Closed samlobe closed 2 years ago
gitesei
commented
2 years ago Hi Sam,
Thanks for letting us know about the issue. I will make a new PyPI release that works on Monterey soon. Meanwhile it should work fine to install it from source:
git clone https://github.com/KULL-Centre/DEERpredict.git
cd DEERpredict
pip install -e . Please let me know if that works for you.
Best wishes, Giulio
samlobe
commented
2 years ago I tried those commands and I'm getting the exact same errors when it tries to build MDAnalysis. I pasted the error message below.
I have a feeling it may be because of the M1 chip in my Mac. Most Macs have the Intel chip; they just started using Apple's own M1 chip for the newer models. I'm seeing "build/lib.macosx-10.9-x86_64-3.8" in the error message. I think x86_64 refers to the architecture of the intel chip. I think 10.9 refers to the operating system (Monterey is 12.0). 3.8 refers to the python version I believe. I tried the install with older python versions and it failed in the same way.
Let me know if there's an easy fix for this. Until then I'll try out DEER-PREdict from this Windows where I successfully installed it (it's annoying because I have to remotely access it and frequently transfer files between my Mac and the Windows).
Thanks, -Sam
Building wheels for collected packages: MDAnalysis
Building wheel for MDAnalysis (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /Users/sam/opt/anaconda3/bin/python3.8 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/1j/qkb9f5hj7mv7hv82l2t7zb2r0000gn/T/pip-install-oma7ihcx/mdanalysis_f2d9dd09bbf746a0b179be5e9255b8cc/setup.py'"'"'; file='"'"'/private/var/folders/1j/qkb9f5hj7mv7hv82l2t7zb2r0000gn/T/pip-install-oma7ihcx/mdanalysis_f2d9dd09bbf746a0b179be5e9255b8cc/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' bdist_wheel -d /private/var/folders/1j/qkb9f5hj7mv7hv82l2t7zb2r0000gn/T/pip-wheel-r9kui30v
cwd:/private/var/folders/1j/qkb9f5hj7mv7hv82l2t7zb2r0000gn/T/pip-install-oma7ihcx/mdanalysis_f2d9dd09bbf746a0b179be5e9255b8cc/
Complete output (751 lines):
/private/var/folders/1j/qkb9f5hj7mv7hv82l2t7zb2r0000gn/T/pip-install-oma7ihcx/mdanalysis_f2d9dd09bbf746a0b179be5e9255b8cc/setup.py:126: DeprecationWarning: The SafeConfigParser class has been renamed to ConfigParser in Python 3.2. This alias will be removed in future versions. Use ConfigParser directly instead.
self.config = configparser.SafeConfigParser()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.macosx-10.9-x86_64-3.8
creating build/lib.macosx-10.9-x86_64-3.8/MDAnalysis
copying MDAnalysis/units.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis
copying MDAnalysis/version.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis
copying MDAnalysis/init.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis
copying MDAnalysis/due.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis
copying MDAnalysis/authors.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis
copying MDAnalysis/exceptions.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis
creating build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/visualization
copying MDAnalysis/visualization/streamlines_3D.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/visualization
copying MDAnalysis/visualization/init.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/visualization
copying MDAnalysis/visualization/streamlines.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/visualization
creating build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/topology
copying MDAnalysis/topology/HoomdXMLParser.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/topology
copying MDAnalysis/topology/XYZParser.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/topology
copying MDAnalysis/topology/CRDParser.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/topology
copying MDAnalysis/topology/MMTFParser.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/topology
copying MDAnalysis/topology/ExtendedPDBParser.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/topology
copying MDAnalysis/topology/MinimalParser.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/topology
copying MDAnalysis/topology/guessers.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/topology
copying MDAnalysis/topology/TXYZParser.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/topology
copying MDAnalysis/topology/ITPParser.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/topology
copying MDAnalysis/topology/GMSParser.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/topology
copying MDAnalysis/topology/init.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/topology
copying MDAnalysis/topology/PQRParser.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/topology
copying MDAnalysis/topology/core.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/topology
copying MDAnalysis/topology/LAMMPSParser.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/topology
copying MDAnalysis/topology/TOPParser.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/topology
copying MDAnalysis/topology/MOL2Parser.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/topology
copying MDAnalysis/topology/DLPolyParser.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/topology
copying MDAnalysis/topology/PDBQTParser.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/topology
copying MDAnalysis/topology/PDBParser.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/topology
copying MDAnalysis/topology/GROParser.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/topology
copying MDAnalysis/topology/DMSParser.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/topology
copying MDAnalysis/topology/TPRParser.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/topology
copying MDAnalysis/topology/ParmEdParser.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/topology
copying MDAnalysis/topology/tables.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/topology
copying MDAnalysis/topology/PSFParser.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/topology
copying MDAnalysis/topology/FHIAIMSParser.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/topology
copying MDAnalysis/topology/base.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/topology
copying MDAnalysis/topology/GSDParser.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/topology
creating build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/core
copying MDAnalysis/core/topologyattrs.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/core
copying MDAnalysis/core/init.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/core
copying MDAnalysis/core/groups.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/core
copying MDAnalysis/core/_get_readers.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/core
copying MDAnalysis/core/universe.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/core
copying MDAnalysis/core/topology.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/core
copying MDAnalysis/core/selection.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/core
copying MDAnalysis/core/topologyobjects.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/core
creating build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/transformations
copying MDAnalysis/transformations/translate.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/transformations
copying MDAnalysis/transformations/fit.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/transformations
copying MDAnalysis/transformations/init.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/transformations
copying MDAnalysis/transformations/positionaveraging.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/transformations
copying MDAnalysis/transformations/rotate.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/transformations
copying MDAnalysis/transformations/wrap.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/transformations
creating build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis
