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MDAnalysis is a Python library to analyze molecular dynamics simulations.
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MDA compilation crash with aarch64 #3374

Closed IAlibay closed 3 years ago

IAlibay commented 3 years ago

For some reason our latest aarch64 builds are reproducibly failing on aarch64, see: https://travis-ci.com/github/MDAnalysis/mdanalysis/jobs/526646721#L1562-L1582

Issue seems to coincide with the release of cython 0.29.24.

@tylerjereddy sorry to bug you here, are you seeing anything similar upstream?

IAlibay commented 3 years ago

Looking at the logs a bit more, looks like an issue with GSD? I don't have an ARM machine on hand to test this unfortunately :(

IAlibay commented 3 years ago

Remembered I had access to a ThunderX2 machine.

I can reproduce this issue:

pip install cython==0.29.24 numpy==1.19.1 scipy==1.7.0
pip install --no-build-isolation hypothesis matplotlib pytest pytest-cov pytest-xdist tqdm threadpoolctl
git clone https://github.com/MDAnalysis/mdanalysis.git
cd mdanalysis/package
python setup.py install
Details ``` Attempting to autodetect OpenMP support... Compiler supports OpenMP Will attempt to use Cython. Compiling MDAnalysis/lib/formats/libdcd.pyx because it changed. Compiling MDAnalysis/lib/c_distances.pyx because it changed. Compiling MDAnalysis/lib/c_distances_openmp.pyx because it changed. Compiling MDAnalysis/lib/qcprot.pyx because it changed. Compiling MDAnalysis/lib/formats/libmdaxdr.pyx because it changed. Compiling MDAnalysis/lib/formats/cython_util.pyx because it changed. Compiling MDAnalysis/analysis/encore/cutils.pyx because it changed. Compiling MDAnalysis/analysis/encore/clustering/affinityprop.pyx because it changed. Compiling MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx because it changed. Compiling MDAnalysis/lib/_cutil.pyx because it changed. Compiling MDAnalysis/lib/_augment.pyx because it changed. Compiling MDAnalysis/lib/nsgrid.pyx because it changed. [ 1/12] Cythonizing MDAnalysis/analysis/encore/clustering/affinityprop.pyx [ 2/12] Cythonizing MDAnalysis/analysis/encore/cutils.pyx [ 3/12] Cythonizing MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx [ 4/12] Cythonizing MDAnalysis/lib/_augment.pyx [ 5/12] Cythonizing MDAnalysis/lib/_cutil.pyx [ 6/12] Cythonizing MDAnalysis/lib/c_distances.pyx [ 7/12] Cythonizing MDAnalysis/lib/c_distances_openmp.pyx [ 8/12] Cythonizing MDAnalysis/lib/formats/cython_util.pyx [ 9/12] Cythonizing MDAnalysis/lib/formats/libdcd.pyx [10/12] Cythonizing MDAnalysis/lib/formats/libmdaxdr.pyx [11/12] Cythonizing MDAnalysis/lib/nsgrid.pyx [12/12] Cythonizing MDAnalysis/lib/qcprot.pyx /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/setuptools/dist.py:461: UserWarning: Normalizing '2.0.0-dev0' to '2.0.0.dev0' warnings.warn(tmpl.format(**locals())) running install running bdist_egg running egg_info creating MDAnalysis.egg-info writing MDAnalysis.egg-info/PKG-INFO writing dependency_links to MDAnalysis.egg-info/dependency_links.txt writing requirements to MDAnalysis.egg-info/requires.txt writing top-level names to MDAnalysis.egg-info/top_level.txt writing manifest file 'MDAnalysis.egg-info/SOURCES.txt' reading manifest file 'MDAnalysis.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files matching 'doc/html/html' found anywhere in distribution warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution warning: no previously-included files matching '*.pyd' found anywhere in distribution warning: no previously-included files matching '*~' found anywhere in distribution warning: no previously-included files matching '.git' found anywhere in distribution writing manifest file 'MDAnalysis.egg-info/SOURCES.txt' installing library code to build/bdist.linux-aarch64/egg running install_lib running build_py creating build creating build/lib.linux-aarch64-3.8 creating build/lib.linux-aarch64-3.8/MDAnalysis copying MDAnalysis/authors.py -> build/lib.linux-aarch64-3.8/MDAnalysis copying MDAnalysis/version.py -> build/lib.linux-aarch64-3.8/MDAnalysis copying MDAnalysis/due.py -> build/lib.linux-aarch64-3.8/MDAnalysis copying MDAnalysis/__init__.py -> build/lib.linux-aarch64-3.8/MDAnalysis copying MDAnalysis/exceptions.py -> build/lib.linux-aarch64-3.8/MDAnalysis copying MDAnalysis/units.py -> build/lib.linux-aarch64-3.8/MDAnalysis creating build/lib.linux-aarch64-3.8/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/core.py -> build/lib.linux-aarch64-3.8/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/XVG.py -> build/lib.linux-aarch64-3.8/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/__init__.py -> build/lib.linux-aarch64-3.8/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/base.py -> build/lib.linux-aarch64-3.8/MDAnalysis/auxiliary creating build/lib.linux-aarch64-3.8/MDAnalysis/coordinates copying MDAnalysis/coordinates/null.py -> build/lib.linux-aarch64-3.8/MDAnalysis/coordinates copying MDAnalysis/coordinates/DMS.py -> build/lib.linux-aarch64-3.8/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRZ.py -> build/lib.linux-aarch64-3.8/MDAnalysis/coordinates copying MDAnalysis/coordinates/chain.py -> build/lib.linux-aarch64-3.8/MDAnalysis/coordinates copying MDAnalysis/coordinates/GMS.py -> build/lib.linux-aarch64-3.8/MDAnalysis/coordinates copying MDAnalysis/coordinates/TXYZ.py -> build/lib.linux-aarch64-3.8/MDAnalysis/coordinates copying MDAnalysis/coordinates/PQR.py -> build/lib.linux-aarch64-3.8/MDAnalysis/coordinates copying MDAnalysis/coordinates/FHIAIMS.py -> build/lib.linux-aarch64-3.8/MDAnalysis/coordinates copying MDAnalysis/coordinates/ParmEd.py -> build/lib.linux-aarch64-3.8/MDAnalysis/coordinates copying MDAnalysis/coordinates/memory.py -> build/lib.linux-aarch64-3.8/MDAnalysis/coordinates copying MDAnalysis/coordinates/GSD.py -> build/lib.linux-aarch64-3.8/MDAnalysis/coordinates copying MDAnalysis/coordinates/H5MD.py -> build/lib.linux-aarch64-3.8/MDAnalysis/coordinates copying MDAnalysis/coordinates/CRD.py -> build/lib.linux-aarch64-3.8/MDAnalysis/coordinates copying MDAnalysis/coordinates/DCD.py -> build/lib.linux-aarch64-3.8/MDAnalysis/coordinates copying MDAnalysis/coordinates/INPCRD.py -> build/lib.linux-aarch64-3.8/MDAnalysis/coordinates copying MDAnalysis/coordinates/core.py -> build/lib.linux-aarch64-3.8/MDAnalysis/coordinates copying MDAnalysis/coordinates/XTC.py -> build/lib.linux-aarch64-3.8/MDAnalysis/coordinates copying MDAnalysis/coordinates/GRO.py -> build/lib.linux-aarch64-3.8/MDAnalysis/coordinates copying MDAnalysis/coordinates/XYZ.py -> build/lib.linux-aarch64-3.8/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRR.py -> build/lib.linux-aarch64-3.8/MDAnalysis/coordinates copying MDAnalysis/coordinates/MOL2.py -> build/lib.linux-aarch64-3.8/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRJ.py -> build/lib.linux-aarch64-3.8/MDAnalysis/coordinates copying MDAnalysis/coordinates/chemfiles.py -> build/lib.linux-aarch64-3.8/MDAnalysis/coordinates copying MDAnalysis/coordinates/__init__.py -> build/lib.linux-aarch64-3.8/MDAnalysis/coordinates copying MDAnalysis/coordinates/NAMDBIN.py -> build/lib.linux-aarch64-3.8/MDAnalysis/coordinates copying MDAnalysis/coordinates/XDR.py -> build/lib.linux-aarch64-3.8/MDAnalysis/coordinates copying MDAnalysis/coordinates/PDB.py -> build/lib.linux-aarch64-3.8/MDAnalysis/coordinates copying MDAnalysis/coordinates/PDBQT.py -> build/lib.linux-aarch64-3.8/MDAnalysis/coordinates copying MDAnalysis/coordinates/LAMMPS.py -> build/lib.linux-aarch64-3.8/MDAnalysis/coordinates copying MDAnalysis/coordinates/MMTF.py -> build/lib.linux-aarch64-3.8/MDAnalysis/coordinates copying MDAnalysis/coordinates/base.py -> build/lib.linux-aarch64-3.8/MDAnalysis/coordinates copying MDAnalysis/coordinates/DLPoly.py -> build/lib.linux-aarch64-3.8/MDAnalysis/coordinates creating build/lib.linux-aarch64-3.8/MDAnalysis/core copying MDAnalysis/core/topologyobjects.py -> build/lib.linux-aarch64-3.8/MDAnalysis/core copying MDAnalysis/core/accessors.py -> build/lib.linux-aarch64-3.8/MDAnalysis/core copying MDAnalysis/core/universe.py -> build/lib.linux-aarch64-3.8/MDAnalysis/core copying MDAnalysis/core/topology.py -> build/lib.linux-aarch64-3.8/MDAnalysis/core copying MDAnalysis/core/__init__.py -> build/lib.linux-aarch64-3.8/MDAnalysis/core copying MDAnalysis/core/groups.py -> build/lib.linux-aarch64-3.8/MDAnalysis/core copying MDAnalysis/core/selection.py -> build/lib.linux-aarch64-3.8/MDAnalysis/core copying MDAnalysis/core/_get_readers.py -> build/lib.linux-aarch64-3.8/MDAnalysis/core copying MDAnalysis/core/topologyattrs.py -> build/lib.linux-aarch64-3.8/MDAnalysis/core creating build/lib.linux-aarch64-3.8/MDAnalysis/tests copying MDAnalysis/tests/datafiles.py -> build/lib.linux-aarch64-3.8/MDAnalysis/tests copying MDAnalysis/tests/__init__.py -> build/lib.linux-aarch64-3.8/MDAnalysis/tests creating build/lib.linux-aarch64-3.8/MDAnalysis/topology copying MDAnalysis/topology/XYZParser.py -> build/lib.linux-aarch64-3.8/MDAnalysis/topology copying MDAnalysis/topology/LAMMPSParser.py -> build/lib.linux-aarch64-3.8/MDAnalysis/topology copying MDAnalysis/topology/MinimalParser.py -> build/lib.linux-aarch64-3.8/MDAnalysis/topology copying MDAnalysis/topology/HoomdXMLParser.py -> build/lib.linux-aarch64-3.8/MDAnalysis/topology copying MDAnalysis/topology/GMSParser.py -> build/lib.linux-aarch64-3.8/MDAnalysis/topology copying MDAnalysis/topology/PDBParser.py -> build/lib.linux-aarch64-3.8/MDAnalysis/topology copying MDAnalysis/topology/core.py -> build/lib.linux-aarch64-3.8/MDAnalysis/topology copying MDAnalysis/topology/GROParser.py -> build/lib.linux-aarch64-3.8/MDAnalysis/topology copying MDAnalysis/topology/DMSParser.py -> build/lib.linux-aarch64-3.8/MDAnalysis/topology copying MDAnalysis/topology/ITPParser.py -> build/lib.linux-aarch64-3.8/MDAnalysis/topology copying MDAnalysis/topology/FHIAIMSParser.py -> build/lib.linux-aarch64-3.8/MDAnalysis/topology copying MDAnalysis/topology/__init__.py -> build/lib.linux-aarch64-3.8/MDAnalysis/topology copying MDAnalysis/topology/GSDParser.py -> build/lib.linux-aarch64-3.8/MDAnalysis/topology copying MDAnalysis/topology/guessers.py -> build/lib.linux-aarch64-3.8/MDAnalysis/topology copying MDAnalysis/topology/TXYZParser.py -> build/lib.linux-aarch64-3.8/MDAnalysis/topology copying MDAnalysis/topology/PQRParser.py -> build/lib.linux-aarch64-3.8/MDAnalysis/topology copying MDAnalysis/topology/ParmEdParser.py -> build/lib.linux-aarch64-3.8/MDAnalysis/topology copying MDAnalysis/topology/CRDParser.py -> build/lib.linux-aarch64-3.8/MDAnalysis/topology copying MDAnalysis/topology/MOL2Parser.py -> build/lib.linux-aarch64-3.8/MDAnalysis/topology copying MDAnalysis/topology/ExtendedPDBParser.py -> build/lib.linux-aarch64-3.8/MDAnalysis/topology copying MDAnalysis/topology/MMTFParser.py -> build/lib.linux-aarch64-3.8/MDAnalysis/topology copying MDAnalysis/topology/PSFParser.py -> build/lib.linux-aarch64-3.8/MDAnalysis/topology copying MDAnalysis/topology/base.py -> build/lib.linux-aarch64-3.8/MDAnalysis/topology copying MDAnalysis/topology/tables.py -> build/lib.linux-aarch64-3.8/MDAnalysis/topology copying MDAnalysis/topology/PDBQTParser.py -> build/lib.linux-aarch64-3.8/MDAnalysis/topology copying MDAnalysis/topology/TOPParser.py -> build/lib.linux-aarch64-3.8/MDAnalysis/topology copying MDAnalysis/topology/TPRParser.py -> build/lib.linux-aarch64-3.8/MDAnalysis/topology copying MDAnalysis/topology/DLPolyParser.py -> build/lib.linux-aarch64-3.8/MDAnalysis/topology creating build/lib.linux-aarch64-3.8/MDAnalysis/selections copying MDAnalysis/selections/pymol.py -> build/lib.linux-aarch64-3.8/MDAnalysis/selections copying MDAnalysis/selections/charmm.py -> build/lib.linux-aarch64-3.8/MDAnalysis/selections copying MDAnalysis/selections/jmol.py -> build/lib.linux-aarch64-3.8/MDAnalysis/selections copying MDAnalysis/selections/vmd.py -> build/lib.linux-aarch64-3.8/MDAnalysis/selections copying MDAnalysis/selections/__init__.py -> build/lib.linux-aarch64-3.8/MDAnalysis/selections copying MDAnalysis/selections/base.py -> build/lib.linux-aarch64-3.8/MDAnalysis/selections copying MDAnalysis/selections/gromacs.py -> build/lib.linux-aarch64-3.8/MDAnalysis/selections creating build/lib.linux-aarch64-3.8/MDAnalysis/transformations copying MDAnalysis/transformations/wrap.py -> build/lib.linux-aarch64-3.8/MDAnalysis/transformations copying MDAnalysis/transformations/__init__.py -> build/lib.linux-aarch64-3.8/MDAnalysis/transformations copying MDAnalysis/transformations/boxdimensions.py -> build/lib.linux-aarch64-3.8/MDAnalysis/transformations copying MDAnalysis/transformations/positionaveraging.py -> build/lib.linux-aarch64-3.8/MDAnalysis/transformations copying MDAnalysis/transformations/translate.py -> build/lib.linux-aarch64-3.8/MDAnalysis/transformations copying MDAnalysis/transformations/fit.py -> build/lib.linux-aarch64-3.8/MDAnalysis/transformations copying MDAnalysis/transformations/rotate.py -> build/lib.linux-aarch64-3.8/MDAnalysis/transformations copying MDAnalysis/transformations/base.py -> build/lib.linux-aarch64-3.8/MDAnalysis/transformations creating build/lib.linux-aarch64-3.8/MDAnalysis/lib copying MDAnalysis/lib/distances.py -> build/lib.linux-aarch64-3.8/MDAnalysis/lib copying MDAnalysis/lib/NeighborSearch.py -> build/lib.linux-aarch64-3.8/MDAnalysis/lib copying MDAnalysis/lib/log.py -> build/lib.linux-aarch64-3.8/MDAnalysis/lib copying MDAnalysis/lib/__init__.py -> build/lib.linux-aarch64-3.8/MDAnalysis/lib copying MDAnalysis/lib/util.py -> build/lib.linux-aarch64-3.8/MDAnalysis/lib copying MDAnalysis/lib/picklable_file_io.py -> build/lib.linux-aarch64-3.8/MDAnalysis/lib copying MDAnalysis/lib/mdamath.py -> build/lib.linux-aarch64-3.8/MDAnalysis/lib copying MDAnalysis/lib/correlations.py -> build/lib.linux-aarch64-3.8/MDAnalysis/lib copying MDAnalysis/lib/transformations.py -> build/lib.linux-aarch64-3.8/MDAnalysis/lib copying MDAnalysis/lib/pkdtree.py -> build/lib.linux-aarch64-3.8/MDAnalysis/lib creating build/lib.linux-aarch64-3.8/MDAnalysis/analysis copying MDAnalysis/analysis/distances.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis copying MDAnalysis/analysis/diffusionmap.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis copying MDAnalysis/analysis/density.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis copying MDAnalysis/analysis/psa.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis copying MDAnalysis/analysis/align.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis copying MDAnalysis/analysis/helix_analysis.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis copying MDAnalysis/analysis/gnm.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis copying MDAnalysis/analysis/pca.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis copying MDAnalysis/analysis/polymer.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis copying MDAnalysis/analysis/dihedrals.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis copying MDAnalysis/analysis/__init__.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis copying MDAnalysis/analysis/leaflet.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis copying MDAnalysis/analysis/lineardensity.