/analysis/encore/cutils.c:592:/mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION"
gcc -shared -Wl,--rpath=/sw/bw/bwpy/0.3.0/python-single/usr/lib -Wl,--rpath=/sw/bw/bwpy/0.3.0/python-single/lib -Wl,-O1 -Wl,--enable-new-dtags -I/usr/include/ncures -lncurses -lrt -Wl,--rpath=/opt/gcc/4.9.3/snos/lib64 -L. -L/sw/bw/bwpy/0.3.0/python-single/lib -L/sw/bw/bwpy/0.3.0/python-single/usr/lib -L/usr/lib64 -L/usr/lib -L/lib64 build/temp.linux-x86_64-2.7/MDAnalysis/analysis/encore/cutils.o -L/sw/bw/bwpy/0.3.0/python-single/usr/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/MDAnalysis/analysis/encore/cutils.so
building 'MDAnalysis.analysis.encore.clustering.affinityprop' extension
creating build/temp.linux-x86_64-2.7/MDAnalysis/analysis/encore/clustering
creating build/temp.linux-x86_64-2.7/MDAnalysis/analysis/encore/clustering/src
gcc -fPIC -I/mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include -IMDAnalysis/analysis/encore/clustering/include -I/sw/bw/bwpy/0.3.0/python-single/usr/include/python2.7 -c MDAnalysis/analysis/encore/clustering/affinityprop.c -o build/temp.linux-x86_64-2.7/MDAnalysis/analysis/encore/clustering/affinityprop.o -std=c99 -ffast-math -O3 -funroll-loops
In file included from /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1821,
from /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
from /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from MDAnalysis/analysis/encore/clustering/affinityprop.c:598:/mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION"
gcc -fPIC -I/mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include -IMDAnalysis/analysis/encore/clustering/include -I/sw/bw/bwpy/0.3.0/python-single/usr/include/python2.7 -c MDAnalysis/analysis/encore/clustering/src/ap.c -o build/temp.linux-x86_64-2.7/MDAnalysis/analysis/encore/clustering/src/ap.o -std=c99 -ffast-math -O3 -funroll-loops
gcc -shared -Wl,--rpath=/sw/bw/bwpy/0.3.0/python-single/usr/lib -Wl,--rpath=/sw/bw/bwpy/0.3.0/python-single/lib -Wl,-O1 -Wl,--enable-new-dtags -I/usr/include/ncures -lncurses -lrt -Wl,--rpath=/opt/gcc/4.9.3/snos/lib64 -L. -L/sw/bw/bwpy/0.3.0/python-single/lib -L/sw/bw/bwpy/0.3.0/python-single/usr/lib -L/usr/lib64 -L/usr/lib -L/lib64 build/temp.linux-x86_64-2.7/MDAnalysis/analysis/encore/clustering/affinityprop.o build/temp.linux-x86_64-2.7/MDAnalysis/analysis/encore/clustering/src/ap.o -L/sw/bw/bwpy/0.3.0/python-single/usr/lib -lm -lpython2.7 -o build/lib.linux-x86_64-2.7/MDAnalysis/analysis/encore/clustering/affinityprop.so
building 'MDAnalysis.analysis.encore.dimensionality_reduction.stochasticproxembed' extension
creating build/temp.linux-x86_64-2.7/MDAnalysis/analysis/encore/dimensionality_reduction
creating build/temp.linux-x86_64-2.7/MDAnalysis/analysis/encore/dimensionality_reduction/src
gcc -fPIC -I/mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include -IMDAnalysis/analysis/encore/dimensionality_reduction/include -I/sw/bw/bwpy/0.3.0/python-single/usr/include/python2.7 -c MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -o build/temp.linux-x86_64-2.7/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.o -std=c99 -ffast-math -O3 -funroll-loops
In file included from /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1821,
from /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
from /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c:598:/mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION"
gcc -fPIC -I/mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include -IMDAnalysis/analysis/encore/dimensionality_reduction/include -I/sw/bw/bwpy/0.3.0/python-single/usr/include/python2.7 -c MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -o build/temp.linux-x86_64-2.7/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.o -std=c99 -ffast-math -O3 -funroll-loops
gcc -shared -Wl,--rpath=/sw/bw/bwpy/0.3.0/python-single/usr/lib -Wl,--rpath=/sw/bw/bwpy/0.3.0/python-single/lib -Wl,-O1 -Wl,--enable-new-dtags -I/usr/include/ncures -lncurses -lrt -Wl,--rpath=/opt/gcc/4.9.3/snos/lib64 -L. -L/sw/bw/bwpy/0.3.0/python-single/lib -L/sw/bw/bwpy/0.3.0/python-single/usr/lib -L/usr/lib64 -L/usr/lib -L/lib64 build/temp.linux-x86_64-2.7/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.o build/temp.linux-x86_64-2.7/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.o -L/sw/bw/bwpy/0.3.0/python-single/usr/lib -lm -lpython2.7 -o build/lib.linux-x86_64-2.7/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.so