copying MDAnalysis/analysis/gnm.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis
copying MDAnalysis/analysis/hole.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis
copying MDAnalysis/analysis/contacts.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis
copying MDAnalysis/analysis/align.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis
copying MDAnalysis/analysis/distances.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis
copying MDAnalysis/analysis/leaflet.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis
copying MDAnalysis/analysis/lineardensity.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis
copying MDAnalysis/analysis/waterdynamics.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis
copying MDAnalysis/analysis/init.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis
copying MDAnalysis/analysis/diffusionmap.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis
copying MDAnalysis/analysis/helanal.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis
copying MDAnalysis/analysis/dihedrals.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis
copying MDAnalysis/analysis/psa.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis
copying MDAnalysis/analysis/density.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis
copying MDAnalysis/analysis/rdf.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis
copying MDAnalysis/analysis/pca.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis
copying MDAnalysis/analysis/nuclinfo.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis
copying MDAnalysis/analysis/polymer.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis
copying MDAnalysis/analysis/rms.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis
copying MDAnalysis/analysis/base.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis
creating build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/selections
copying MDAnalysis/selections/charmm.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/selections
copying MDAnalysis/selections/vmd.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/selections
copying MDAnalysis/selections/jmol.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/selections
copying MDAnalysis/selections/init.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/selections
copying MDAnalysis/selections/gromacs.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/selections
copying MDAnalysis/selections/pymol.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/selections
copying MDAnalysis/selections/base.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/selections
creating build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/coordinates
copying MDAnalysis/coordinates/GRO.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/coordinates
copying MDAnalysis/coordinates/FHIAIMS.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/coordinates
copying MDAnalysis/coordinates/DMS.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/coordinates
copying MDAnalysis/coordinates/XYZ.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/coordinates
copying MDAnalysis/coordinates/INPCRD.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/coordinates
copying MDAnalysis/coordinates/chemfiles.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/coordinates
copying MDAnalysis/coordinates/memory.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/coordinates
copying MDAnalysis/coordinates/DLPoly.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/coordinates
copying MDAnalysis/coordinates/chain.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/coordinates
copying MDAnalysis/coordinates/MOL2.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/coordinates
copying MDAnalysis/coordinates/null.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/coordinates
copying MDAnalysis/coordinates/init.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/coordinates
copying MDAnalysis/coordinates/XDR.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/coordinates
copying MDAnalysis/coordinates/core.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/coordinates
copying MDAnalysis/coordinates/TXYZ.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/coordinates
copying MDAnalysis/coordinates/TRR.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/coordinates
copying MDAnalysis/coordinates/TRJ.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/coordinates
copying MDAnalysis/coordinates/GSD.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/coordinates
copying MDAnalysis/coordinates/PDB.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/coordinates
copying MDAnalysis/coordinates/MMTF.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/coordinates
copying MDAnalysis/coordinates/DCD.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/coordinates
copying MDAnalysis/coordinates/ParmEd.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/coordinates
copying MDAnalysis/coordinates/PDBQT.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/coordinates
copying MDAnalysis/coordinates/GMS.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/coordinates
copying MDAnalysis/coordinates/NAMDBIN.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/coordinates
copying MDAnalysis/coordinates/TRZ.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/coordinates
copying MDAnalysis/coordinates/base.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/coordinates
copying MDAnalysis/coordinates/XTC.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/coordinates
copying MDAnalysis/coordinates/CRD.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/coordinates
copying MDAnalysis/coordinates/LAMMPS.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/coordinates
copying MDAnalysis/coordinates/PQR.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/coordinates
creating build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/tests
copying MDAnalysis/tests/init.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/tests
copying MDAnalysis/tests/datafiles.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/tests
creating build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/lib
copying MDAnalysis/lib/distances.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/lib
copying MDAnalysis/lib/transformations.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/lib
copying MDAnalysis/lib/log.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/lib
copying MDAnalysis/lib/util.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/lib
copying MDAnalysis/lib/init.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/lib
copying MDAnalysis/lib/NeighborSearch.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/lib
copying MDAnalysis/lib/correlations.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/lib
copying MDAnalysis/lib/mdamath.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/lib
copying MDAnalysis/lib/pkdtree.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/lib
creating build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/auxiliary
copying MDAnalysis/auxiliary/init.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/auxiliary
copying MDAnalysis/auxiliary/core.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/auxiliary
copying MDAnalysis/auxiliary/XVG.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/auxiliary
copying MDAnalysis/auxiliary/base.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/auxiliary
creating build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/topology/tpr
copying MDAnalysis/topology/tpr/init.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/topology/tpr
copying MDAnalysis/topology/tpr/setting.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/topology/tpr
copying MDAnalysis/topology/tpr/obj.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/topology/tpr
copying MDAnalysis/topology/tpr/utils.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/topology/tpr
creating build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis/hole2