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis copying MDAnalysis/analysis/contacts.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis copying MDAnalysis/analysis/msd.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis copying MDAnalysis/analysis/nuclinfo.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis copying MDAnalysis/analysis/rdf.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis copying MDAnalysis/analysis/base.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis copying MDAnalysis/analysis/bat.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis copying MDAnalysis/analysis/rms.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis copying MDAnalysis/analysis/waterdynamics.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis creating build/lib.linux-aarch64-3.8/MDAnalysis/converters copying MDAnalysis/converters/OpenMMParser.py -> build/lib.linux-aarch64-3.8/MDAnalysis/converters copying MDAnalysis/converters/ParmEd.py -> build/lib.linux-aarch64-3.8/MDAnalysis/converters copying MDAnalysis/converters/__init__.py -> build/lib.linux-aarch64-3.8/MDAnalysis/converters copying MDAnalysis/converters/RDKit.py -> build/lib.linux-aarch64-3.8/MDAnalysis/converters copying MDAnalysis/converters/OpenMM.py -> build/lib.linux-aarch64-3.8/MDAnalysis/converters copying MDAnalysis/converters/ParmEdParser.py -> build/lib.linux-aarch64-3.8/MDAnalysis/converters copying MDAnalysis/converters/RDKitParser.py -> build/lib.linux-aarch64-3.8/MDAnalysis/converters creating build/lib.linux-aarch64-3.8/MDAnalysis/visualization copying MDAnalysis/visualization/streamlines_3D.py -> build/lib.linux-aarch64-3.8/MDAnalysis/visualization copying MDAnalysis/visualization/__init__.py -> build/lib.linux-aarch64-3.8/MDAnalysis/visualization copying MDAnalysis/visualization/streamlines.py -> build/lib.linux-aarch64-3.8/MDAnalysis/visualization creating build/lib.linux-aarch64-3.8/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/obj.py -> build/lib.linux-aarch64-3.8/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/utils.py -> build/lib.linux-aarch64-3.8/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/__init__.py -> build/lib.linux-aarch64-3.8/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/setting.py -> build/lib.linux-aarch64-3.8/MDAnalysis/topology/tpr creating build/lib.linux-aarch64-3.8/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/__init__.py -> build/lib.linux-aarch64-3.8/MDAnalysis/lib/formats creating build/lib.linux-aarch64-3.8/MDAnalysis/analysis/data copying MDAnalysis/analysis/data/__init__.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis/data copying MDAnalysis/analysis/data/filenames.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis/data creating build/lib.linux-aarch64-3.8/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/confdistmatrix.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/utils.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/similarity.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/covariance.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/__init__.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/bootstrap.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis/encore creating build/lib.linux-aarch64-3.8/MDAnalysis/analysis/legacy copying MDAnalysis/analysis/legacy/x3dna.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis/legacy copying MDAnalysis/analysis/legacy/__init__.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis/legacy creating build/lib.linux-aarch64-3.8/MDAnalysis/analysis/hbonds copying MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis/hbonds copying MDAnalysis/analysis/hbonds/__init__.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis/hbonds creating build/lib.linux-aarch64-3.8/MDAnalysis/analysis/hole2 copying MDAnalysis/analysis/hole2/templates.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis/hole2 copying MDAnalysis/analysis/hole2/utils.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis/hole2 copying MDAnalysis/analysis/hole2/hole.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis/hole2 copying MDAnalysis/analysis/hole2/__init__.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis/hole2 creating build/lib.linux-aarch64-3.8/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis/hydrogenbonds creating build/lib.linux-aarch64-3.8/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis/encore/dimensionality_reduction creating build/lib.linux-aarch64-3.8/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/__init__.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/cluster.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/data/janin_ref_data.npy -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis/data copying MDAnalysis/analysis/data/rama_ref_data.npy -> build/lib.linux-aarch64-3.8/MDAnalysis/analysis/data running build_ext building 'MDAnalysis.lib.formats.libdcd' extension creating build/temp.linux-aarch64-3.8 creating build/temp.linux-aarch64-3.8/MDAnalysis creating build/temp.linux-aarch64-3.8/MDAnalysis/lib creating build/temp.linux-aarch64-3.8/MDAnalysis/lib/formats gcc -pthread -B /home/ri-ialibay/software/miniconda/install/envs/test-gsd/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/formats -I/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include -I/lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/formats/include -I/home/ri-ialibay/software/miniconda/install/envs/test-gsd/include/python3.8 -c MDAnalysis/lib/formats/libdcd.c -o build/temp.linux-aarch64-3.8/MDAnalysis/lib/formats/libdcd.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros cc1: warning: -fassociative-math disabled; other options take precedence In file included from /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:0, from /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/lib/formats/libdcd.c:650: /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ In file included from MDAnalysis/lib/formats/libdcd.c:659:0: MDAnalysis/lib/formats/include/readdcd.h: In function ‘read_dcdstep’: MDAnalysis/lib/formats/include/readdcd.h:549:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (readlen != (6*sizeof(int) + 3*N*sizeof(float))) ^~ MDAnalysis/lib/formats/include/readdcd.h:562:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (tmpbuf[i] != sizeof(float)*N) return DCD_BADFORMAT; ^~ MDAnalysis/lib/formats/include/readdcd.h: In function ‘write_dcdheader’: 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; ^~~~~~~~ In file included from MDAnalysis/lib/formats/include/readdcd.h:25:0, from MDAnalysis/lib/formats/libdcd.c:659: At top level: MDAnalysis/lib/formats/include/endianswap.h:96:13: warning: ‘swap2_aligned’ defined but not used [-Wunused-function] static void swap2_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ MDAnalysis/lib/formats/include/endianswap.h:32:13: warning: ‘swap2_unaligned’ defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ In file included from MDAnalysis/lib/formats/libdcd.c:658:0: MDAnalysis/lib/formats/include/fastio.h:453:12: warning: ‘fio_write_str’ defined but not used [-Wunused-function] static int fio_write_str(fio_fd fd, const char *str) { ^~~~~~~~~~~~~ MDAnalysis/lib/formats/include/fastio.h:449:12: warning: ‘fio_read_int32’ defined but not used [-Wunused-function] static int fio_read_int32(fio_fd fd, int *i) { ^~~~~~~~~~~~~~ gcc -pthread -shared -B /home/ri-ialibay/software/miniconda/install/envs/test-gsd/compiler_compat -L/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib -Wl,-rpath=/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-aarch64-3.8/MDAnalysis/lib/formats/libdcd.o -o build/lib.linux-aarch64-3.8/MDAnalysis/lib/formats/libdcd.cpython-38-aarch64-linux-gnu.so building 'MDAnalysis.lib.c_distances' extension gcc -pthread -B /home/ri-ialibay/software/miniconda/install/envs/test-gsd/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include -I/lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/include -I/home/ri-ialibay/software/miniconda/install/envs/test-gsd/include/python3.8 -c MDAnalysis/lib/c_distances.c -o build/temp.linux-aarch64-3.8/MDAnalysis/lib/c_distances.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros cc1: warning: -fassociative-math disabled; other options take precedence In file included from /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:0, from /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/lib/c_distances.c:651: /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ gcc -pthread -shared -B /home/ri-ialibay/software/miniconda/install/envs/test-gsd/compiler_compat -L/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib -Wl,-rpath=/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-aarch64-3.8/MDAnalysis/lib/c_distances.o -lm -o build/lib.linux-aarch64-3.8/MDAnalysis/lib/c_distances.cpython-38-aarch64-linux-gnu.so building 'MDAnalysis.lib.c_distances_openmp' extension gcc -pthread -B /home/ri-ialibay/software/miniconda/install/envs/test-gsd/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DPARALLEL -I/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include -I/lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/include -I/home/ri-ialibay/software/miniconda/install/envs/test-gsd/include/python3.8 -c MDAnalysis/lib/c_distances_openmp.c -o build/temp.linux-aarch64-3.8/MDAnalysis/lib/c_distances_openmp.o -fopenmp -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros cc1: warning: -fassociative-math disabled; other options take precedence In file included from /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:0, from /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/lib/c_distances_openmp.c:662: /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ gcc -pthread -shared -B /home/ri-ialibay/software/miniconda/install/envs/test-gsd/compiler_compat -L/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib -Wl,-rpath=/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-aarch64-3.8/MDAnalysis/lib/c_distances_openmp.o -lm -lgomp -o build/lib.linux-aarch64-3.8/MDAnalysis/lib/c_distances_openmp.cpython-38-aarch64-linux-gnu.so -fopenmp building 'MDAnalysis.lib.qcprot' extension gcc -pthread -B /home/ri-ialibay/software/miniconda/install/envs/test-gsd/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include -I/home/ri-ialibay/software/miniconda/install/envs/test-gsd/include/python3.8 -c MDAnalysis/lib/qcprot.c -o build/temp.linux-aarch64-3.8/MDAnalysis/lib/qcprot.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros cc1: warning: -fassociative-math disabled; other options take precedence In file included from /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:0, from /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/lib/qcprot.c:646: /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ MDAnalysis/lib/qcprot.c: In function ‘__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct’: MDAnalysis/lib/qcprot.c:2274:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { ^ MDAnalysis/lib/qcprot.c:2482:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { ^ gcc -pthread -shared -B /home/ri-ialibay/software/miniconda/install/envs/test-gsd/compiler_compat -L/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib -Wl,-rpath=/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-aarch64-3.8/MDAnalysis/lib/qcprot.o -o build/lib.linux-aarch64-3.8/MDAnalysis/lib/qcprot.cpython-38-aarch64-linux-gnu.so building 'MDAnalysis.lib._transformations' extension creating build/temp.linux-aarch64-3.8/MDAnalysis/lib/src creating build/temp.linux-aarch64-3.8/MDAnalysis/lib/src/transformations gcc -pthread -B /home/ri-ialibay/software/miniconda/install/envs/test-gsd/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include -I/home/ri-ialibay/software/miniconda/install/envs/test-gsd/include/python3.8 -c MDAnalysis/lib/src/transformations/transformations.c -o build/temp.linux-aarch64-3.8/MDAnalysis/lib/src/transformations/transformations.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros cc1: warning: -fassociative-math disabled; other options take precedence In file included from /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:0, from /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/lib/src/transformations/transformations.c:73: /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ MDAnalysis/lib/src/transformations/transformations.c: In function ‘py_superimposition_matrix’: MDAnalysis/lib/src/transformations/transformations.c:1845:0: warning: ignoring #pragma vector always [-Wunknown-pragmas] #pragma vector always MDAnalysis/lib/src/transformations/transformations.c:1962:0: warning: ignoring #pragma vector always [-Wunknown-pragmas] #pragma vector always MDAnalysis/lib/src/transformations/transformations.c:1986:0: warning: ignoring #pragma vector always [-Wunknown-pragmas] #pragma vector always MDAnalysis/lib/src/transformations/transformations.c: In function ‘axis2tuple’: MDAnalysis/lib/src/transformations/transformations.c:2122:5: warning: ‘PyUnicode_GetSize’ is deprecated [-Wdeprecated-declarations] if (PyUnicode_Check(axes) && (PyUnicode_GetSize(axes) == 4)) { ^~ In file included from /home/ri-ialibay/software/miniconda/install/envs/test-gsd/include/python3.8/Python.h:97:0, from MDAnalysis/lib/src/transformations/transformations.c:68: /home/ri-ialibay/software/miniconda/install/envs/test-gsd/include/python3.8/unicodeobject.h:177:43: note: declared here Py_DEPRECATED(3.3) PyAPI_FUNC(Py_ssize_t) PyUnicode_GetSize( ^~~~~~~~~~~~~~~~~ MDAnalysis/lib/src/transformations/transformations.c: In function ‘py_vector_norm’: MDAnalysis/lib/src/transformations/transformations.c:3427:0: warning: ignoring #pragma vector always [-Wunknown-pragmas] #pragma vector always MDAnalysis/lib/src/transformations/transformations.c:3508:0: warning: ignoring #pragma vector always [-Wunknown-pragmas] #pragma vector always MDAnalysis/lib/src/transformations/transformations.c: In function ‘py_unit_vector’: MDAnalysis/lib/src/transformations/transformations.c:3610:0: warning: ignoring #pragma vector always [-Wunknown-pragmas] #pragma vector always MDAnalysis/lib/src/transformations/transformations.c:3615:0: warning: ignoring #pragma vector always [-Wunknown-pragmas] #pragma vector always MDAnalysis/lib/src/transformations/transformations.c:3679:0: warning: ignoring #pragma vector always [-Wunknown-pragmas] #pragma vector always MDAnalysis/lib/src/transformations/transformations.c:3684:0: warning: ignoring #pragma vector always [-Wunknown-pragmas] #pragma vector always At top level: MDAnalysis/lib/src/transformations/transformations.c:910:1: warning: ‘PyConverter_DoubleVector4Copy’ defined but not used [-Wunused-function] PyConverter_DoubleVector4Copy( ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MDAnalysis/lib/src/transformations/transformations.c:804:1: warning: ‘PyConverter_DoubleArrayOrNone’ defined but not used [-Wunused-function] PyConverter_DoubleArrayOrNone( ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MDAnalysis/lib/src/transformations/transformations.c:774:1: warning: ‘PyConverter_DoubleArray’ defined but not used [-Wunused-function] PyConverter_DoubleArray( ^~~~~~~~~~~~~~~~~~~~~~~ gcc -pthread -shared -B /home/ri-ialibay/software/miniconda/install/envs/test-gsd/compiler_compat -L/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib -Wl,-rpath=/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-aarch64-3.8/MDAnalysis/lib/src/transformations/transformations.o -lm -o build/lib.linux-aarch64-3.8/MDAnalysis/lib/_transformations.cpython-38-aarch64-linux-gnu.so building 'MDAnalysis.lib.formats.libmdaxdr' extension creating build/temp.linux-aarch64-3.8/MDAnalysis/lib/formats/src gcc -pthread -B /home/ri-ialibay/software/miniconda/install/envs/test-gsd/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/formats -I/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include -I/lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/formats/include -I/lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/formats -I/home/ri-ialibay/software/miniconda/install/envs/test-gsd/include/python3.8 -c MDAnalysis/lib/formats/libmdaxdr.c -o build/temp.linux-aarch64-3.8/MDAnalysis/lib/formats/libmdaxdr.