building 'MDAnalysis.lib._cutil' extension
g++ -fPIC -I/mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/lib/python2.7/site-packages/numpy/core/include -IMDAnalysis/lib/include -I/sw/bw/bwpy/0.3.0/python-single/usr/include/python2.7 -c MDAnalysis/lib/_cutil.cpp -o build/temp.linux-x86_64-2.7/MDAnalysis/lib/_cutil.o -ffast-math -O3 -funroll-loops -std=c++11
cc1plus: error: unrecognized command line option "-std=c++11"
error: command 'g++' failed with exit status 1
Failed building wheel for MDAnalysis
Running setup.py clean for MDAnalysis
Failed to build MDAnalysis
extasy-gromacs-coco 0.1 requires extasy.coco, which is not installed.
extasy-gromacs-coco 0.1 has requirement MDAnalysis==0.9.0, but you'll have mdanalysis 0.19.2 which is incompatible.
Installing collected packages: biopython, GridDataFormats, msgpack, mmtf-python, joblib, pbr, funcsigs, mock, gsd, MDAnalysis
Running setup.py install for MDAnalysis ... error
Complete output from command /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/bin/python2.7 -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-ZVYZEf/MDAnalysis/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-0dGT2Q/install-record.txt --single-version-externally-managed --compile --install-headers /mnt/a/u/sciteam/bettenco/coco_test_build_15_12_2018/ve-coco/include/site/python2.7/MDAnalysis:
Attempting to autodetect OpenMP support... Did not detect OpenMP support.
No openmp compatible compiler found default to serial build.
Will not attempt to use Cython.
running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/MDAnalysis
copying MDAnalysis/exceptions.py -> build/lib.linux-x86_64-2.7/MDAnalysis
copying MDAnalysis/units.py -> build/lib.linux-x86_64-2.7/MDAnalysis
copying MDAnalysis/version.py -> build/lib.linux-x86_64-2.7/MDAnalysis
copying MDAnalysis/KDTree.py -> build/lib.linux-x86_64-2.7/MDAnalysis
copying MDAnalysis/due.py -> build/lib.linux-x86_64-2.7/MDAnalysis
copying MDAnalysis/__init__.py -> build/lib.linux-x86_64-2.7/MDAnalysis
copying MDAnalysis/authors.py -> build/lib.linux-x86_64-2.7/MDAnalysis
creating build/lib.linux-x86_64-2.7/MDAnalysis/transformations
copying MDAnalysis/transformations/rotate.py -> build/lib.linux-x86_64-2.7/MDAnalysis/transformations
copying MDAnalysis/transformations/translate.py -> build/lib.linux-x86_64-2.7/MDAnalysis/transformations
copying MDAnalysis/transformations/__init__.py -> build/lib.linux-x86_64-2.7/MDAnalysis/transformations
creating build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/DCD.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/GSD.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/null.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/XYZ.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/TXYZ.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/DLPoly.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/TRJ.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/MOL2.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/LAMMPS.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/chain.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/MMTF.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/PDBQT.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/base.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/PQR.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/DMS.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/PDB.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/CRD.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/INPCRD.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/__init__.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/memory.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/XTC.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/GRO.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/GMS.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/TRZ.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/core.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/TRR.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/XDR.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
creating build/lib.linux-x86_64-2.7/MDAnalysis/tests
copying MDAnalysis/tests/datafiles.py -> build/lib.linux-x86_64-2.7/MDAnalysis/tests
copying MDAnalysis/tests/__init__.py -> build/lib.linux-x86_64-2.7/MDAnalysis/tests
creating build/lib.linux-x86_64-2.7/MDAnalysis/lib
copying MDAnalysis/lib/NeighborSearch.py -> build/lib.linux-x86_64-2.7/MDAnalysis/lib