copying MDAnalysis/analysis/hole2/hole.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis/hole2
copying MDAnalysis/analysis/hole2/init.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis/hole2
copying MDAnalysis/analysis/hole2/templates.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis/hole2
copying MDAnalysis/analysis/hole2/utils.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis/hole2
creating build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis/encore
copying MDAnalysis/analysis/encore/bootstrap.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis/encore
copying MDAnalysis/analysis/encore/similarity.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis/encore
copying MDAnalysis/analysis/encore/covariance.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis/encore
copying MDAnalysis/analysis/encore/init.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis/encore
copying MDAnalysis/analysis/encore/confdistmatrix.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis/encore
copying MDAnalysis/analysis/encore/utils.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis/encore
creating build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis/legacy
copying MDAnalysis/analysis/legacy/x3dna.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis/legacy
copying MDAnalysis/analysis/legacy/init.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis/legacy
creating build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis/hydrogenbonds
copying MDAnalysis/analysis/hydrogenbonds/init.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis/hydrogenbonds
copying MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis/hydrogenbonds
creating build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis/utils
copying MDAnalysis/analysis/utils/init.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis/utils
creating build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis/hbonds
copying MDAnalysis/analysis/hbonds/init.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis/hbonds
copying MDAnalysis/analysis/hbonds/hbond_analysis.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis/hbonds
copying MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis/hbonds
copying MDAnalysis/analysis/hbonds/wbridge_analysis.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis/hbonds
creating build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis/data
copying MDAnalysis/analysis/data/filenames.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis/data
copying MDAnalysis/analysis/data/init.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis/data
creating build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis/encore/clustering
copying MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis/encore/clustering
copying MDAnalysis/analysis/encore/clustering/init.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis/encore/clustering
copying MDAnalysis/analysis/encore/clustering/cluster.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis/encore/clustering
copying MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis/encore/clustering
creating build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis/encore/dimensionality_reduction
copying MDAnalysis/analysis/encore/dimensionality_reduction/init.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis/encore/dimensionality_reduction
copying MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis/encore/dimensionality_reduction
copying MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis/encore/dimensionality_reduction
creating build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/lib/formats
copying MDAnalysis/lib/formats/init.py -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/lib/formats
copying MDAnalysis/analysis/data/janin_ref_data.npy -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis/data
copying MDAnalysis/analysis/data/rama_ref_data.npy -> build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/analysis/data
running build_ext
building 'MDAnalysis.lib.formats.libdcd' extension
creating build/temp.macosx-10.9-x86_64-3.8
creating build/temp.macosx-10.9-x86_64-3.8/MDAnalysis
creating build/temp.macosx-10.9-x86_64-3.8/MDAnalysis/lib
creating build/temp.macosx-10.9-x86_64-3.8/MDAnalysis/lib/formats
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/sam/opt/anaconda3/include -arch x86_64 -I/Users/sam/opt/anaconda3/include -arch x86_64 -I/Users/sam/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -I/Users/sam/opt/anaconda3/include/python3.8 -c MDAnalysis/lib/formats/libdcd.c -o build/temp.macosx-10.9-x86_64-3.8/MDAnalysis/lib/formats/libdcd.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros
In file included from MDAnalysis/lib/formats/libdcd.c:629:
In file included from /Users/sam/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /Users/sam/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /Users/sam/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944:
/Users/sam/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
^
In file included from MDAnalysis/lib/formats/libdcd.c:635:
MDAnalysis/lib/formats/include/readdcd.h:698:14: warning: unused variable 'tmbuf' [-Wunused-variable]
struct tm *tmbuf;
^MDAnalysis/lib/formats/include/readdcd.h:697:10: warning: unused variable 'cur_time' [-Wunused-variable]
time_t cur_time;
^MDAnalysis/lib/formats/libdcd.c:26672:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^/Users/sam/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^/Users/sam/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
^MDAnalysis/lib/formats/libdcd.c:26787:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^/Users/sam/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^/Users/sam/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
^MDAnalysis/lib/formats/libdcd.c:26901:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^/Users/sam/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^/Users/sam/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
^MDAnalysis/lib/formats/libdcd.c:27090:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^/Users/sam/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^/Users/sam/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
^MDAnalysis/lib/formats/libdcd.c:27209:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^/Users/sam/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^/Users/sam/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
^MDAnalysis/lib/formats/libdcd.c:27470:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^/Users/sam/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^/Users/sam/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
^MDAnalysis/lib/formats/libdcd.c:27616:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^/Users/sam/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^/Users/sam/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
^MDAnalysis/lib/formats/libdcd.c:34780:5: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0,
^/Users/sam/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^/Users/sam/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
^In file included from MDAnalysis/lib/formats/libdcd.c:634:
MDAnalysis/lib/formats/include/fastio.h:449:12: warning: unused function 'fio_read_int32' [-Wunused-function]
static int fio_read_int32(fio_fd fd, int *i) {
^MDAnalysis/lib/formats/include/fastio.h:453:12: warning: unused function 'fio_write_str' [-Wunused-function]
static int fio_write_str(fio_fd fd, const char *str) {
^In file included from MDAnalysis/lib/formats/libdcd.c:635:
In file included from MDAnalysis/lib/formats/include/readdcd.h:25:
MDAnalysis/lib/formats/include/endianswap.h:32:13: warning: unused function 'swap2_unaligned' [-Wunused-function]
static void swap2_unaligned(void *v, long ndata) {
^MDAnalysis/lib/formats/include/endianswap.h:96:13: warning: unused function 'swap2_aligned' [-Wunused-function]
static void swap2_aligned(void *v, long ndata) {
^15 warnings generated.