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros cc1: warning: -fassociative-math disabled; other options take precedence In file included from /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:0, from /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/lib/formats/libmdaxdr.c:673: /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ In file included from MDAnalysis/lib/formats/libmdaxdr.c:679:0: MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- In file included from MDAnalysis/lib/formats/libmdaxdr.c:680:0: MDAnalysis/lib/formats/include/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- In file included from MDAnalysis/lib/formats/include/xdrfile_xtc.h:43:0, from MDAnalysis/lib/formats/libmdaxdr.c:680: MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- In file included from MDAnalysis/lib/formats/libmdaxdr.c:681:0: MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- gcc -pthread -B /home/ri-ialibay/software/miniconda/install/envs/test-gsd/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/formats -I/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include -I/lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/formats/include -I/lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/formats -I/home/ri-ialibay/software/miniconda/install/envs/test-gsd/include/python3.8 -c MDAnalysis/lib/formats/src/xdrfile.c -o build/temp.linux-aarch64-3.8/MDAnalysis/lib/formats/src/xdrfile.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros cc1: warning: -fassociative-math disabled; other options take precedence In file included from MDAnalysis/lib/formats/src/xdrfile.c:62:0: /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- MDAnalysis/lib/formats/src/xdrfile.c: In function ‘sizeofint’: MDAnalysis/lib/formats/src/xdrfile.c:501:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while (size >= num && num_of_bits < 32) ^~ MDAnalysis/lib/formats/src/xdrfile.c: In function ‘sizeofints’: MDAnalysis/lib/formats/src/xdrfile.c:547:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while (bytes[num_of_bytes] >= num) ^~ MDAnalysis/lib/formats/src/xdrfile.c: In function ‘encodeints’: MDAnalysis/lib/formats/src/xdrfile.c:656:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (num_of_bits >= num_of_bytes * 8) ^~ MDAnalysis/lib/formats/src/xdrfile.c:658:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (i = 0; i < num_of_bytes; i++) ^ MDAnalysis/lib/formats/src/xdrfile.c:666:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (i = 0; i < num_of_bytes-1; i++) ^ MDAnalysis/lib/formats/src/xdrfile.c: In function ‘decodebits’: MDAnalysis/lib/formats/src/xdrfile.c:706:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (lastbits < num_of_bits) ^ MDAnalysis/lib/formats/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: MDAnalysis/lib/formats/src/xdrfile.c:816:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(size3>xfp->buf1size) ^ MDAnalysis/lib/formats/src/xdrfile.c:868:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] maxidx = (LASTIDXxfp->buf1size) ^ MDAnalysis/lib/formats/src/xdrfile.c:1135:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while (smallidx < LASTIDX && magicints[smallidx] < mindiff) ^ MDAnalysis/lib/formats/src/xdrfile.c:1141:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] maxidx = (LASTIDXxfp->buf1size) ^ MDAnalysis/lib/formats/src/xdrfile.c:1368:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] maxidx = (LASTIDXxfp->buf1size) { ^ MDAnalysis/lib/formats/src/xdrfile.c:1619:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while (smallidx < LASTIDX && magicints[smallidx] < mindiff) { ^ MDAnalysis/lib/formats/src/xdrfile.c:1624:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] maxidx = (LASTIDX maxsize) ^ MDAnalysis/lib/formats/src/xdrfile.c:2335:15: note: ‘size’ was declared here unsigned int size; ^~~~ MDAnalysis/lib/formats/src/xdrfile.c: In function ‘xdrfile_write_string’: MDAnalysis/lib/formats/src/xdrfile.c:2361:5: warning: ‘size’ may be used uninitialized in this function [-Wmaybe-uninitialized] if (size > maxsize) ^ MDAnalysis/lib/formats/src/xdrfile.c:2335:15: note: ‘size’ was declared here unsigned int size; ^~~~ MDAnalysis/lib/formats/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: MDAnalysis/lib/formats/src/xdrfile.c:1157:21: warning: ‘prevcoord[2]’ may be used uninitialized in this function [-Wmaybe-uninitialized] abs(thiscoord[2] - prevcoord[2]) < larger) { ~~~~~~~~~~~~~^~~~~~~~~~~~~~ MDAnalysis/lib/formats/src/xdrfile.c:1156:21: warning: ‘prevcoord[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] abs(thiscoord[1] - prevcoord[1]) < larger && ~~~~~~~~~~~~~^~~~~~~~~~~~~~ MDAnalysis/lib/formats/src/xdrfile.c:1155:21: warning: ‘prevcoord[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized] abs(thiscoord[0] - prevcoord[0]) < larger && ~~~~~~~~~~~~~^~~~~~~~~~~~~~ MDAnalysis/lib/formats/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: MDAnalysis/lib/formats/src/xdrfile.c:1639:21: warning: ‘prevcoord[2]’ may be used uninitialized in this function [-Wmaybe-uninitialized] abs(thiscoord[2] - prevcoord[2]) < larger) { ~~~~~~~~~~~~~^~~~~~~~~~~~~~ MDAnalysis/lib/formats/src/xdrfile.c:1638:21: warning: ‘prevcoord[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] abs(thiscoord[1] - prevcoord[1]) < larger && ~~~~~~~~~~~~~^~~~~~~~~~~~~~ MDAnalysis/lib/formats/src/xdrfile.c:1637:21: warning: ‘prevcoord[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized] abs(thiscoord[0] - prevcoord[0]) < larger && ~~~~~~~~~~~~~^~~~~~~~~~~~~~ gcc -pthread -B /home/ri-ialibay/software/miniconda/install/envs/test-gsd/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/formats -I/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include -I/lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/formats/include -I/lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/formats -I/home/ri-ialibay/software/miniconda/install/envs/test-gsd/include/python3.8 -c MDAnalysis/lib/formats/src/xdrfile_xtc.c -o build/temp.linux-aarch64-3.8/MDAnalysis/lib/formats/src/xdrfile_xtc.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros cc1: warning: -fassociative-math disabled; other options take precedence In file included from MDAnalysis/lib/formats/src/xdrfile_xtc.c:30:0: /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within 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:31:0: /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/formats/include/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- In file included from /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/formats/include/xdrfile_xtc.h:43:0, from MDAnalysis/lib/formats/src/xdrfile_xtc.c:31: /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- gcc -pthread -B /home/ri-ialibay/software/miniconda/install/envs/test-gsd/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/formats -I/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include -I/lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/formats/include -I/lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/formats -I/home/ri-ialibay/software/miniconda/install/envs/test-gsd/include/python3.8 -c MDAnalysis/lib/formats/src/xdrfile_trr.c -o build/temp.linux-aarch64-3.8/MDAnalysis/lib/formats/src/xdrfile_trr.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros cc1: warning: -fassociative-math disabled; other options take precedence In file included from MDAnalysis/lib/formats/src/xdrfile_trr.c:38:0: /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within 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:39:0: /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- In file included from /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/formats/include/xdrfile_trr.h:42:0, from MDAnalysis/lib/formats/src/xdrfile_trr.c:39: /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- MDAnalysis/lib/formats/src/xdrfile_trr.c: In function ‘do_trnheader’: MDAnalysis/lib/formats/src/xdrfile_trr.c:78:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (slen != strlen(version) + 1) ^~ MDAnalysis/lib/formats/src/xdrfile_trr.c:86:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (xdrfile_write_string(version, xd) != (strlen(version) + 1)) ^~ MDAnalysis/lib/formats/src/xdrfile_trr.c: In function ‘write_trr’: MDAnalysis/lib/formats/src/xdrfile_trr.c:408:10: warning: ‘plcholder’ is used uninitialized in this function [-Wuninitialized] return do_trn(xd, 0, &step, &t, &lambda, box, &natoms, x, v, f, plcholder); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -pthread -B /home/ri-ialibay/software/miniconda/install/envs/test-gsd/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/formats -I/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include -I/lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/formats/include -I/lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/formats -I/home/ri-ialibay/software/miniconda/install/envs/test-gsd/include/python3.8 -c MDAnalysis/lib/formats/src/trr_seek.c -o build/temp.linux-aarch64-3.8/MDAnalysis/lib/formats/src/trr_seek.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros cc1: warning: -fassociative-math disabled; other options take precedence In file included from MDAnalysis/lib/formats/src/trr_seek.c:30:0: /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within 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:31:0: /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- In file included from /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/formats/include/xdrfile_trr.h:42:0, from MDAnalysis/lib/formats/src/trr_seek.c:31: /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- MDAnalysis/lib/formats/src/trr_seek.c: In function ‘read_trr_n_frames’: MDAnalysis/lib/formats/src/trr_seek.c:39:27: warning: unused variable ‘totalframebytes’ [-Wunused-variable] int result, framebytes, totalframebytes; ^~~~~~~~~~~~~~~ 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; ^~~~ gcc -pthread -B /home/ri-ialibay/software/miniconda/install/envs/test-gsd/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/formats -I/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include -I/lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/formats/include -I/lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/formats -I/home/ri-ialibay/software/miniconda/install/envs/test-gsd/include/python3.8 -c MDAnalysis/lib/formats/src/xtc_seek.c -o build/temp.linux-aarch64-3.8/MDAnalysis/lib/formats/src/xtc_seek.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros cc1: warning: -fassociative-math disabled; other options take precedence In file included from MDAnalysis/lib/formats/src/xtc_seek.c:25:0: /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within 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:26:0: /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/formats/include/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- In file included from /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/formats/include/xdrfile_xtc.h:43:0, from MDAnalysis/lib/formats/src/xtc_seek.c:26: /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- gcc -pthread -shared -B /home/ri-ialibay/software/miniconda/install/envs/test-gsd/compiler_compat -L/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib -Wl,-rpath=/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-aarch64-3.8/MDAnalysis/lib/formats/libmdaxdr.o build/temp.linux-aarch64-3.8/MDAnalysis/lib/formats/src/xdrfile.o build/temp.linux-aarch64-3.8/MDAnalysis/lib/formats/src/xdrfile_xtc.o build/temp.linux-aarch64-3.8/MDAnalysis/lib/formats/src/xdrfile_trr.o build/temp.linux-aarch64-3.8/MDAnalysis/lib/formats/src/trr_seek.o build/temp.linux-aarch64-3.8/MDAnalysis/lib/formats/src/xtc_seek.o -o build/lib.linux-aarch64-3.8/MDAnalysis/lib/formats/libmdaxdr.cpython-38-aarch64-linux-gnu.so building 'MDAnalysis.lib.formats.cython_util' extension gcc -pthread -B /home/ri-ialibay/software/miniconda/install/envs/test-gsd/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include -I/home/ri-ialibay/software/miniconda/install/envs/test-gsd/include/python3.8 -c MDAnalysis/lib/formats/cython_util.c -o build/temp.linux-aarch64-3.8/MDAnalysis/lib/formats/cython_util.