copying MDAnalysis/lib/util.py -> build/lib.linux-x86_64-2.7/MDAnalysis/lib
copying MDAnalysis/lib/transformations.py -> build/lib.linux-x86_64-2.7/MDAnalysis/lib
copying MDAnalysis/lib/log.py -> build/lib.linux-x86_64-2.7/MDAnalysis/lib
copying MDAnalysis/lib/pkdtree.py -> build/lib.linux-x86_64-2.7/MDAnalysis/lib
copying MDAnalysis/lib/__init__.py -> build/lib.linux-x86_64-2.7/MDAnalysis/lib
copying MDAnalysis/lib/distances.py -> build/lib.linux-x86_64-2.7/MDAnalysis/lib
copying MDAnalysis/lib/mdamath.py -> build/lib.linux-x86_64-2.7/MDAnalysis/lib
creating build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/PDBParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/HoomdXMLParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/DMSParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/TOPParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/GSDParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/MOL2Parser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/ExtendedPDBParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/GROParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/PSFParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/tables.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/PQRParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/_elements.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/TXYZParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/XYZParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/base.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/MMTFParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/GMSParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/TPRParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/guessers.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/__init__.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/LAMMPSParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/PDBQTParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/CRDParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/DLPolyParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/core.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/MinimalParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
creating build/lib.linux-x86_64-2.7/MDAnalysis/migration
copying MDAnalysis/migration/test_dummy_old_MDA_code.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration
copying MDAnalysis/migration/ten2eleven.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration
copying MDAnalysis/migration/test_dummy_torsion.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration
copying MDAnalysis/migration/__init__.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration
creating build/lib.linux-x86_64-2.7/MDAnalysis/selections
copying MDAnalysis/selections/base.py -> build/lib.linux-x86_64-2.7/MDAnalysis/selections
copying MDAnalysis/selections/charmm.py -> build/lib.linux-x86_64-2.7/MDAnalysis/selections
copying MDAnalysis/selections/vmd.py -> build/lib.linux-x86_64-2.7/MDAnalysis/selections
copying MDAnalysis/selections/gromacs.py -> build/lib.linux-x86_64-2.7/MDAnalysis/selections
copying MDAnalysis/selections/__init__.py -> build/lib.linux-x86_64-2.7/MDAnalysis/selections
copying MDAnalysis/selections/pymol.py -> build/lib.linux-x86_64-2.7/MDAnalysis/selections
copying MDAnalysis/selections/jmol.py -> build/lib.linux-x86_64-2.7/MDAnalysis/selections
creating build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/topologyattrs.py -> build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/AtomGroup.py -> build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/parallel.py -> build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/topologyobjects.py -> build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/universe.py -> build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/util.py -> build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/units.py -> build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/qcprot.py -> build/lib.linux-x86_64
shantenujha
commented
5 years ago @FranklinBetten -- ping
I could not used the exact commands listed in the instructions.md file of this git. I need to run that issue by Vivek so I will make a ticket for that as well. For now though the bitbucket I was using is listed below in the installation commands.
I think this is a different error than Vivek and I got when we were trying to install pyCoCo before.
The installation commands I used were