gcc -bundle -undefined dynamic_lookup -L/Users/sam/opt/anaconda3/lib -arch x86_64 -L/Users/sam/opt/anaconda3/lib -arch x86_64 -arch x86_64 build/temp.macosx-10.9-x86_64-3.8/MDAnalysis/lib/formats/libdcd.o -o build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/lib/formats/ libdcd.cpython-38-darwin.so
building 'MDAnalysis.lib.c_distances' extension
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/sam/opt/anaconda3/include -arch x86_64 -I/Users/sam/opt/anaconda3/include -arch x86_64 -I/Users/sam/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include -IMDAnalysis/lib/include -I/Users/sam/opt/anaconda3/include/python3.8 -c MDAnalysis/lib/c_distances.c -o build/temp.macosx-10.9-x86_64-3.8/MDAnalysis/lib/c_distances.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros
In file included from MDAnalysis/lib/c_distances.c:630:
In file included from /Users/sam/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /Users/sam/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /Users/sam/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944:
/Users/sam/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
^
MDAnalysis/lib/c_distances.c:21567:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^/Users/sam/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^/Users/sam/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
^MDAnalysis/lib/c_distances.c:21686:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^/Users/sam/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^/Users/sam/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
^MDAnalysis/lib/c_distances.c:21947:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^/Users/sam/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^/Users/sam/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
^MDAnalysis/lib/c_distances.c:22093:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^/Users/sam/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^/Users/sam/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
^5 warnings generated.
gcc -bundle -undefined dynamic_lookup -L/Users/sam/opt/anaconda3/lib -arch x86_64 -L/Users/sam/opt/anaconda3/lib -arch x86_64 -arch x86_64 build/temp.macosx-10.9-x86_64-3.8/MDAnalysis/lib/c_distances.o -lm -o build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/lib/ c_distances.cpython-38-darwin.so
building 'MDAnalysis.lib.c_distances_openmp' extension
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/sam/opt/anaconda3/include -arch x86_64 -I/Users/sam/opt/anaconda3/include -arch x86_64 -I/Users/sam/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include -IMDAnalysis/lib/include -I/Users/sam/opt/anaconda3/include/python3.8 -c MDAnalysis/lib/c_distances_openmp.c -o build/temp.macosx-10.9-x86_64-3.8/MDAnalysis/lib/c_distances_openmp.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros
In file included from MDAnalysis/lib/c_distances_openmp.c:630:
In file included from /Users/sam/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /Users/sam/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /Users/sam/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944:
/Users/sam/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
^
1 warning generated.
gcc -bundle -undefined dynamic_lookup -L/Users/sam/opt/anaconda3/lib -arch x86_64 -L/Users/sam/opt/anaconda3/lib -arch x86_64 -arch x86_64 build/temp.macosx-10.9-x86_64-3.8/MDAnalysis/lib/c_distances_openmp.o -lm -o build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/lib/ c_distances_openmp.cpython-38-darwin.so
building 'MDAnalysis.lib.qcprot' extension
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/sam/opt/anaconda3/include -arch x86_64 -I/Users/sam/opt/anaconda3/include -arch x86_64 -I/Users/sam/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include -I/Users/sam/opt/anaconda3/include/python3.8 -c MDAnalysis/lib/qcprot.c -o build/temp.macosx-10.9-x86_64-3.8/MDAnalysis/lib/qcprot.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros
In file included from MDAnalysis/lib/qcprot.c:625:
In file included from /Users/sam/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /Users/sam/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /Users/sam/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944:
/Users/sam/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
^
MDAnalysis/lib/qcprot.c:2276:37: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare]
for (__pyx_t_14 = 0; __pyx_t_14 < __pyx_t_13; __pyx_t_14+=1) {
~~~~~~~~~~ ^ ~~~~~~~~~~MDAnalysis/lib/qcprot.c:2484:37: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare]
for (__pyx_t_14 = 0; __pyx_t_14 < __pyx_t_13; __pyx_t_14+=1) {
~~~~~~~~~~ ^ ~~~~~~~~~~3 warnings generated.