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros cc1: warning: -fassociative-math disabled; other options take precedence In file included from /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:0, from /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/lib/formats/cython_util.c:646: /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ gcc -pthread -shared -B /home/ri-ialibay/software/miniconda/install/envs/test-gsd/compiler_compat -L/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib -Wl,-rpath=/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-aarch64-3.8/MDAnalysis/lib/formats/cython_util.o -o build/lib.linux-aarch64-3.8/MDAnalysis/lib/formats/cython_util.cpython-38-aarch64-linux-gnu.so building 'MDAnalysis.analysis.encore.cutils' extension creating build/temp.linux-aarch64-3.8/MDAnalysis/analysis creating build/temp.linux-aarch64-3.8/MDAnalysis/analysis/encore gcc -pthread -B /home/ri-ialibay/software/miniconda/install/envs/test-gsd/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include -I/home/ri-ialibay/software/miniconda/install/envs/test-gsd/include/python3.8 -c MDAnalysis/analysis/encore/cutils.c -o build/temp.linux-aarch64-3.8/MDAnalysis/analysis/encore/cutils.o -std=c99 -ffast-math -funroll-loops -fsigned-zeros -O1 cc1: warning: -fassociative-math disabled; other options take precedence In file included from /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:0, from /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/analysis/encore/cutils.c:646: /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ gcc -pthread -shared -B /home/ri-ialibay/software/miniconda/install/envs/test-gsd/compiler_compat -L/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib -Wl,-rpath=/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-aarch64-3.8/MDAnalysis/analysis/encore/cutils.o -o build/lib.linux-aarch64-3.8/MDAnalysis/analysis/encore/cutils.cpython-38-aarch64-linux-gnu.so building 'MDAnalysis.analysis.encore.clustering.affinityprop' extension creating build/temp.linux-aarch64-3.8/MDAnalysis/analysis/encore/clustering creating build/temp.linux-aarch64-3.8/MDAnalysis/analysis/encore/clustering/src gcc -pthread -B /home/ri-ialibay/software/miniconda/install/envs/test-gsd/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include -I/lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/analysis/encore/clustering/include -I/home/ri-ialibay/software/miniconda/install/envs/test-gsd/include/python3.8 -c MDAnalysis/analysis/encore/clustering/affinityprop.c -o build/temp.linux-aarch64-3.8/MDAnalysis/analysis/encore/clustering/affinityprop.o -std=c99 -ffast-math -funroll-loops -fsigned-zeros -O1 cc1: warning: -fassociative-math disabled; other options take precedence In file included from /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:0, from /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/analysis/encore/clustering/affinityprop.c:652: /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ gcc -pthread -B /home/ri-ialibay/software/miniconda/install/envs/test-gsd/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include -I/lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/analysis/encore/clustering/include -I/home/ri-ialibay/software/miniconda/install/envs/test-gsd/include/python3.8 -c MDAnalysis/analysis/encore/clustering/src/ap.c -o build/temp.linux-aarch64-3.8/MDAnalysis/analysis/encore/clustering/src/ap.o -std=c99 -ffast-math -funroll-loops -fsigned-zeros -O1 cc1: warning: -fassociative-math disabled; other options take precedence gcc -pthread -shared -B /home/ri-ialibay/software/miniconda/install/envs/test-gsd/compiler_compat -L/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib -Wl,-rpath=/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-aarch64-3.8/MDAnalysis/analysis/encore/clustering/affinityprop.o build/temp.linux-aarch64-3.8/MDAnalysis/analysis/encore/clustering/src/ap.o -lm -o build/lib.linux-aarch64-3.8/MDAnalysis/analysis/encore/clustering/affinityprop.cpython-38-aarch64-linux-gnu.so building 'MDAnalysis.analysis.encore.dimensionality_reduction.stochasticproxembed' extension creating build/temp.linux-aarch64-3.8/MDAnalysis/analysis/encore/dimensionality_reduction creating build/temp.linux-aarch64-3.8/MDAnalysis/analysis/encore/dimensionality_reduction/src gcc -pthread -B /home/ri-ialibay/software/miniconda/install/envs/test-gsd/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include -I/lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/analysis/encore/dimensionality_reduction/include -I/home/ri-ialibay/software/miniconda/install/envs/test-gsd/include/python3.8 -c MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -o build/temp.linux-aarch64-3.8/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.o -std=c99 -ffast-math -funroll-loops -fsigned-zeros -O1 cc1: warning: -fassociative-math disabled; other options take precedence In file included from /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:0, from /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c:652: /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ gcc -pthread -B /home/ri-ialibay/software/miniconda/install/envs/test-gsd/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include -I/lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/analysis/encore/dimensionality_reduction/include -I/home/ri-ialibay/software/miniconda/install/envs/test-gsd/include/python3.8 -c MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -o build/temp.linux-aarch64-3.8/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.o -std=c99 -ffast-math -funroll-loops -fsigned-zeros -O1 cc1: warning: -fassociative-math disabled; other options take precedence gcc -pthread -shared -B /home/ri-ialibay/software/miniconda/install/envs/test-gsd/compiler_compat -L/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib -Wl,-rpath=/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-aarch64-3.8/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.o build/temp.linux-aarch64-3.8/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.o -lm -o build/lib.linux-aarch64-3.8/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-38-aarch64-linux-gnu.so building 'MDAnalysis.lib._cutil' extension gcc -pthread -B /home/ri-ialibay/software/miniconda/install/envs/test-gsd/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include -I/lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/include -I/home/ri-ialibay/software/miniconda/install/envs/test-gsd/include/python3.8 -c MDAnalysis/lib/_cutil.cpp -o build/temp.linux-aarch64-3.8/MDAnalysis/lib/_cutil.o -ffast-math -O3 -funroll-loops -fsigned-zeros -std=c++11 cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ cc1plus: warning: -fassociative-math disabled; other options take precedence In file included from /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:0, from /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/lib/_cutil.cpp:666: /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ In file included from MDAnalysis/lib/_cutil.cpp:691:0: /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/include/calc_distances.h:854:13: warning: ‘void _calc_dihedral_triclinic(float (*)[3], float (*)[3], float (*)[3], float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] static void _calc_dihedral_triclinic(coordinate* atom1, coordinate* atom2, ^~~~~~~~~~~~~~~~~~~~~~~~ /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/include/calc_distances.h:818:13: warning: ‘void _calc_dihedral_ortho(float (*)[3], float (*)[3], float (*)[3], float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] static void _calc_dihedral_ortho(coordinate* atom1, coordinate* atom2, ^~~~~~~~~~~~~~~~~~~~ /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/include/calc_distances.h:790:13: warning: ‘void _calc_dihedral(float (*)[3], float (*)[3], float (*)[3], float (*)[3], int, double*)’ defined but not used [-Wunused-function] static void _calc_dihedral(coordinate* atom1, coordinate* atom2, ^~~~~~~~~~~~~~ /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/include/calc_distances.h:713:13: warning: ‘void _calc_angle_triclinic(float (*)[3], float (*)[3], float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] static void _calc_angle_triclinic(coordinate* atom1, coordinate* atom2, ^~~~~~~~~~~~~~~~~~~~~ /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/include/calc_distances.h:670:13: warning: ‘void _calc_angle_ortho(float (*)[3], float (*)[3], float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] static void _calc_angle_ortho(coordinate* atom1, coordinate* atom2, ^~~~~~~~~~~~~~~~~ /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/include/calc_distances.h:639:13: warning: ‘void _calc_angle(float (*)[3], float (*)[3], float (*)[3], int, double*)’ defined but not used [-Wunused-function] static void _calc_angle(coordinate* atom1, coordinate* atom2, ^~~~~~~~~~~ /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/include/calc_distances.h:614:13: warning: ‘void _calc_bond_distance_triclinic(float (*)[3], float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] static void _calc_bond_distance_triclinic(coordinate* atom1, coordinate* atom2, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/include/calc_distances.h:589:13: warning: ‘void _calc_bond_distance_ortho(float (*)[3], float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] static void _calc_bond_distance_ortho(coordinate* atom1, coordinate* atom2, ^~~~~~~~~~~~~~~~~~~~~~~~~ /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/include/calc_distances.h:570:13: warning: ‘void _calc_bond_distance(float (*)[3], float (*)[3], int, double*)’ defined but not used [-Wunused-function] static void _calc_bond_distance(coordinate* atom1, coordinate* atom2, ^~~~~~~~~~~~~~~~~~~ /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/include/calc_distances.h:515:13: warning: ‘void _calc_self_distance_array_triclinic(float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] static void _calc_self_distance_array_triclinic(coordinate* ref, int numref, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/include/calc_distances.h:482:13: warning: ‘void _calc_self_distance_array_ortho(float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] static void _calc_self_distance_array_ortho(coordinate* ref, int numref, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/include/calc_distances.h:455:13: warning: ‘void _calc_self_distance_array(float (*)[3], int, double*)’ defined but not used [-Wunused-function] static void _calc_self_distance_array(coordinate* ref, int numref, ^~~~~~~~~~~~~~~~~~~~~~~~~ /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/include/calc_distances.h:428:13: warning: ‘void _calc_distance_array_triclinic(float (*)[3], int, float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] static void _calc_distance_array_triclinic(coordinate* ref, int numref, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/include/calc_distances.h:401:13: warning: ‘void _calc_distance_array_ortho(float (*)[3], int, float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] static void _calc_distance_array_ortho(coordinate* ref, int numref, coordinate* conf, ^~~~~~~~~~~~~~~~~~~~~~~~~~ /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/include/calc_distances.h:380:13: warning: ‘void _calc_distance_array(float (*)[3], int, float (*)[3], int, double*)’ defined but not used [-Wunused-function] static void _calc_distance_array(coordinate* ref, int numref, coordinate* conf, ^~~~~~~~~~~~~~~~~~~~ /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/include/calc_distances.h:111:13: warning: ‘void _ortho_pbc(float (*)[3], int, float*)’ defined but not used [-Wunused-function] static void _ortho_pbc(coordinate* coords, int numcoords, float* box) ^~~~~~~~~~ g++ -pthread -shared -B /home/ri-ialibay/software/miniconda/install/envs/test-gsd/compiler_compat -L/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib -Wl,-rpath=/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-aarch64-3.8/MDAnalysis/lib/_cutil.o -lm -o build/lib.linux-aarch64-3.8/MDAnalysis/lib/_cutil.cpython-38-aarch64-linux-gnu.so building 'MDAnalysis.lib._augment' extension gcc -pthread -B /home/ri-ialibay/software/miniconda/install/envs/test-gsd/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include -I/home/ri-ialibay/software/miniconda/install/envs/test-gsd/include/python3.8 -c MDAnalysis/lib/_augment.cpp -o build/temp.linux-aarch64-3.8/MDAnalysis/lib/_augment.o -ffast-math -O3 -funroll-loops -fsigned-zeros -std=c++11 cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ cc1plus: warning: -fassociative-math disabled; other options take precedence In file included from /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:0, from /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4, from MDAnalysis/lib/_augment.cpp:661: /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ g++ -pthread -shared -B /home/ri-ialibay/software/miniconda/install/envs/test-gsd/compiler_compat -L/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib -Wl,-rpath=/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-aarch64-3.8/MDAnalysis/lib/_augment.o -o build/lib.linux-aarch64-3.8/MDAnalysis/lib/_augment.cpython-38-aarch64-linux-gnu.so building 'MDAnalysis.lib.nsgrid' extension gcc -pthread -B /home/ri-ialibay/software/miniconda/install/envs/test-gsd/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/core/include -I/lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/include -I/home/ri-ialibay/software/miniconda/install/envs/test-gsd/include/python3.8 -c MDAnalysis/lib/nsgrid.cpp -o build/temp.linux-aarch64-3.8/MDAnalysis/lib/nsgrid.o -ffast-math -O3 -funroll-loops -fsigned-zeros -std=c++11 cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ cc1plus: warning: -fassociative-math disabled; other options take precedence In file included from MDAnalysis/lib/nsgrid.cpp:665:0: /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/include/calc_distances.h:854:13: warning: ‘void _calc_dihedral_triclinic(float (*)[3], float (*)[3], float (*)[3], float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] static void _calc_dihedral_triclinic(coordinate* atom1, coordinate* atom2, ^~~~~~~~~~~~~~~~~~~~~~~~ /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/include/calc_distances.h:818:13: warning: ‘void _calc_dihedral_ortho(float (*)[3], float (*)[3], float (*)[3], float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] static void _calc_dihedral_ortho(coordinate* atom1, coordinate* atom2, ^~~~~~~~~~~~~~~~~~~~ /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/include/calc_distances.h:790:13: warning: ‘void _calc_dihedral(float (*)[3], float (*)[3], float (*)[3], float (*)[3], int, double*)’ defined but not used [-Wunused-function] static void _calc_dihedral(coordinate* atom1, coordinate* atom2, ^~~~~~~~~~~~~~ /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/include/calc_distances.h:713:13: warning: ‘void _calc_angle_triclinic(float (*)[3], float (*)[3], float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] static void _calc_angle_triclinic(coordinate* atom1, coordinate* atom2, ^~~~~~~~~~~~~~~~~~~~~ /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/include/calc_distances.h:670:13: warning: ‘void _calc_angle_ortho(float (*)[3], float (*)[3], float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] static void _calc_angle_ortho(coordinate* atom1, coordinate* atom2, ^~~~~~~~~~~~~~~~~ /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/include/calc_distances.h:639:13: warning: ‘void _calc_angle(float (*)[3], float (*)[3], float (*)[3], int, double*)’ defined but not used [-Wunused-function] static void _calc_angle(coordinate* atom1, coordinate* atom2, ^~~~~~~~~~~ /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/include/calc_distances.h:614:13: warning: ‘void _calc_bond_distance_triclinic(float (*)[3], float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] static void _calc_bond_distance_triclinic(coordinate* atom1, coordinate* atom2, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/include/calc_distances.h:589:13: warning: ‘void _calc_bond_distance_ortho(float (*)[3], float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] static void _calc_bond_distance_ortho(coordinate* atom1, coordinate* atom2, ^~~~~~~~~~~~~~~~~~~~~~~~~ /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/include/calc_distances.h:570:13: warning: ‘void _calc_bond_distance(float (*)[3], float (*)[3], int, double*)’ defined but not used [-Wunused-function] static void _calc_bond_distance(coordinate* atom1, coordinate* atom2, ^~~~~~~~~~~~~~~~~~~ /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/include/calc_distances.h:515:13: warning: ‘void _calc_self_distance_array_triclinic(float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] static void _calc_self_distance_array_triclinic(coordinate* ref, int numref, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/include/calc_distances.h:482:13: warning: ‘void _calc_self_distance_array_ortho(float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] static void _calc_self_distance_array_ortho(coordinate* ref, int numref, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/include/calc_distances.h:455:13: warning: ‘void _calc_self_distance_array(float (*)[3], int, double*)’ defined but not used [-Wunused-function] static void _calc_self_distance_array(coordinate* ref, int numref, ^~~~~~~~~~~~~~~~~~~~~~~~~ /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/include/calc_distances.h:428:13: warning: ‘void _calc_distance_array_triclinic(float (*)[3], int, float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] static void _calc_distance_array_triclinic(coordinate* ref, int numref, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/include/calc_distances.h:401:13: warning: ‘void _calc_distance_array_ortho(float (*)[3], int, float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] static void _calc_distance_array_ortho(coordinate* ref, int numref, coordinate* conf, ^~~~~~~~~~~~~~~~~~~~~~~~~~ /lustre/home/ri-ialibay/test-mda/mdanalysis/package/MDAnalysis/lib/include/calc_distances.h:380:13: warning: ‘void _calc_distance_array(float (*)[3], int, float (*)[3], int, double*)’ defined but not used [-Wunused-function] static void _calc_distance_array(coordinate* ref, int numref, coordinate* conf, ^~~~~~~~~~~~~~~~~~~~ g++ -pthread -shared -B /home/ri-ialibay/software/miniconda/install/envs/test-gsd/compiler_compat -L/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib -Wl,-rpath=/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-aarch64-3.8/MDAnalysis/lib/nsgrid.o -o build/lib.linux-aarch64-3.8/MDAnalysis/lib/nsgrid.cpython-38-aarch64-linux-gnu.so creating build/bdist.linux-aarch64 creating build/bdist.linux-aarch64/egg creating build/bdist.linux-aarch64/egg/MDAnalysis creating build/bdist.linux-aarch64/egg/MDAnalysis/auxiliary copying build/lib.linux-aarch64-3.8/MDAnalysis/auxiliary/core.py -> build/bdist.linux-aarch64/egg/MDAnalysis/auxiliary copying build/lib.linux-aarch64-3.8/MDAnalysis/auxiliary/XVG.py -> build/bdist.linux-aarch64/egg/MDAnalysis/auxiliary copying build/lib.linux-aarch64-3.8/MDAnalysis/auxiliary/__init__.py -> build/bdist.linux-aarch64/egg/MDAnalysis/auxiliary copying build/lib.linux-aarch64-3.8/MDAnalysis/auxiliary/base.py -> build/bdist.linux-aarch64/egg/MDAnalysis/auxiliary creating build/bdist.linux-aarch64/egg/MDAnalysis/coordinates copying build/lib.linux-aarch64-3.8/MDAnalysis/coordinates/null.py -> build/bdist.linux-aarch64/egg/MDAnalysis/coordinates copying build/lib.linux-aarch64-3.8/MDAnalysis/coordinates/DMS.py -> build/bdist.linux-aarch64/egg/MDAnalysis/coordinates copying build/lib.linux-aarch64-3.8/MDAnalysis/coordinates/TRZ.py -> build/bdist.linux-aarch64/egg/MDAnalysis/coordinates copying build/lib.linux-aarch64-3.8/MDAnalysis/coordinates/chain.py -> build/bdist.linux-aarch64/egg/MDAnalysis/coordinates copying build/lib.linux-aarch64-3.8/MDAnalysis/coordinates/GMS.py -> build/bdist.linux-aarch64/egg/MDAnalysis/coordinates copying build/lib.linux-aarch64-3.8/MDAnalysis/coordinates/TXYZ.py -> build/bdist.linux-aarch64/egg/MDAnalysis/coordinates copying build/lib.linux-aarch64-3.8/MDAnalysis/coordinates/PQR.py -> build/bdist.linux-aarch64/egg/MDAnalysis/coordinates copying build/lib.linux-aarch64-3.8/MDAnalysis/coordinates/FHIAIMS.py -> build/bdist.linux-aarch64/egg/MDAnalysis/coordinates copying build/lib.linux-aarch64-3.8/MDAnalysis/coordinates/ParmEd.py -> build/bdist.linux-aarch64/egg/MDAnalysis/coordinates copying build/lib.linux-aarch64-3.8/MDAnalysis/coordinates/memory.py -> build/bdist.linux-aarch64/egg/MDAnalysis/coordinates copying build/lib.linux-aarch64-3.8/MDAnalysis/coordinates/GSD.py -> build/bdist.linux-aarch64/egg/MDAnalysis/coordinates copying build/lib.linux-aarch64-3.8/MDAnalysis/coordinates/H5MD.py -> build/bdist.linux-aarch64/egg/MDAnalysis/coordinates copying build/lib.linux-aarch64-3.8/MDAnalysis/coordinates/CRD.py -> build/bdist.linux-aarch64/egg/MDAnalysis/coordinates copying build/lib.linux-aarch64-3.8/MDAnalysis/coordinates/DCD.py -> build/bdist.linux-aarch64/egg/MDAnalysis/coordinates copying build/lib.linux-aarch64-3.8/MDAnalysis/coordinates/INPCRD.py -> build/bdist.linux-aarch64/egg/MDAnalysis/coordinates copying build/lib.linux-aarch64-3.8/MDAnalysis/coordinates/core.py -> build/bdist.linux-aarch64/egg/MDAnalysis/coordinates copying build/lib.linux-aarch64-3.8/MDAnalysis/coordinates/XTC.py -> build/bdist.linux-aarch64/egg/MDAnalysis/coordinates copying build/lib.linux-aarch64-3.8/MDAnalysis/coordinates/GRO.py -> build/bdist.linux-aarch64/egg/MDAnalysis/coordinates copying build/lib.linux-aarch64-3.8/MDAnalysis/coordinates/XYZ.py -> build/bdist.linux-aarch64/egg/MDAnalysis/coordinates copying build/lib.linux-aarch64-3.8/MDAnalysis/coordinates/TRR.py -> build/bdist.linux-aarch64/egg/MDAnalysis/coordinates copying build/lib.linux-aarch64-3.8/MDAnalysis/coordinates/MOL2.py -> build/bdist.linux-aarch64/egg/MDAnalysis/coordinates copying build/lib.linux-aarch64-3.8/MDAnalysis/coordinates/TRJ.py -> build/bdist.linux-aarch64/egg/MDAnalysis/coordinates copying build/lib.linux-aarch64-3.8/MDAnalysis/coordinates/chemfiles.py -> build/bdist.linux-aarch64/egg/MDAnalysis/coordinates copying build/lib.linux-aarch64-3.8/MDAnalysis/coordinates/__init__.py -> build/bdist.linux-aarch64/egg/MDAnalysis/coordinates copying build/lib.linux-aarch64-3.8/MDAnalysis/coordinates/NAMDBIN.py -> build/bdist.linux-aarch64/egg/MDAnalysis/coordinates copying build/lib.linux-aarch64-3.8/MDAnalysis/coordinates/XDR.py -> build/bdist.linux-aarch64/egg/MDAnalysis/coordinates copying build/lib.linux-aarch64-3.8/MDAnalysis/coordinates/PDB.py -> build/bdist.linux-aarch64/egg/MDAnalysis/coordinates copying build/lib.linux-aarch64-3.8/MDAnalysis/coordinates/PDBQT.py -> build/bdist.linux-aarch64/egg/MDAnalysis/coordinates copying build/lib.linux-aarch64-3.8/MDAnalysis/coordinates/LAMMPS.py -> build/bdist.linux-aarch64/egg/MDAnalysis/coordinates copying build/lib.linux-aarch64-3.8/MDAnalysis/coordinates/MMTF.py -> build/bdist.linux-aarch64/egg/MDAnalysis/coordinates copying build/lib.linux-aarch64-3.8/MDAnalysis/coordinates/base.py -> build/bdist.linux-aarch64/egg/MDAnalysis/coordinates copying build/lib.linux-aarch64-3.8/MDAnalysis/coordinates/DLPoly.py -> build/bdist.linux-aarch64/egg/MDAnalysis/coordinates creating build/bdist.linux-aarch64/egg/MDAnalysis/core copying build/lib.linux-aarch64-3.8/MDAnalysis/core/topologyobjects.py -> build/bdist.linux-aarch64/egg/MDAnalysis/core copying build/lib.linux-aarch64-3.8/MDAnalysis/core/accessors.py -> build/bdist.linux-aarch64/egg/MDAnalysis/core copying build/lib.linux-aarch64-3.8/MDAnalysis/core/universe.py -> build/bdist.linux-aarch64/egg/MDAnalysis/core copying build/lib.linux-aarch64-3.8/MDAnalysis/core/topology.py -> build/bdist.linux-aarch64/egg/MDAnalysis/core copying build/lib.linux-aarch64-3.8/MDAnalysis/core/__init__.py -> build/bdist.linux-aarch64/egg/MDAnalysis/core copying build/lib.linux-aarch64-3.8/MDAnalysis/core/groups.py -> build/bdist.linux-aarch64/egg/MDAnalysis/core copying build/lib.linux-aarch64-3.8/MDAnalysis/core/selection.py -> build/bdist.linux-aarch64/egg/MDAnalysis/core copying build/lib.linux-aarch64-3.8/MDAnalysis/core/_get_readers.py -> build/bdist.linux-aarch64/egg/MDAnalysis/core copying build/lib.linux-aarch64-3.8/MDAnalysis/core/topologyattrs.py -> build/bdist.linux-aarch64/egg/MDAnalysis/core copying build/lib.linux-aarch64-3.8/MDAnalysis/authors.py -> build/bdist.linux-aarch64/egg/MDAnalysis creating build/bdist.linux-aarch64/egg/MDAnalysis/tests copying build/lib.linux-aarch64-3.8/MDAnalysis/tests/datafiles.py -> build/bdist.linux-aarch64/egg/MDAnalysis/tests copying build/lib.linux-aarch64-3.8/MDAnalysis/tests/__init__.py -> build/bdist.linux-aarch64/egg/MDAnalysis/tests creating build/bdist.linux-aarch64/egg/MDAnalysis/topology copying build/lib.linux-aarch64-3.8/MDAnalysis/topology/XYZParser.py -> build/bdist.linux-aarch64/egg/MDAnalysis/topology copying build/lib.linux-aarch64-3.8/MDAnalysis/topology/LAMMPSParser.py -> build/bdist.linux-aarch64/egg/MDAnalysis/topology copying build/lib.linux-aarch64-3.8/MDAnalysis/topology/MinimalParser.py -> build/bdist.linux-aarch64/egg/MDAnalysis/topology copying build/lib.linux-aarch64-3.8/MDAnalysis/topology/HoomdXMLParser.py -> build/bdist.linux-aarch64/egg/MDAnalysis/topology copying build/lib.linux-aarch64-3.8/MDAnalysis/topology/GMSParser.py -> build/bdist.linux-aarch64/egg/MDAnalysis/topology copying build/lib.linux-aarch64-3.8/MDAnalysis/topology/PDBParser.py -> build/bdist.linux-aarch64/egg/MDAnalysis/topology copying build/lib.linux-aarch64-3.8/MDAnalysis/topology/core.py -> build/bdist.linux-aarch64/egg/MDAnalysis/topology copying build/lib.linux-aarch64-3.8/MDAnalysis/topology/GROParser.py -> build/bdist.linux-aarch64/egg/MDAnalysis/topology copying build/lib.linux-aarch64-3.8/MDAnalysis/topology/DMSParser.py -> build/bdist.linux-aarch64/egg/MDAnalysis/topology copying build/lib.linux-aarch64-3.8/MDAnalysis/topology/ITPParser.py -> build/bdist.linux-aarch64/egg/MDAnalysis/topology copying build/lib.linux-aarch64-3.8/MDAnalysis/topology/FHIAIMSParser.py -> build/bdist.linux-aarch64/egg/MDAnalysis/topology copying build/lib.linux-aarch64-3.8/MDAnalysis/topology/__init__.py -> build/bdist.linux-aarch64/egg/MDAnalysis/topology copying build/lib.linux-aarch64-3.8/MDAnalysis/topology/GSDParser.py -> build/bdist.linux-aarch64/egg/MDAnalysis/topology copying build/lib.linux-aarch64-3.8/MDAnalysis/topology/guessers.py -> build/bdist.linux-aarch64/egg/MDAnalysis/topology copying build/lib.linux-aarch64-3.8/MDAnalysis/topology/TXYZParser.py -> build/bdist.linux-aarch64/egg/MDAnalysis/topology copying build/lib.linux-aarch64-3.8/MDAnalysis/topology/PQRParser.py -> build/bdist.linux-aarch64/egg/MDAnalysis/topology copying build/lib.linux-aarch64-3.8/MDAnalysis/topology/ParmEdParser.py -> build/bdist.linux-aarch64/egg/MDAnalysis/topology copying build/lib.linux-aarch64-3.8/MDAnalysis/topology/CRDParser.py -> build/bdist.linux-aarch64/egg/MDAnalysis/topology creating build/bdist.linux-aarch64/egg/MDAnalysis/topology/tpr copying build/lib.linux-aarch64-3.8/MDAnalysis/topology/tpr/obj.py -> build/bdist.linux-aarch64/egg/MDAnalysis/topology/tpr copying build/lib.linux-aarch64-3.8/MDAnalysis/topology/tpr/utils.py -> build/bdist.linux-aarch64/egg/MDAnalysis/topology/tpr copying build/lib.linux-aarch64-3.8/MDAnalysis/topology/tpr/__init__.py -> build/bdist.linux-aarch64/egg/MDAnalysis/topology/tpr copying build/lib.linux-aarch64-3.8/MDAnalysis/topology/tpr/setting.py -> build/bdist.linux-aarch64/egg/MDAnalysis/topology/tpr copying build/lib.linux-aarch64-3.8/MDAnalysis/topology/MOL2Parser.py -> build/bdist.linux-aarch64/egg/MDAnalysis/topology copying build/lib.linux-aarch64-3.8/MDAnalysis/topology/ExtendedPDBParser.py -> build/bdist.linux-aarch64/egg/MDAnalysis/topology copying build/lib.linux-aarch64-3.8/MDAnalysis/topology/MMTFParser.py -> build/bdist.linux-aarch64/egg/MDAnalysis/topology copying build/lib.linux-aarch64-3.8/MDAnalysis/topology/PSFParser.py -> build/bdist.linux-aarch64/egg/MDAnalysis/topology copying build/lib.linux-aarch64-3.8/MDAnalysis/topology/base.py -> build/bdist.linux-aarch64/egg/MDAnalysis/topology copying build/lib.linux-aarch64-3.8/MDAnalysis/topology/tables.py -> build/bdist.linux-aarch64/egg/MDAnalysis/topology copying build/lib.linux-aarch64-3.8/MDAnalysis/topology/PDBQTParser.py -> build/bdist.linux-aarch64/egg/MDAnalysis/topology copying build/lib.linux-aarch64-3.8/MDAnalysis/topology/TOPParser.py -> build/bdist.linux-aarch64/egg/MDAnalysis/topology copying build/lib.linux-aarch64-3.8/MDAnalysis/topology/TPRParser.py -> build/bdist.linux-aarch64/egg/MDAnalysis/topology copying build/lib.linux-aarch64-3.8/MDAnalysis/topology/DLPolyParser.py -> build/bdist.linux-aarch64/egg/MDAnalysis/topology creating build/bdist.linux-aarch64/egg/MDAnalysis/selections copying build/lib.linux-aarch64-3.8/MDAnalysis/selections/pymol.py -> build/bdist.linux-aarch64/egg/MDAnalysis/selections copying build/lib.linux-aarch64-3.8/MDAnalysis/selections/charmm.py -> build/bdist.linux-aarch64/egg/MDAnalysis/selections copying build/lib.linux-aarch64-3.8/MDAnalysis/selections/jmol.py -> build/bdist.linux-aarch64/egg/MDAnalysis/selections copying build/lib.linux-aarch64-3.8/MDAnalysis/selections/vmd.py -> build/bdist.linux-aarch64/egg/MDAnalysis/selections copying build/lib.linux-aarch64-3.8/MDAnalysis/selections/__init__.py -> build/bdist.linux-aarch64/egg/MDAnalysis/selections copying build/lib.linux-aarch64-3.8/MDAnalysis/selections/base.py -> build/bdist.linux-aarch64/egg/MDAnalysis/selections copying build/lib.linux-aarch64-3.8/MDAnalysis/selections/gromacs.py -> build/bdist.linux-aarch64/egg/MDAnalysis/selections copying build/lib.linux-aarch64-3.8/MDAnalysis/version.py -> build/bdist.linux-aarch64/egg/MDAnalysis copying build/lib.linux-aarch64-3.8/MDAnalysis/due.py -> build/bdist.linux-aarch64/egg/MDAnalysis copying build/lib.linux-aarch64-3.8/MDAnalysis/__init__.py -> build/bdist.linux-aarch64/egg/MDAnalysis creating build/bdist.linux-aarch64/egg/MDAnalysis/transformations copying build/lib.linux-aarch64-3.8/MDAnalysis/transformations/wrap.py -> build/bdist.linux-aarch64/egg/MDAnalysis/transformations copying build/lib.linux-aarch64-3.8/MDAnalysis/transformations/__init__.py -> build/bdist.linux-aarch64/egg/MDAnalysis/transformations copying build/lib.linux-aarch64-3.8/MDAnalysis/transformations/boxdimensions.py -> build/bdist.linux-aarch64/egg/MDAnalysis/transformations copying build/lib.linux-aarch64-3.8/MDAnalysis/transformations/positionaveraging.py -> build/bdist.linux-aarch64/egg/MDAnalysis/transformations copying build/lib.linux-aarch64-3.8/MDAnalysis/transformations/translate.py -> build/bdist.linux-aarch64/egg/MDAnalysis/transformations copying build/lib.linux-aarch64-3.8/MDAnalysis/transformations/fit.py -> build/bdist.linux-aarch64/egg/MDAnalysis/transformations copying build/lib.linux-aarch64-3.8/MDAnalysis/transformations/rotate.py -> build/bdist.linux-aarch64/egg/MDAnalysis/transformations copying build/lib.linux-aarch64-3.8/MDAnalysis/transformations/base.py -> build/bdist.linux-aarch64/egg/MDAnalysis/transformations copying build/lib.linux-aarch64-3.8/MDAnalysis/exceptions.py -> build/bdist.linux-aarch64/egg/MDAnalysis creating build/bdist.linux-aarch64/egg/MDAnalysis/lib copying build/lib.linux-aarch64-3.8/MDAnalysis/lib/distances.py -> build/bdist.linux-aarch64/egg/MDAnalysis/lib copying build/lib.linux-aarch64-3.8/MDAnalysis/lib/qcprot.cpython-38-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/egg/MDAnalysis/lib copying build/lib.linux-aarch64-3.8/MDAnalysis/lib/_augment.cpython-38-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/egg/MDAnalysis/lib creating build/bdist.linux-aarch64/egg/MDAnalysis/lib/formats copying build/lib.linux-aarch64-3.8/MDAnalysis/lib/formats/__init__.py -> build/bdist.linux-aarch64/egg/MDAnalysis/lib/formats copying build/lib.linux-aarch64-3.8/MDAnalysis/lib/formats/libmdaxdr.cpython-38-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/egg/MDAnalysis/lib/formats copying build/lib.linux-aarch64-3.8/MDAnalysis/lib/formats/libdcd.cpython-38-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/egg/MDAnalysis/lib/formats copying build/lib.linux-aarch64-3.8/MDAnalysis/lib/formats/cython_util.cpython-38-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/egg/MDAnalysis/lib/formats copying build/lib.linux-aarch64-3.8/MDAnalysis/lib/NeighborSearch.py -> build/bdist.linux-aarch64/egg/MDAnalysis/lib copying build/lib.linux-aarch64-3.8/MDAnalysis/lib/log.py -> build/bdist.linux-aarch64/egg/MDAnalysis/lib copying build/lib.linux-aarch64-3.8/MDAnalysis/lib/c_distances.cpython-38-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/egg/MDAnalysis/lib copying build/lib.linux-aarch64-3.8/MDAnalysis/lib/__init__.py -> build/bdist.linux-aarch64/egg/MDAnalysis/lib copying build/lib.linux-aarch64-3.8/MDAnalysis/lib/util.py -> build/bdist.linux-aarch64/egg/MDAnalysis/lib copying build/lib.linux-aarch64-3.8/MDAnalysis/lib/picklable_file_io.py -> build/bdist.linux-aarch64/egg/MDAnalysis/lib copying build/lib.linux-aarch64-3.8/MDAnalysis/lib/_transformations.cpython-38-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/egg/MDAnalysis/libcopying build/lib.linux-aarch64-3.8/MDAnalysis/lib/mdamath.py -> build/bdist.linux-aarch64/egg/MDAnalysis/lib copying build/lib.linux-aarch64-3.8/MDAnalysis/lib/c_distances_openmp.cpython-38-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/egg/MDAnalysis/lib copying build/lib.linux-aarch64-3.8/MDAnalysis/lib/correlations.py -> build/bdist.linux-aarch64/egg/MDAnalysis/lib copying build/lib.linux-aarch64-3.8/MDAnalysis/lib/transformations.py -> build/bdist.linux-aarch64/egg/MDAnalysis/lib copying build/lib.linux-aarch64-3.8/MDAnalysis/lib/_cutil.cpython-38-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/egg/MDAnalysis/lib copying build/lib.linux-aarch64-3.8/MDAnalysis/lib/pkdtree.py -> build/bdist.linux-aarch64/egg/MDAnalysis/lib copying build/lib.linux-aarch64-3.8/MDAnalysis/lib/nsgrid.cpython-38-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/egg/MDAnalysis/lib copying build/lib.linux-aarch64-3.8/MDAnalysis/units.py -> build/bdist.linux-aarch64/egg/MDAnalysis creating build/bdist.linux-aarch64/egg/MDAnalysis/analysis creating build/bdist.linux-aarch64/egg/MDAnalysis/analysis/data copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/data/janin_ref_data.npy -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis/data copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/data/__init__.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis/data copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/data/rama_ref_data.npy -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis/data copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/data/filenames.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis/data copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/distances.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/diffusionmap.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis creating build/bdist.linux-aarch64/egg/MDAnalysis/analysis/encore copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/encore/confdistmatrix.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis/encore copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/encore/utils.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis/encore copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/encore/similarity.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis/encore copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/encore/covariance.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis/encore copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/encore/cutils.cpython-38-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis/encore creating build/bdist.linux-aarch64/egg/MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-38-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/encore/__init__.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis/encore creating build/bdist.linux-aarch64/egg/MDAnalysis/analysis/encore/clustering copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis/encore/clustering copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/encore/clustering/__init__.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis/encore/clustering copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/encore/clustering/cluster.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis/encore/clustering copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis/encore/clustering copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/encore/clustering/affinityprop.cpython-38-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis/encore/clustering copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/encore/bootstrap.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis/encore copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/density.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/psa.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/align.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/helix_analysis.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis creating build/bdist.linux-aarch64/egg/MDAnalysis/analysis/legacy copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/legacy/x3dna.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis/legacy copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/legacy/__init__.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis/legacy copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/gnm.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/pca.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/polymer.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/dihedrals.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/__init__.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis creating build/bdist.linux-aarch64/egg/MDAnalysis/analysis/hbonds copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis/hbonds copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/hbonds/__init__.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis/hbonds copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/leaflet.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis creating build/bdist.linux-aarch64/egg/MDAnalysis/analysis/hole2 copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/hole2/templates.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis/hole2 copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/hole2/utils.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis/hole2 copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/hole2/hole.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis/hole2 copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/hole2/__init__.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis/hole2 copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/lineardensity.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/contacts.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/msd.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/nuclinfo.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/rdf.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis creating build/bdist.linux-aarch64/egg/MDAnalysis/analysis/hydrogenbonds copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis/hydrogenbonds copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis/hydrogenbonds copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis/hydrogenbonds copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis/hydrogenbonds copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/base.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/bat.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/rms.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis copying build/lib.linux-aarch64-3.8/MDAnalysis/analysis/waterdynamics.py -> build/bdist.linux-aarch64/egg/MDAnalysis/analysis creating build/bdist.linux-aarch64/egg/MDAnalysis/converters copying build/lib.linux-aarch64-3.8/MDAnalysis/converters/OpenMMParser.py -> build/bdist.linux-aarch64/egg/MDAnalysis/converters copying build/lib.linux-aarch64-3.8/MDAnalysis/converters/ParmEd.py -> build/bdist.linux-aarch64/egg/MDAnalysis/converters copying build/lib.linux-aarch64-3.8/MDAnalysis/converters/__init__.py -> build/bdist.linux-aarch64/egg/MDAnalysis/converters copying build/lib.linux-aarch64-3.8/MDAnalysis/converters/RDKit.py -> build/bdist.linux-aarch64/egg/MDAnalysis/converters copying build/lib.linux-aarch64-3.8/MDAnalysis/converters/OpenMM.py -> build/bdist.linux-aarch64/egg/MDAnalysis/converters copying build/lib.linux-aarch64-3.8/MDAnalysis/converters/ParmEdParser.py -> build/bdist.linux-aarch64/egg/MDAnalysis/converters copying build/lib.linux-aarch64-3.8/MDAnalysis/converters/RDKitParser.py -> build/bdist.linux-aarch64/egg/MDAnalysis/converters creating build/bdist.linux-aarch64/egg/MDAnalysis/visualization copying build/lib.linux-aarch64-3.8/MDAnalysis/visualization/streamlines_3D.py -> build/bdist.linux-aarch64/egg/MDAnalysis/visualization copying build/lib.linux-aarch64-3.8/MDAnalysis/visualization/__init__.py -> build/bdist.linux-aarch64/egg/MDAnalysis/visualization copying build/lib.linux-aarch64-3.8/MDAnalysis/visualization/streamlines.py -> build/bdist.linux-aarch64/egg/MDAnalysis/visualization byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/auxiliary/core.py to core.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/auxiliary/XVG.py to XVG.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/auxiliary/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/auxiliary/base.py to base.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/coordinates/null.py to null.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/coordinates/DMS.py to DMS.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/coordinates/TRZ.py to TRZ.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/coordinates/chain.py to chain.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/coordinates/GMS.py to GMS.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/coordinates/TXYZ.py to TXYZ.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/coordinates/PQR.py to PQR.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/coordinates/FHIAIMS.py to FHIAIMS.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/coordinates/ParmEd.py to ParmEd.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/coordinates/memory.py to memory.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/coordinates/GSD.py to GSD.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/coordinates/H5MD.py to H5MD.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/coordinates/CRD.py to CRD.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/coordinates/DCD.py to DCD.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/coordinates/INPCRD.py to INPCRD.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/coordinates/core.py to core.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/coordinates/XTC.py to XTC.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/coordinates/GRO.py to GRO.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/coordinates/XYZ.py to XYZ.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/coordinates/TRR.py to TRR.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/coordinates/MOL2.py to MOL2.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/coordinates/TRJ.py to TRJ.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/coordinates/chemfiles.py to chemfiles.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/coordinates/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/coordinates/NAMDBIN.py to NAMDBIN.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/coordinates/XDR.py to XDR.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/coordinates/PDB.py to PDB.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/coordinates/PDBQT.py to PDBQT.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/coordinates/LAMMPS.py to LAMMPS.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/coordinates/MMTF.py to MMTF.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/coordinates/base.py to base.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/coordinates/DLPoly.py to DLPoly.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/core/topologyobjects.py to topologyobjects.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/core/accessors.py to accessors.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/core/universe.py to universe.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/core/topology.py to topology.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/core/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/core/groups.py to groups.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/core/selection.py to selection.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/core/_get_readers.py to _get_readers.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/core/topologyattrs.py to topologyattrs.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/authors.py to authors.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/tests/datafiles.py to datafiles.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/tests/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/topology/XYZParser.py to XYZParser.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/topology/LAMMPSParser.py to LAMMPSParser.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/topology/MinimalParser.py to MinimalParser.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/topology/HoomdXMLParser.py to HoomdXMLParser.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/topology/GMSParser.py to GMSParser.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/topology/PDBParser.py to PDBParser.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/topology/core.py to core.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/topology/GROParser.py to GROParser.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/topology/DMSParser.py to DMSParser.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/topology/ITPParser.py to ITPParser.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/topology/FHIAIMSParser.py to FHIAIMSParser.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/topology/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/topology/GSDParser.py to GSDParser.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/topology/guessers.py to guessers.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/topology/TXYZParser.py to TXYZParser.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/topology/PQRParser.py to PQRParser.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/topology/ParmEdParser.py to ParmEdParser.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/topology/CRDParser.py to CRDParser.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/topology/tpr/obj.py to obj.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/topology/tpr/utils.py to utils.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/topology/tpr/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/topology/tpr/setting.py to setting.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/topology/MOL2Parser.py to MOL2Parser.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/topology/ExtendedPDBParser.py to ExtendedPDBParser.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/topology/MMTFParser.py to MMTFParser.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/topology/PSFParser.py to PSFParser.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/topology/base.py to base.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/topology/tables.py to tables.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/topology/PDBQTParser.py to PDBQTParser.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/topology/TOPParser.py to TOPParser.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/topology/TPRParser.py to TPRParser.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/topology/DLPolyParser.py to DLPolyParser.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/selections/pymol.py to pymol.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/selections/charmm.py to charmm.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/selections/jmol.py to jmol.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/selections/vmd.py to vmd.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/selections/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/selections/base.py to base.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/selections/gromacs.py to gromacs.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/version.py to version.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/due.py to due.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/transformations/wrap.py to wrap.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/transformations/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/transformations/boxdimensions.py to boxdimensions.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/transformations/positionaveraging.py to positionaveraging.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/transformations/translate.py to translate.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/transformations/fit.py to fit.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/transformations/rotate.py to rotate.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/transformations/base.py to base.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/exceptions.py to exceptions.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/lib/distances.py to distances.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/lib/formats/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/lib/NeighborSearch.py to NeighborSearch.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/lib/log.py to log.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/lib/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/lib/util.py to util.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/lib/picklable_file_io.py to picklable_file_io.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/lib/mdamath.py to mdamath.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/lib/correlations.py to correlations.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/lib/transformations.py to transformations.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/lib/pkdtree.py to pkdtree.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/units.py to units.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/data/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/data/filenames.py to filenames.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/distances.py to distances.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/diffusionmap.py to diffusionmap.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/encore/confdistmatrix.py to confdistmatrix.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/encore/utils.py to utils.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/encore/similarity.py to similarity.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/encore/covariance.py to covariance.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py to DimensionalityReductionMethod.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py to reduce_dimensionality.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/encore/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py to ClusteringMethod.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/encore/clustering/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/encore/clustering/cluster.py to cluster.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/encore/clustering/ClusterCollection.py to ClusterCollection.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/encore/bootstrap.py to bootstrap.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/density.py to density.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/psa.py to psa.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/align.py to align.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/helix_analysis.py to helix_analysis.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/legacy/x3dna.py to x3dna.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/legacy/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/gnm.py to gnm.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/pca.py to pca.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/polymer.py to polymer.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/dihedrals.py to dihedrals.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/hbonds/hbond_autocorrel.py to hbond_autocorrel.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/hbonds/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/leaflet.py to leaflet.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/hole2/templates.py to templates.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/hole2/utils.py to utils.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/hole2/hole.py to hole.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/hole2/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/lineardensity.py to lineardensity.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/contacts.py to contacts.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/msd.py to msd.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/nuclinfo.py to nuclinfo.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/rdf.py to rdf.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py to hbond_autocorrel.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py to wbridge_analysis.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/hydrogenbonds/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py to hbond_analysis.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/base.py to base.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/bat.py to bat.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/rms.py to rms.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/waterdynamics.py to waterdynamics.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/converters/OpenMMParser.py to OpenMMParser.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/converters/ParmEd.py to ParmEd.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/converters/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/converters/RDKit.py to RDKit.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/converters/OpenMM.py to OpenMM.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/converters/ParmEdParser.py to ParmEdParser.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/converters/RDKitParser.py to RDKitParser.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/visualization/streamlines_3D.py to streamlines_3D.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/visualization/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/visualization/streamlines.py to streamlines.cpython-38.pyc creating stub loader for MDAnalysis/lib/formats/libdcd.cpython-38-aarch64-linux-gnu.so creating stub loader for MDAnalysis/lib/c_distances.cpython-38-aarch64-linux-gnu.so creating stub loader for MDAnalysis/lib/c_distances_openmp.cpython-38-aarch64-linux-gnu.so creating stub loader for MDAnalysis/lib/qcprot.cpython-38-aarch64-linux-gnu.so creating stub loader for MDAnalysis/lib/_transformations.cpython-38-aarch64-linux-gnu.so creating stub loader for MDAnalysis/lib/formats/libmdaxdr.cpython-38-aarch64-linux-gnu.so creating stub loader for MDAnalysis/lib/formats/cython_util.cpython-38-aarch64-linux-gnu.so creating stub loader for MDAnalysis/analysis/encore/cutils.cpython-38-aarch64-linux-gnu.so creating stub loader for MDAnalysis/analysis/encore/clustering/affinityprop.cpython-38-aarch64-linux-gnu.so creating stub loader for MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-38-aarch64-linux-gnu.so creating stub loader for MDAnalysis/lib/_cutil.cpython-38-aarch64-linux-gnu.so creating stub loader for MDAnalysis/lib/_augment.cpython-38-aarch64-linux-gnu.so creating stub loader for MDAnalysis/lib/nsgrid.cpython-38-aarch64-linux-gnu.so byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/lib/formats/libdcd.py to libdcd.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/lib/c_distances.py to c_distances.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/lib/c_distances_openmp.py to c_distances_openmp.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/lib/qcprot.py to qcprot.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/lib/_transformations.py to _transformations.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/lib/formats/libmdaxdr.py to libmdaxdr.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/lib/formats/cython_util.py to cython_util.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/encore/cutils.py to cutils.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/encore/clustering/affinityprop.py to affinityprop.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.py to stochasticproxembed.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/lib/_cutil.py to _cutil.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/lib/_augment.py to _augment.cpython-38.pyc byte-compiling build/bdist.linux-aarch64/egg/MDAnalysis/lib/nsgrid.py to nsgrid.cpython-38.pyc creating build/bdist.linux-aarch64/egg/EGG-INFO copying MDAnalysis.egg-info/PKG-INFO -> build/bdist.linux-aarch64/egg/EGG-INFO copying MDAnalysis.egg-info/SOURCES.txt -> build/bdist.linux-aarch64/egg/EGG-INFO copying MDAnalysis.egg-info/dependency_links.txt -> build/bdist.linux-aarch64/egg/EGG-INFO copying MDAnalysis.egg-info/not-zip-safe -> build/bdist.linux-aarch64/egg/EGG-INFO copying MDAnalysis.egg-info/requires.txt -> build/bdist.linux-aarch64/egg/EGG-INFO copying MDAnalysis.egg-info/top_level.txt -> build/bdist.linux-aarch64/egg/EGG-INFO writing build/bdist.linux-aarch64/egg/EGG-INFO/native_libs.txt creating dist creating 'dist/MDAnalysis-2.0.0.dev0-py3.8-linux-aarch64.egg' and adding 'build/bdist.linux-aarch64/egg' to it removing 'build/bdist.linux-aarch64/egg' (and everything under it) Processing MDAnalysis-2.0.0.dev0-py3.8-linux-aarch64.egg creating /lustre/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/MDAnalysis-2.0.0.dev0-py3.8-linux-aarch64.eggExtracting MDAnalysis-2.0.0.dev0-py3.8-linux-aarch64.egg to /lustre/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages Adding MDAnalysis 2.0.0.dev0 to easy-install.pth file Installed /lustre/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/MDAnalysis-2.0.0.dev0-py3.8-linux-aarch64.egg Processing dependencies for MDAnalysis==2.0.0.dev0 Searching for gsd>=1.4.0 Reading https://pypi.org/simple/gsd/ Downloading https://files.pythonhosted.org/packages/6f/85/53ac84ef5467979c58d89383e6ba4cf88729877c8e931be1d8e11cb19a2b/gsd-2.4.2.tar.gz#sha256=fa2ed62da3eb2cbfea02a22dadc1d84e80c16d874535de4bace6941c6d805851 Best match: gsd 2.4.2 Processing gsd-2.4.2.tar.gz Writing /tmp/easy_install-3o9utvai/gsd-2.4.2/setup.cfg Running gsd-2.4.2/setup.py -q bdist_egg --dist-dir /tmp/easy_install-3o9utvai/gsd-2.4.2/egg-dist-tmp-4nnyphc4 Compiling gsd/fl.pyx because it depends on /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Includes/libc/string.pxd. [1/1] Cythonizing gsd/fl.pyx Traceback (most recent call last): File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/ParseTreeTransforms.py", line 2218, in visit_FuncDefNode node.body = node.body.analyse_expressions(node.local_scope) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/Nodes.py", line 435, in analyse_expressions self.stats = [stat.analyse_expressions(env) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/Nodes.py", line 435, in self.stats = [stat.analyse_expressions(env) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/Nodes.py", line 6702, in analyse_expressions self.item = self.item.coerce_to(self.target.type, env) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/ExprNodes.py", line 952, in coerce_to src = PyTypeTestNode(src, dst_type, env) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/ExprNodes.py", line 13015, in __init__ assert dst_type.is_extension_type or dst_type.is_builtin_type, "PyTypeTest on non extension type" AssertionError: PyTypeTest on non extension type During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/setuptools/sandbox.py", line 152, in save_modules yield saved File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/setuptools/sandbox.py", line 193, in setup_context yield File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/setuptools/sandbox.py", line 254, in run_setup _execfile(setup_script, ns) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/setuptools/sandbox.py", line 43, in _execfile exec(code, globals, locals) File "/tmp/easy_install-3o9utvai/gsd-2.4.2/setup.py", line 7, in # (see the file AUTHORS for the full list of names) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Build/Dependencies.py", line 1102, in cythonize cythonize_one(*args) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Build/Dependencies.py", line 1208, in cythonize_one result = compile_single(pyx_file, options, full_module_name=full_module_name) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/Main.py", line 727, in compile_single return run_pipeline(source, options, full_module_name) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/Main.py", line 515, in run_pipeline err, enddata = Pipeline.run_pipeline(pipeline, source) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/Pipeline.py", line 355, in run_pipeline data = run(phase, data) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/Pipeline.py", line 335, in run return phase(data) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/ParseTreeTransforms.py", line 1598, in __call__ return super_class.__call__(root) File "Cython/Compiler/Visitor.py", line 355, in Cython.Compiler.Visitor.EnvTransform.__call__ File "Cython/Compiler/Visitor.py", line 302, in Cython.Compiler.Visitor.CythonTransform.__call__ File "Cython/Compiler/Visitor.py", line 284, in Cython.Compiler.Visitor.VisitorTransform.