gcc -bundle -undefined dynamic_lookup -L/Users/sam/opt/anaconda3/lib -arch x86_64 -L/Users/sam/opt/anaconda3/lib -arch x86_64 -arch x86_64 build/temp.macosx-10.9-x86_64-3.8/MDAnalysis/lib/qcprot.o -o build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/lib/qcprot.cpython-38-darwin.so
building 'MDAnalysis.lib._transformations' extension
creating build/temp.macosx-10.9-x86_64-3.8/MDAnalysis/lib/src
creating build/temp.macosx-10.9-x86_64-3.8/MDAnalysis/lib/src/transformations
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/sam/opt/anaconda3/include -arch x86_64 -I/Users/sam/opt/anaconda3/include -arch x86_64 -I/Users/sam/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include -I/Users/sam/opt/anaconda3/include/python3.8 -c MDAnalysis/lib/src/transformations/transformations.c -o build/temp.macosx-10.9-x86_64-3.8/MDAnalysis/lib/src/transformations/transformations.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros
In file included from MDAnalysis/lib/src/transformations/transformations.c:73:
In file included from /Users/sam/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /Users/sam/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /Users/sam/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944:
/Users/sam/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
^
MDAnalysis/lib/src/transformations/transformations.c:1845:25: warning: unknown pragma ignored [-Wunknown-pragmas]
#pragma vector always
^MDAnalysis/lib/src/transformations/transformations.c:1962:29: warning: unknown pragma ignored [-Wunknown-pragmas]
#pragma vector always
^MDAnalysis/lib/src/transformations/transformations.c:1986:29: warning: unknown pragma ignored [-Wunknown-pragmas]
#pragma vector always
^MDAnalysis/lib/src/transformations/transformations.c:2122:35: warning: 'PyUnicode_GetSize' is deprecated [-Wdeprecated-declarations]
if (PyUnicode_Check(axes) && (PyUnicode_GetSize(axes) == 4)) {
^/Users/sam/opt/anaconda3/include/python3.8/unicodeobject.h:177:1: note: 'PyUnicode_GetSize' has been explicitly marked deprecated here
Py_DEPRECATED(3.3) PyAPI_FUNC(Py_ssize_t) PyUnicode_GetSize(
^
/Users/sam/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
^MDAnalysis/lib/src/transformations/transformations.c:3427:21: warning: unknown pragma ignored [-Wunknown-pragmas]
#pragma vector always
^MDAnalysis/lib/src/transformations/transformations.c:3508:25: warning: unknown pragma ignored [-Wunknown-pragmas]
#pragma vector always
^MDAnalysis/lib/src/transformations/transformations.c:3610:21: warning: unknown pragma ignored [-Wunknown-pragmas]
#pragma vector always
^MDAnalysis/lib/src/transformations/transformations.c:3615:21: warning: unknown pragma ignored [-Wunknown-pragmas]
#pragma vector always
^MDAnalysis/lib/src/transformations/transformations.c:3679:25: warning: unknown pragma ignored [-Wunknown-pragmas]
#pragma vector always
^MDAnalysis/lib/src/transformations/transformations.c:3684:25: warning: unknown pragma ignored [-Wunknown-pragmas]
#pragma vector always
^MDAnalysis/lib/src/transformations/transformations.c:774:1: warning: unused function 'PyConverter_DoubleArray' [-Wunused-function]
PyConverter_DoubleArray(
^
MDAnalysis/lib/src/transformations/transformations.c:804:1: warning: unused function 'PyConverter_DoubleArrayOrNone' [-Wunused-function]
PyConverter_DoubleArrayOrNone(
^
MDAnalysis/lib/src/transformations/transformations.c:910:1: warning: unused function 'PyConverter_DoubleVector4Copy' [-Wunused-function]
PyConverter_DoubleVector4Copy(
^
14 warnings generated.
gcc -bundle -undefined dynamic_lookup -L/Users/sam/opt/anaconda3/lib -arch x86_64 -L/Users/sam/opt/anaconda3/lib -arch x86_64 -arch x86_64 build/temp.macosx-10.9-x86_64-3.8/MDAnalysis/lib/src/transformations/transformations.o -lm -o build/lib.macosx-10.9-x8664-3.8/MDAnalysis/lib/ transformations.cpython-38-darwin.so
building 'MDAnalysis.lib.formats.libmdaxdr' extension
creating build/temp.macosx-10.9-x86_64-3.8/MDAnalysis/lib/formats/src
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/sam/opt/anaconda3/include -arch x86_64 -I/Users/sam/opt/anaconda3/include -arch x86_64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/Users/sam/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/Users/sam/opt/anaconda3/include/python3.8 -c MDAnalysis/lib/formats/libmdaxdr.c -o build/temp.macosx-10.9-x86_64-3.8/MDAnalysis/lib/formats/libmdaxdr.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros
In file included from MDAnalysis/lib/formats/libmdaxdr.c:651:
In file included from /Users/sam/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /Users/sam/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /Users/sam/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944:
/Users/sam/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
^
In file included from MDAnalysis/lib/formats/libmdaxdr.c:654:
MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: '/*' within block comment [-Wcomment]
/ -- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
^
In file included from MDAnalysis/lib/formats/libmdaxdr.c:655:
MDAnalysis/lib/formats/include/xdrfile_xtc.h:5:2: warning: '/*' within block comment [-Wcomment]
/ -- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
^
In file included from MDAnalysis/lib/formats/libmdaxdr.c:656:
MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: '/*' within block comment [-Wcomment]
/ -- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
^
MDAnalysis/lib/formats/libmdaxdr.c:25954:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^/Users/sam/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^/Users/sam/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
^MDAnalysis/lib/formats/libmdaxdr.c:26045:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^/Users/sam/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^/Users/sam/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
^MDAnalysis/lib/formats/libmdaxdr.c:26136:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^/Users/sam/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^/Users/sam/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
^MDAnalysis/lib/formats/libmdaxdr.c:26325:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^/Users/sam/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^/Users/sam/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
^MDAnalysis/lib/formats/libmdaxdr.c:26444:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^/Users/sam/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^/Users/sam/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
^MDAnalysis/lib/formats/libmdaxdr.c:26705:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^/Users/sam/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^/Users/sam/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
^MDAnalysis/lib/formats/libmdaxdr.c:26851:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^/Users/sam/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^/Users/sam/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
^11 warnings generated.
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/sam/opt/anaconda3/include -arch x86_64 -I/Users/sam/opt/anaconda3/include -arch x86_64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/Users/sam/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/Users/sam/opt/anaconda3/include/python3.8 -c MDAnalysis/lib/formats/src/xdrfile.c -o build/temp.macosx-10.9-x86_64-3.8/MDAnalysis/lib/formats/src/xdrfile.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros
In file included from MDAnalysis/lib/formats/src/xdrfile.c:62:
MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: '/*' within block comment [-Wcomment]
/ -- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
^
MDAnalysis/lib/formats/src/xdrfile.c:501:17: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
while (size >= num && num_of_bits < 32)
~~~~ ^ ~~~MDAnalysis/lib/formats/src/xdrfile.c:547:32: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare]
while (bytes[num_of_bytes] >= num)
~~~~~~~~~~~~~~~~~~~ ^ ~~~MDAnalysis/lib/formats/src/xdrfile.c:656:21: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
if (num_of_bits >= num_of_bytes * 8)
~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~MDAnalysis/lib/formats/src/xdrfile.c:658:17: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
for (i = 0; i < num_of_bytes; i++)
~ ^ ~~~~~~~~~~~~MDAnalysis/lib/formats/src/xdrfile.c:666:17: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
for (i = 0; i < num_of_bytes-1; i++)
~ ^ ~~~~~~~~~~~~~~MDAnalysis/lib/formats/src/xdrfile.c:706:16: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare]
if (lastbits < num_of_bits)
~~~~~~~~ ^ ~~~~~~~~~~~MDAnalysis/lib/formats/src/xdrfile.c:816:10: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare]
if(size3>xfp->buf1size)
~~~~~^~~~~~~~~~~~~~MDAnalysis/lib/formats/src/xdrfile.c:868:19: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare]
maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
~~~~~~~^~~~MDAnalysis/lib/formats/src/xdrfile.c:1012:10: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare]
if(size3>xfp->buf1size)
~~~~~^~~~~~~~~~~~~~MDAnalysis/lib/formats/src/xdrfile.c:1135:18: warning: comparison of integers of different signs: 'int' and 'unsigned long' [-Wsign-compare]
while (smallidx < LASTIDX && magicints[smallidx] < mindiff)
~~~~~~~~ ^ ~~~~~~~MDAnalysis/lib/formats/src/xdrfile.c:1141:19: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare]
maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
~~~~~~~^~~~MDAnalysis/lib/formats/src/xdrfile.c:1273:8: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
if(tmp==(unsigned int)buf2[0])
~~~^ ~~~~~~~~~~~~~~~~~~~~~MDAnalysis/lib/formats/src/xdrfile.c:1313:10: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare]
if(size3>xfp->buf1size)
~~~~~^~~~~~~~~~~~~~MDAnalysis/lib/formats/src/xdrfile.c:1368:19: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare]
maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
~~~~~~~^~~~MDAnalysis/lib/formats/src/xdrfile.c:1504:10: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare]
if(size3>xfp->buf1size) {
~~~~~^~~~~~~~~~~~~~MDAnalysis/lib/formats/src/xdrfile.c:1619:18: warning: comparison of integers of different signs: 'int' and 'unsigned long' [-Wsign-compare]
while (smallidx < LASTIDX && magicints[smallidx] < mindiff) {
~~~~~~~~ ^ ~~~~~~~MDAnalysis/lib/formats/src/xdrfile.c:1624:19: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare]
maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
~~~~~~~^~~~MDAnalysis/lib/formats/src/xdrfile.c:1734:8: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
if(tmp==(unsigned int)buf2[0])
~~~^ ~~~~~~~~~~~~~~~~~~~~~MDAnalysis/lib/formats/src/xdrfile.c:2535:3: warning: incompatible function pointer types initializing 'unsigned int ()(XDR )' (aka 'unsigned int ()(struct XDR )') with an expression of type 'int64_t (XDR )' (aka 'long long (struct XDR )') [-Wincompatible-function-pointer-types]
xdrstdio_getpos, /* get offset in thestream */
^~~~~~~~~~~~~~~MDAnalysis/lib/formats/src/xdrfile.c:2536:3: warning: incompatible function pointer types initializing 'int ()(XDR , unsigned int)' (aka 'int ()(struct XDR , unsigned int)') with an expression of type 'int (XDR , int64_t, int)' (aka 'int (struct XDR , long long, int)') [-Wincompatible-function-pointer-types]
xdrstdio_setpos, /* set offset in thestream */
^~~~~~~~~~~~~~~21 warnings generated.