__call__ File "Cython/Compiler/Visitor.py", line 182, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/ParseTreeTransforms.py", line 1608, in visit_ModuleNode node.analyse_declarations(self.current_env()) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/ModuleNode.py", line 124, in analyse_declarations self.body.analyse_declarations(env) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/Nodes.py", line 431, in analyse_declarations stat.analyse_declarations(env) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/Nodes.py", line 431, in analyse_declarations stat.analyse_declarations(env) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/Nodes.py", line 7941, in analyse_declarations module_scope = env.find_module( File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/Symtab.py", line 1273, in find_module return module_scope.context.find_module( File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/Main.py", line 232, in find_module err, result = self.process_pxd(source_desc, scope, qualified_name) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/Main.py", line 146, in process_pxd result = Pipeline.run_pipeline(pipeline, source_desc) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/Pipeline.py", line 355, in run_pipeline data = run(phase, data) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/Pipeline.py", line 335, in run return phase(data) File "Cython/Compiler/Visitor.py", line 302, in Cython.Compiler.Visitor.CythonTransform.__call__ File "Cython/Compiler/Visitor.py", line 284, in Cython.Compiler.Visitor.VisitorTransform.__call__ File "Cython/Compiler/Visitor.py", line 182, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/ParseTreeTransforms.py", line 2213, in visit_ModuleNode self.visitchildren(node) File "Cython/Compiler/Visitor.py", line 247, in Cython.Compiler.Visitor.VisitorTransform.visitchildren File "Cython/Compiler/Visitor.py", line 251, in Cython.Compiler.Visitor.VisitorTransform.visitchildren File "Cython/Compiler/Visitor.py", line 260, in Cython.Compiler.Visitor.VisitorTransform._process_children File "Cython/Compiler/Visitor.py", line 221, in Cython.Compiler.Visitor.TreeVisitor._visitchildren File "Cython/Compiler/Visitor.py", line 193, in Cython.Compiler.Visitor.TreeVisitor._visitchild File "Cython/Compiler/Visitor.py", line 182, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 312, in Cython.Compiler.Visitor.CythonTransform.visit_Node File "Cython/Compiler/Visitor.py", line 260, in Cython.Compiler.Visitor.VisitorTransform._process_children File "Cython/Compiler/Visitor.py", line 219, in Cython.Compiler.Visitor.TreeVisitor._visitchildren File "Cython/Compiler/Visitor.py", line 193, in Cython.Compiler.Visitor.TreeVisitor._visitchild File "Cython/Compiler/Visitor.py", line 182, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 312, in Cython.Compiler.Visitor.CythonTransform.visit_Node File "Cython/Compiler/Visitor.py", line 260, in Cython.Compiler.Visitor.VisitorTransform._process_children File "Cython/Compiler/Visitor.py", line 219, in Cython.Compiler.Visitor.TreeVisitor._visitchildren File "Cython/Compiler/Visitor.py", line 193, in Cython.Compiler.Visitor.TreeVisitor._visitchild File "Cython/Compiler/Visitor.py", line 188, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 148, in Cython.Compiler.Visitor.TreeVisitor._raise_compiler_error Cython.Compiler.Errors.CompilerCrash: Error compiling Cython file: ------------------------------------------------------------ ... if PyDataType_HASSUBARRAY(d): return d.subarray.shape else: return () cdef inline char* _util_dtypestring(dtype descr, char* f, char* end, int* offset) except NULL: ^ ------------------------------------------------------------ /home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/numpy/__init__.pxd:763:5: Compiler crash in AnalyseExpressionsTransform ModuleNode.body = StatListNode(__init__.pxd:17:0) StatListNode.stats[42] = StatListNode(__init__.pxd:763:5) StatListNode.stats[0] = CFuncDefNode(__init__.pxd:763:5, args = [...]/4, inline_in_pxd = True, modifiers = [...]/1, visibility = 'private') Compiler crash traceback from this point on: File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/ParseTreeTransforms.py", line 2218, in visit_FuncDefNode node.body = node.body.analyse_expressions(node.local_scope) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/Nodes.py", line 435, in analyse_expressions self.stats = [stat.analyse_expressions(env) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/Nodes.py", line 435, in self.stats = [stat.analyse_expressions(env) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/Nodes.py", line 6702, in analyse_expressions self.item = self.item.coerce_to(self.target.type, env) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/ExprNodes.py", line 952, in coerce_to src = PyTypeTestNode(src, dst_type, env) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/ExprNodes.py", line 13015, in __init__ assert dst_type.is_extension_type or dst_type.is_builtin_type, "PyTypeTest on non extension type" AssertionError: PyTypeTest on non extension type During handling of the above exception, another exception occurred: Traceback (most recent call last): File "setup.py", line 608, in setup(name='MDAnalysis', File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/setuptools/__init__.py", line 153, in setup return distutils.core.setup(**attrs) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/distutils/core.py", line 148, in setup dist.run_commands() File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/distutils/dist.py", line 966, in run_commands self.run_command(cmd) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/distutils/dist.py", line 985, in run_command cmd_obj.run() File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/setuptools/command/install.py", line 67, in run self.do_egg_install() File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/setuptools/command/install.py", line 117, in do_egg_install cmd.run(show_deprecation=False) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/setuptools/command/easy_install.py", line 408, in run self.easy_install(spec, not self.no_deps) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/setuptools/command/easy_install.py", line 650, in easy_install return self.install_item(None, spec, tmpdir, deps, True) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/setuptools/command/easy_install.py", line 697, in install_item self.process_distribution(spec, dist, deps) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/setuptools/command/easy_install.py", line 744, in process_distribution distros = WorkingSet([]).resolve( File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/pkg_resources/__init__.py", line 766, in resolve dist = best[req.key] = env.best_match( File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/pkg_resources/__init__.py", line 1051, in best_match return self.obtain(req, installer) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/pkg_resources/__init__.py", line 1063, in obtain return installer(requirement) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/setuptools/command/easy_install.py", line 669, in easy_install return self.install_item(spec, dist.location, tmpdir, deps) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/setuptools/command/easy_install.py", line 695, in install_item dists = self.install_eggs(spec, download, tmpdir) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/setuptools/command/easy_install.py", line 890, in install_eggs return self.build_and_install(setup_script, setup_base) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/setuptools/command/easy_install.py", line 1162, in build_and_install self.run_setup(setup_script, setup_base, args) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/setuptools/command/easy_install.py", line 1146, in run_setup run_setup(setup_script, args) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/setuptools/sandbox.py", line 257, in run_setup raise File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/contextlib.py", line 131, in __exit__ self.gen.throw(type, value, traceback) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/setuptools/sandbox.py", line 193, in setup_context yield File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/contextlib.py", line 131, in __exit__ self.gen.throw(type, value, traceback) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/setuptools/sandbox.py", line 164, in save_modules saved_exc.resume() File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/setuptools/sandbox.py", line 139, in resume raise exc.with_traceback(self._tb) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/setuptools/sandbox.py", line 152, in save_modules yield saved File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/setuptools/sandbox.py", line 193, in setup_context yield File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/setuptools/sandbox.py", line 254, in run_setup _execfile(setup_script, ns) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/setuptools/sandbox.py", line 43, in _execfile exec(code, globals, locals) File "/tmp/easy_install-3o9utvai/gsd-2.4.2/setup.py", line 7, in # (see the file AUTHORS for the full list of names) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Build/Dependencies.py", line 1102, in cythonize cythonize_one(*args) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Build/Dependencies.py", line 1208, in cythonize_one result = compile_single(pyx_file, options, full_module_name=full_module_name) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/Main.py", line 727, in compile_single return run_pipeline(source, options, full_module_name) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/Main.py", line 515, in run_pipeline err, enddata = Pipeline.run_pipeline(pipeline, source) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/Pipeline.py", line 355, in run_pipeline data = run(phase, data) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/Pipeline.py", line 335, in run return phase(data) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/ParseTreeTransforms.py", line 1598, in __call__ return super_class.__call__(root) File "Cython/Compiler/Visitor.py", line 355, in Cython.Compiler.Visitor.EnvTransform.__call__ File "Cython/Compiler/Visitor.py", line 302, in Cython.Compiler.Visitor.CythonTransform.__call__ File "Cython/Compiler/Visitor.py", line 284, in Cython.Compiler.Visitor.VisitorTransform.__call__ File "Cython/Compiler/Visitor.py", line 182, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/ParseTreeTransforms.py", line 1608, in visit_ModuleNode node.analyse_declarations(self.current_env()) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/ModuleNode.py", line 124, in analyse_declarations self.body.analyse_declarations(env) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/Nodes.py", line 431, in analyse_declarations stat.analyse_declarations(env) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/Nodes.py", line 431, in analyse_declarations stat.analyse_declarations(env) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/Nodes.py", line 7941, in analyse_declarations module_scope = env.find_module( File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/Symtab.py", line 1273, in find_module return module_scope.context.find_module( File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/Main.py", line 232, in find_module err, result = self.process_pxd(source_desc, scope, qualified_name) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/Main.py", line 146, in process_pxd result = Pipeline.run_pipeline(pipeline, source_desc) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/Pipeline.py", line 355, in run_pipeline data = run(phase, data) File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/Pipeline.py", line 335, in run return phase(data) File "Cython/Compiler/Visitor.py", line 302, in Cython.Compiler.Visitor.CythonTransform.__call__ File "Cython/Compiler/Visitor.py", line 284, in Cython.Compiler.Visitor.VisitorTransform.__call__ File "Cython/Compiler/Visitor.py", line 182, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/ParseTreeTransforms.py", line 2213, in visit_ModuleNode self.visitchildren(node) File "Cython/Compiler/Visitor.py", line 247, in Cython.Compiler.Visitor.VisitorTransform.visitchildren File "Cython/Compiler/Visitor.py", line 251, in Cython.Compiler.Visitor.VisitorTransform.visitchildren File "Cython/Compiler/Visitor.py", line 260, in Cython.Compiler.Visitor.VisitorTransform._process_children File "Cython/Compiler/Visitor.py", line 221, in Cython.Compiler.Visitor.TreeVisitor._visitchildren File "Cython/Compiler/Visitor.py", line 193, in Cython.Compiler.Visitor.TreeVisitor._visitchild File "Cython/Compiler/Visitor.py", line 182, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 312, in Cython.Compiler.Visitor.CythonTransform.visit_Node File "Cython/Compiler/Visitor.py", line 260, in Cython.Compiler.Visitor.VisitorTransform._process_children File "Cython/Compiler/Visitor.py", line 219, in Cython.Compiler.Visitor.TreeVisitor._visitchildren File "Cython/Compiler/Visitor.py", line 193, in Cython.Compiler.Visitor.TreeVisitor._visitchild File "Cython/Compiler/Visitor.py", line 182, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 312, in Cython.Compiler.Visitor.CythonTransform.visit_Node File "Cython/Compiler/Visitor.py", line 260, in Cython.Compiler.Visitor.VisitorTransform._process_children File "Cython/Compiler/Visitor.py", line 219, in Cython.Compiler.Visitor.TreeVisitor._visitchildren File "Cython/Compiler/Visitor.py", line 193, in Cython.Compiler.Visitor.TreeVisitor._visitchild File "Cython/Compiler/Visitor.py", line 188, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 148, in Cython.Compiler.Visitor.TreeVisitor._raise_compiler_error setuptools.sandbox.UnpickleableException: CompilerCrash((, 763, 5), 'AnalyseExpressionsTransform', 'Compiler crash in AnalyseExpressionsTransform\n\nModuleNode.body = StatListNode(__init__.pxd:17:0)\nStatListNode.stats[42] = StatListNode(__init__.pxd:763:5)\nStatListNode.stats[0] = CFuncDefNode(__init__.pxd:763:5,\n args = [...]/4,\n inline_in_pxd = True,\n modifiers = [...]/1,\n visibility = \'private\')\n\nCompiler crash traceback from this point on:\n File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit\n File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/ParseTreeTransforms.py", line 2218, in visit_FuncDefNode\n node.body = node.body.analyse_expressions(node.local_scope)\n File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/Nodes.py", line 435, in analyse_expressions\n self.stats = [stat.analyse_expressions(env)\n File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/Nodes.py", line 435, in \n self.stats = [stat.analyse_expressions(env)\n File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/Nodes.py", line 6702, in analyse_expressions\n self.item = self.item.coerce_to(self.target.type, env)\n File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/ExprNodes.py", line 952, in coerce_to\n src = PyTypeTestNode(src, dst_type, env)\n File "/home/ri-ialibay/software/miniconda/install/envs/test-gsd/lib/python3.8/site-packages/Cython/Compiler/ExprNodes.py", line 13015, in __init__\n assert dst_type.is_extension_type or dst_type.is_builtin_type, "PyTypeTest on non extension type"\nAssertionError: PyTypeTest on non extension type', AssertionError('PyTypeTest on non extension type'), ) ```
IAlibay commented 3 years ago

Appears to be fine with numpy>=1.19.2

Whilst it would be nice to hunt down for the exact cause here, given that aarch64 is somewhat experimental, I'd perfer just set the numpy lower bound to something a bit higher? (unless there are any objections)