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/sam/opt/anaconda3/include -arch x86_64 -I/Users/sam/opt/anaconda3/include -arch x86_64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/Users/sam/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/Users/sam/opt/anaconda3/include/python3.8 -c MDAnalysis/lib/formats/src/xdrfile_xtc.c -o build/temp.macosx-10.9-x86_64-3.8/MDAnalysis/lib/formats/src/xdrfile_xtc.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros
In file included from MDAnalysis/lib/formats/src/xdrfile_xtc.c:30:
MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: '/*' within block comment [-Wcomment]
/ -- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
^
In file included from MDAnalysis/lib/formats/src/xdrfile_xtc.c:31:
MDAnalysis/lib/formats/include/xdrfile_xtc.h:5:2: warning: '/*' within block comment [-Wcomment]
/ -- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
^
2 warnings generated.
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/sam/opt/anaconda3/include -arch x86_64 -I/Users/sam/opt/anaconda3/include -arch x86_64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/Users/sam/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/Users/sam/opt/anaconda3/include/python3.8 -c MDAnalysis/lib/formats/src/xdrfile_trr.c -o build/temp.macosx-10.9-x86_64-3.8/MDAnalysis/lib/formats/src/xdrfile_trr.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros
In file included from MDAnalysis/lib/formats/src/xdrfile_trr.c:38:
MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: '/*' within block comment [-Wcomment]
/ -- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
^
In file included from MDAnalysis/lib/formats/src/xdrfile_trr.c:39:
MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: '/*' within block comment [-Wcomment]
/ -- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
^
MDAnalysis/lib/formats/src/xdrfile_trr.c:78:14: warning: comparison of integers of different signs: 'int' and 'unsigned long' [-Wsign-compare]
if (slen != strlen(version) + 1)
~~~~ ^ ~~~~~~~~~~~~~~~~~~~MDAnalysis/lib/formats/src/xdrfile_trr.c:86:43: warning: comparison of integers of different signs: 'int' and 'unsigned long' [-Wsign-compare]
if (xdrfile_write_string(version, xd) != (strlen(version) + 1))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~MDAnalysis/lib/formats/src/xdrfile_trr.c:408:67: warning: variable 'plcholder' is uninitialized when used here [-Wuninitialized]
return do_trn(xd, 0, &step, &t, &lambda, box, &natoms, x, v, f,plcholder);
^~~~~
MDAnalysis/lib/formats/src/xdrfile_trr.c:407:17: note: initialize the variable 'plcholder' to silence this warning
int *plcholder;
^
= NULL5 warnings generated.
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/sam/opt/anaconda3/include -arch x86_64 -I/Users/sam/opt/anaconda3/include -arch x86_64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/Users/sam/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/Users/sam/opt/anaconda3/include/python3.8 -c MDAnalysis/lib/formats/src/trr_seek.c -o build/temp.macosx-10.9-x86_64-3.8/MDAnalysis/lib/formats/src/trr_seek.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros
In file included from MDAnalysis/lib/formats/src/trr_seek.c:30:
MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: '/*' within block comment [-Wcomment]
/ -- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
^
In file included from MDAnalysis/lib/formats/src/trr_seek.c:31:
MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: '/*' within block comment [-Wcomment]
/ -- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
^
MDAnalysis/lib/formats/src/trr_seek.c:38:15: warning: unused variable 'lambda' [-Wunused-variable]
float time, lambda;
^MDAnalysis/lib/formats/src/trr_seek.c:38:9: warning: unused variable 'time' [-Wunused-variable]
float time, lambda;
^MDAnalysis/lib/formats/src/trr_seek.c:39:27: warning: unused variable 'totalframebytes' [-Wunused-variable]
int result, framebytes, totalframebytes;
^5 warnings generated.
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/sam/opt/anaconda3/include -arch x86_64 -I/Users/sam/opt/anaconda3/include -arch x86_64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/Users/sam/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/Users/sam/opt/anaconda3/include/python3.8 -c MDAnalysis/lib/formats/src/xtc_seek.c -o build/temp.macosx-10.9-x86_64-3.8/MDAnalysis/lib/formats/src/xtc_seek.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros
In file included from MDAnalysis/lib/formats/src/xtc_seek.c:25:
MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: '/*' within block comment [-Wcomment]
/ -- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
^
In file included from MDAnalysis/lib/formats/src/xtc_seek.c:26:
MDAnalysis/lib/formats/include/xdrfile_xtc.h:5:2: warning: '/*' within block comment [-Wcomment]
/ -- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
^
2 warnings generated.
gcc -bundle -undefined dynamic_lookup -L/Users/sam/opt/anaconda3/lib -arch x86_64 -L/Users/sam/opt/anaconda3/lib -arch x86_64 -arch x86_64 build/temp.macosx-10.9-x86_64-3.8/MDAnalysis/lib/formats/libmdaxdr.o build/temp.macosx-10.9-x86_64-3.8/MDAnalysis/lib/formats/src/xdrfile.o build/temp.macosx-10.9-x86_64-3.8/MDAnalysis/lib/formats/src/xdrfile_xtc.o build/temp.macosx-10.9-x86_64-3.8/MDAnalysis/lib/formats/src/xdrfile_trr.o build/temp.macosx-10.9-x86_64-3.8/MDAnalysis/lib/formats/src/trr_seek.o build/temp.macosx-10.9-x86_64-3.8/MDAnalysis/lib/formats/src/xtc_seek.o -o build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/lib/formats/ libmdaxdr.cpython-38-darwin.so
building 'MDAnalysis.lib.formats.cython_util' extension
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/sam/opt/anaconda3/include -arch x86_64 -I/Users/sam/opt/anaconda3/include -arch x86_64 -I/Users/sam/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include -I/Users/sam/opt/anaconda3/include/python3.8 -c MDAnalysis/lib/formats/cython_util.c -o build/temp.macosx-10.9-x86_64-3.8/MDAnalysis/lib/formats/cython_util.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros
In file included from MDAnalysis/lib/formats/cython_util.c:625:
In file included from /Users/sam/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /Users/sam/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /Users/sam/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944:
/Users/sam/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
^
MDAnalysis/lib/formats/cython_util.c:18589:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^/Users/sam/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^/Users/sam/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
^MDAnalysis/lib/formats/cython_util.c:18778:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^/Users/sam/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^/Users/sam/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
^MDAnalysis/lib/formats/cython_util.c:18897:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^/Users/sam/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^/Users/sam/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
^MDAnalysis/lib/formats/cython_util.c:19158:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^/Users/sam/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^/Users/sam/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
^MDAnalysis/lib/formats/cython_util.c:19304:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^/Users/sam/opt/anaconda3/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^/Users/sam/opt/anaconda3/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
^6 warnings generated.
gcc -bundle -undefined dynamic_lookup -L/Users/sam/opt/anaconda3/lib -arch x86_64 -L/Users/sam/opt/anaconda3/lib -arch x86_64 -arch x86_64 build/temp.macosx-10.9-x86_64-3.8/MDAnalysis/lib/formats/cython_util.o -o build/lib.macosx-10.9-x86_64-3.8/MDAnalysis/lib/formats/ cython_util.cpython-38-darwin.so
building 'MDAnalysis.analysis.encore.cutils' extension
creating build/temp.macosx-10.9-x86_64-3.8/MDAnalysis/analysis
creating build/temp.macosx-10.9-x86_64-3.8/MDAnalysis/analysis/encore
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/sam/opt/anaconda3/include -arch x86_64 -I/Users/sam/opt/anaconda3/include -arch x86_64 -I/Users/sam/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include -I/Users/sam/opt/anaconda3/include/python3.8 -c MDAnalysis/analysis/encore/cutils.c -o build/temp.macosx-10.9-x86_64-3.8/MDAnalysis/analysis/encore/cutils.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros
In file included from MDAnalysis/analysis/encore/cutils.c:625:
In file included from /Users/sam/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /Users/sam/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /Users/sam/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944:
/Users/sam/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
gitesei
commented
2 years ago Thanks, Sam! I got hold of a new MacBook and it turned out that increasing the MDAnalysis version in requirements.txt from 1.0 to 1.1.1 did the trick. I have also made a new PyPI release so that pip install DEERPREdict should now also work.
I hope this helps and please let me know if it doesn't.
Best wishes,
Giulio
samlobe
commented
2 years ago Amazing! Thank you for fixing it! I'm able to import it successfully now from my Mac :) The install had one error, but I can still import it. Maybe it's insignificant. I pasted it below in case it matters.
Take care, -Sam
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
mdanalysistests 2.0.0 requires MDAnalysis==2.0.0, but you have mdanalysis 1.1.1 which is incompatible.
On Mon, Dec 20, 2021 at 3:25 PM Giulio Tesei @.***> wrote:
Thanks, Sam! I got hold of a new MacBook and it turned out that increasing the MDAnalysis version in requirements.txt from 1.0 to 1.1.1 did the trick. I have also made a new PyPI release so that pip install DEERPREdict should now also work. I hope this helps and please let me know if it doesn't. Best wishes, Giulio
— Reply to this email directly, view it on GitHub https://github.com/KULL-Centre/DEERpredict/issues/4#issuecomment-998344243, or unsubscribe https://github.com/notifications/unsubscribe-auth/ARICHHIA3Z2JHCUXWIMWCRDUR63M3ANCNFSM5KMSQLAA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.
You are receiving this because you authored the thread.Message ID: @.***>
gitesei
commented
2 years ago Great! Maybe mdanalysistests==2.0.0 was already in your environment before installing DEERPREdict with pip, which now requires MDAnalysis==1.1.1. Anyhow, that shouldn't cause any problems for DEERPREdict :) Best wishes, Giulio
I tried
pip install DEERPREdicton my Mac terminal and the install failed.I have the Apple M1 chip and I'm on OS Monterey 12.0.1. I believe it's failing because the install seems to be for an older operating system and/or for the Intel chip (I saw "build/lib.macosx-10.9-x86_64-3.8" in the error text).
I was able to install successfully on a Windows. Please let me know if this is fixed because I'd love to have this package on my Mac!
Thanks, -Sam
Here's a list of the install warnings I get: