search

prody / ProDy

A Python Package for Protein Dynamics Analysis
http://prody.csb.pitt.edu
Other
417 stars 153 forks source link

Trouble installing on Mac OS 10.14 $MACOSX_DEPLOYMENT_TARGET mismatch: #925

Closed MooersLab closed 4 years ago

MooersLab commented 4 years ago

I have tried several ways to upgrade from 10.8 to 10.10 but I get $MACOSX_DEPLOYMENT_TARGET error. See the bottom of the log.

sudo -H /opt/local/bin/python3.7 -m pip install --upgrade ProDy Collecting ProDy Using cached https://files.pythonhosted.org/packages/b8/b1/e2dc6bb4e8f5d6f281e8d747dd9bcfe3f4dc82d30ad44131d4433d7da272/ProDy-1.10.10.tar.gz Installing build dependencies ... done Getting requirements to build wheel ... done Preparing wheel metadata ... done Building wheels for collected packages: ProDy Building wheel for ProDy (PEP 517) ... error ERROR: Command errored out with exit status 1: command: /opt/local/bin/python3.7 /opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/pip/_vendor/pep517/_in_process.py build_wheel /tmp/tmpepdkw4os cwd: /private/tmp/pip-install-c0ro_1xd/ProDy Complete output (247 lines): running bdist_wheel running build running build_py creating build creating build/lib.macosx-10.14-x86_64-3.7 creating build/lib.macosx-10.14-x86_64-3.7/prody copying prody/init.py -> build/lib.macosx-10.14-x86_64-3.7/prody creating build/lib.macosx-10.14-x86_64-3.7/prody/atomic copying prody/atomic/functions.py -> build/lib.macosx-10.14-x86_64-3.7/prody/atomic copying prody/atomic/fields.py -> build/lib.macosx-10.14-x86_64-3.7/prody/atomic copying prody/atomic/chain.py -> build/lib.macosx-10.14-x86_64-3.7/prody/atomic copying prody/atomic/flags.py -> build/lib.macosx-10.14-x86_64-3.7/prody/atomic copying prody/atomic/atommap.py -> build/lib.macosx-10.14-x86_64-3.7/prody/atomic copying prody/atomic/init.py -> build/lib.macosx-10.14-x86_64-3.7/prody/atomic copying prody/atomic/atomgroup.py -> build/lib.macosx-10.14-x86_64-3.7/prody/atomic copying prody/atomic/residue.py -> build/lib.macosx-10.14-x86_64-3.7/prody/atomic copying prody/atomic/subset.py -> build/lib.macosx-10.14-x86_64-3.7/prody/atomic copying prody/atomic/pointer.py -> build/lib.macosx-10.14-x86_64-3.7/prody/atomic copying prody/atomic/selection.py -> build/lib.macosx-10.14-x86_64-3.7/prody/atomic copying prody/atomic/segment.py -> build/lib.macosx-10.14-x86_64-3.7/prody/atomic copying prody/atomic/select.py -> build/lib.macosx-10.14-x86_64-3.7/prody/atomic copying prody/atomic/bond.py -> build/lib.macosx-10.14-x86_64-3.7/prody/atomic copying prody/atomic/atomic.py -> build/lib.macosx-10.14-x86_64-3.7/prody/atomic copying prody/atomic/hierview.py -> build/lib.macosx-10.14-x86_64-3.7/prody/atomic copying prody/atomic/atom.py -> build/lib.macosx-10.14-x86_64-3.7/prody/atomic creating build/lib.macosx-10.14-x86_64-3.7/prody/database copying prody/database/uniprot.py -> build/lib.macosx-10.14-x86_64-3.7/prody/database copying prody/database/cath.py -> build/lib.macosx-10.14-x86_64-3.7/prody/database copying prody/database/init.py -> build/lib.macosx-10.14-x86_64-3.7/prody/database copying prody/database/goa.py -> build/lib.macosx-10.14-x86_64-3.7/prody/database copying prody/database/dali.py -> build/lib.macosx-10.14-x86_64-3.7/prody/database copying prody/database/pfam.py -> build/lib.macosx-10.14-x86_64-3.7/prody/database creating build/lib.macosx-10.14-x86_64-3.7/prody/dynamics copying prody/dynamics/functions.py -> build/lib.macosx-10.14-x86_64-3.7/prody/dynamics copying prody/dynamics/gnm.py -> build/lib.macosx-10.14-x86_64-3.7/prody/dynamics copying prody/dynamics/editing.py -> build/lib.macosx-10.14-x86_64-3.7/prody/dynamics copying prody/dynamics/nma.py -> build/lib.macosx-10.14-x86_64-3.7/prody/dynamics copying prody/dynamics/analysis.py -> build/lib.macosx-10.14-x86_64-3.7/prody/dynamics copying prody/dynamics/plotting.py -> build/lib.macosx-10.14-x86_64-3.7/prody/dynamics copying prody/dynamics/bbenm.py -> build/lib.macosx-10.14-x86_64-3.7/prody/dynamics copying prody/dynamics/exanm.py -> build/lib.macosx-10.14-x86_64-3.7/prody/dynamics copying prody/dynamics/anm.py -> build/lib.macosx-10.14-x86_64-3.7/prody/dynamics copying prody/dynamics/init.py -> build/lib.macosx-10.14-x86_64-3.7/prody/dynamics copying prody/dynamics/mode.py -> build/lib.macosx-10.14-x86_64-3.7/prody/dynamics copying prody/dynamics/rtb.py -> build/lib.macosx-10.14-x86_64-3.7/prody/dynamics copying prody/dynamics/sampling.py -> build/lib.macosx-10.14-x86_64-3.7/prody/dynamics copying prody/dynamics/pca.py -> build/lib.macosx-10.14-x86_64-3.7/prody/dynamics copying prody/dynamics/vmdfile.py -> build/lib.macosx-10.14-x86_64-3.7/prody/dynamics copying prody/dynamics/heatmapper.py -> build/lib.macosx-10.14-x86_64-3.7/prody/dynamics copying prody/dynamics/perturb.py -> build/lib.macosx-10.14-x86_64-3.7/prody/dynamics copying prody/dynamics/signature.py -> build/lib.macosx-10.14-x86_64-3.7/prody/dynamics copying prody/dynamics/mechstiff.py -> build/lib.macosx-10.14-x86_64-3.7/prody/dynamics copying prody/dynamics/compare.py -> build/lib.macosx-10.14-x86_64-3.7/prody/dynamics copying prody/dynamics/entropy.py -> build/lib.macosx-10.14-x86_64-3.7/prody/dynamics copying prody/dynamics/nmdfile.py -> build/lib.macosx-10.14-x86_64-3.7/prody/dynamics copying prody/dynamics/modeset.py -> build/lib.macosx-10.14-x86_64-3.7/prody/dynamics copying prody/dynamics/gamma.py -> build/lib.macosx-10.14-x86_64-3.7/prody/dynamics creating build/lib.macosx-10.14-x86_64-3.7/prody/ensemble copying prody/ensemble/pdbensemble.py -> build/lib.macosx-10.14-x86_64-3.7/prody/ensemble copying prody/ensemble/functions.py -> build/lib.macosx-10.14-x86_64-3.7/prody/ensemble copying prody/ensemble/init.py -> build/lib.macosx-10.14-x86_64-3.7/prody/ensemble copying prody/ensemble/ensemble.py -> build/lib.macosx-10.14-x86_64-3.7/prody/ensemble copying prody/ensemble/conformation.py -> build/lib.macosx-10.14-x86_64-3.7/prody/ensemble creating build/lib.macosx-10.14-x86_64-3.7/prody/kdtree copying prody/kdtree/init.py -> build/lib.macosx-10.14-x86_64-3.7/prody/kdtree copying prody/kdtree/kdtree.py -> build/lib.macosx-10.14-x86_64-3.7/prody/kdtree creating build/lib.macosx-10.14-x86_64-3.7/prody/measure copying prody/measure/measure.py -> build/lib.macosx-10.14-x86_64-3.7/prody/measure copying prody/measure/contacts.py -> build/lib.macosx-10.14-x86_64-3.7/prody/measure copying prody/measure/init.py -> build/lib.macosx-10.14-x86_64-3.7/prody/measure copying prody/measure/transform.py -> build/lib.macosx-10.14-x86_64-3.7/prody/measure creating build/lib.macosx-10.14-x86_64-3.7/prody/proteins copying prody/proteins/functions.py -> build/lib.macosx-10.14-x86_64-3.7/prody/proteins copying prody/proteins/dssp.py -> build/lib.macosx-10.14-x86_64-3.7/prody/proteins copying prody/proteins/blastpdbUniProtKB.py -> build/lib.macosx-10.14-x86_64-3.7/prody/proteins copying prody/proteins/header.py -> build/lib.macosx-10.14-x86_64-3.7/prody/proteins copying prody/proteins/starfile.py -> build/lib.macosx-10.14-x86_64-3.7/prody/proteins copying prody/proteins/ciffile.py -> build/lib.macosx-10.14-x86_64-3.7/prody/proteins copying prody/proteins/init.py -> build/lib.macosx-10.14-x86_64-3.7/prody/proteins copying prody/proteins/pdbligands.py -> build/lib.macosx-10.14-x86_64-3.7/prody/proteins copying prody/proteins/localpdb.py -> build/lib.macosx-10.14-x86_64-3.7/prody/proteins copying prody/proteins/blastpdb.py -> build/lib.macosx-10.14-x86_64-3.7/prody/proteins copying prody/proteins/psiblast.py -> build/lib.macosx-10.14-x86_64-3.7/prody/proteins copying prody/proteins/pdbfile.py -> build/lib.macosx-10.14-x86_64-3.7/prody/proteins copying prody/proteins/wwpdb.py -> build/lib.macosx-10.14-x86_64-3.7/prody/proteins copying prody/proteins/stride.py -> build/lib.macosx-10.14-x86_64-3.7/prody/proteins copying prody/proteins/pdbclusters.py -> build/lib.macosx-10.14-x86_64-3.7/prody/proteins copying prody/proteins/compare.py -> build/lib.macosx-10.14-x86_64-3.7/prody/proteins copying prody/proteins/emdfile.py -> build/lib.macosx-10.14-x86_64-3.7/prody/proteins creating build/lib.macosx-10.14-x86_64-3.7/prody/sequence copying prody/sequence/msa.py -> build/lib.macosx-10.14-x86_64-3.7/prody/sequence copying prody/sequence/analysis.py -> build/lib.macosx-10.14-x86_64-3.7/prody/sequence copying prody/sequence/sequence.py -> build/lib.macosx-10.14-x86_64-3.7/prody/sequence copying prody/sequence/plotting.py -> build/lib.macosx-10.14-x86_64-3.7/prody/sequence copying prody/sequence/init.py -> build/lib.macosx-10.14-x86_64-3.7/prody/sequence copying prody/sequence/msafile.py -> build/lib.macosx-10.14-x86_64-3.7/prody/sequence creating build/lib.macosx-10.14-x86_64-3.7/prody/trajectory copying prody/trajectory/trajbase.py -> build/lib.macosx-10.14-x86_64-3.7/prody/trajectory copying prody/trajectory/trajfile.py -> build/lib.macosx-10.14-x86_64-3.7/prody/trajectory copying prody/trajectory/init.py -> build/lib.macosx-10.14-x86_64-3.7/prody/trajectory copying prody/trajectory/trajectory.py -> build/lib.macosx-10.14-x86_64-3.7/prody/trajectory copying prody/trajectory/dcdfile.py -> build/lib.macosx-10.14-x86_64-3.7/prody/trajectory copying prody/trajectory/psffile.py -> build/lib.macosx-10.14-x86_64-3.7/prody/trajectory copying prody/trajectory/frame.py -> build/lib.macosx-10.14-x86_64-3.7/prody/trajectory creating build/lib.macosx-10.14-x86_64-3.7/prody/chromatin copying prody/chromatin/functions.py -> build/lib.macosx-10.14-x86_64-3.7/prody/chromatin copying prody/chromatin/norm.py -> build/lib.macosx-10.14-x86_64-3.7/prody/chromatin copying prody/chromatin/init.py -> build/lib.macosx-10.14-x86_64-3.7/prody/chromatin copying prody/chromatin/hic.py -> build/lib.macosx-10.14-x86_64-3.7/prody/chromatin copying prody/chromatin/cluster.py -> build/lib.macosx-10.14-x86_64-3.7/prody/chromatin copying prody/chromatin/straw.py -> build/lib.macosx-10.14-x86_64-3.7/prody/chromatin creating build/lib.macosx-10.14-x86_64-3.7/prody/domain_decomposition copying prody/domain_decomposition/spectrus.py -> build/lib.macosx-10.14-x86_64-3.7/prody/domain_decomposition copying prody/domain_decomposition/init.py -> build/lib.macosx-10.14-x86_64-3.7/prody/domain_decomposition creating build/lib.macosx-10.14-x86_64-3.7/prody/utilities copying prody/utilities/legacy.py -> build/lib.macosx-10.14-x86_64-3.7/prody/utilities copying prody/utilities/checkers.py -> build/lib.macosx-10.14-x86_64-3.7/prody/utilities copying prody/utilities/init.py -> build/lib.macosx-10.14-x86_64-3.7/prody/utilities copying prody/utilities/logger.py -> build/lib.macosx-10.14-x86_64-3.7/prody/utilities copying prody/utilities/doctools.py -> build/lib.macosx-10.14-x86_64-3.7/prody/utilities copying prody/utilities/settings.py -> build/lib.macosx-10.14-x86_64-3.7/prody/utilities copying prody/utilities/catchall.py -> build/lib.macosx-10.14-x86_64-3.7/prody/utilities copying prody/utilities/misctools.py -> build/lib.macosx-10.14-x86_64-3.7/prody/utilities copying prody/utilities/pathtools.py -> build/lib.macosx-10.14-x86_64-3.7/prody/utilities copying prody/utilities/drawtools.py -> build/lib.macosx-10.14-x86_64-3.7/prody/utilities creating build/lib.macosx-10.14-x86_64-3.7/prody/apps copying prody/apps/init.py -> build/lib.macosx-10.14-x86_64-3.7/prody/apps copying prody/apps/apptools.py -> build/lib.macosx-10.14-x86_64-3.7/prody/apps creating build/lib.macosx-10.14-x86_64-3.7/prody/apps/prody_apps copying prody/apps/prody_apps/prody_fetch.py -> build/lib.macosx-10.14-x86_64-3.7/prody/apps/prody_apps copying prody/apps/prody_apps/prody_pca.py -> build/lib.macosx-10.14-x86_64-3.7/prody/apps/prody_apps copying prody/apps/prody_apps/prody_biomol.py -> build/lib.macosx-10.14-x86_64-3.7/prody/apps/prody_apps copying prody/apps/prody_apps/prody_eda.py -> build/lib.macosx-10.14-x86_64-3.7/prody/apps/prody_apps copying prody/apps/prody_apps/prody_align.py -> build/lib.macosx-10.14-x86_64-3.7/prody/apps/prody_apps copying prody/apps/prody_apps/nmaoptions.py -> build/lib.macosx-10.14-x86_64-3.7/prody/apps/prody_apps copying prody/apps/prody_apps/init.py -> build/lib.macosx-10.14-x86_64-3.7/prody/apps/prody_apps copying prody/apps/prody_apps/prody_catdcd.py -> build/lib.macosx-10.14-x86_64-3.7/prody/apps/prody_apps copying prody/apps/prody_apps/prody_contacts.py -> build/lib.macosx-10.14-x86_64-3.7/prody/apps/prody_apps copying prody/apps/prody_apps/prody_gnm.py -> build/lib.macosx-10.14-x86_64-3.7/prody/apps/prody_apps copying prody/apps/prody_apps/prody_blast.py -> build/lib.macosx-10.14-x86_64-3.7/prody/apps/prody_apps copying prody/apps/prody_apps/prody_select.py -> build/lib.macosx-10.14-x86_64-3.7/prody/apps/prody_apps copying prody/apps/prody_apps/prody_anm.py -> build/lib.macosx-10.14-x86_64-3.7/prody/apps/prody_apps creating build/lib.macosx-10.14-x86_64-3.7/prody/apps/evol_apps copying prody/apps/evol_apps/evol_coevol.py -> build/lib.macosx-10.14-x86_64-3.7/prody/apps/evol_apps copying prody/apps/evol_apps/evol_refine.py -> build/lib.macosx-10.14-x86_64-3.7/prody/apps/evol_apps copying prody/apps/evol_apps/evol_conserv.py -> build/lib.macosx-10.14-x86_64-3.7/prody/apps/evol_apps copying prody/apps/evol_apps/init.py -> build/lib.macosx-10.14-x86_64-3.7/prody/apps/evol_apps copying prody/apps/evol_apps/evol_merge.py -> build/lib.macosx-10.14-x86_64-3.7/prody/apps/evol_apps copying prody/apps/evol_apps/evol_fetch.py -> build/lib.macosx-10.14-x86_64-3.7/prody/apps/evol_apps copying prody/apps/evol_apps/evol_rankorder.py -> build/lib.macosx-10.14-x86_64-3.7/prody/apps/evol_apps copying prody/apps/evol_apps/evol_occupancy.py -> build/lib.macosx-10.14-x86_64-3.7/prody/apps/evol_apps copying prody/apps/evol_apps/evol_filter.py -> build/lib.macosx-10.14-x86_64-3.7/prody/apps/evol_apps copying prody/apps/evol_apps/evol_search.py -> build/lib.macosx-10.14-x86_64-3.7/prody/apps/evol_apps creating build/lib.macosx-10.14-x86_64-3.7/prody/tests copying prody/tests/init.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests creating build/lib.macosx-10.14-x86_64-3.7/prody/tests/apps copying prody/tests/apps/test_prody_gnm.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/apps copying prody/tests/apps/test_prody_catdcd.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/apps copying prody/tests/apps/test_prody_anm.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/apps copying prody/tests/apps/init.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/apps copying prody/tests/apps/test_prody_pca.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/apps copying prody/tests/apps/test_prody_examples.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/apps creating build/lib.macosx-10.14-x86_64-3.7/prody/tests/atomic copying prody/tests/atomic/test_subset.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/atomic copying prody/tests/atomic/test_select.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/atomic copying prody/tests/atomic/test_atomic.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/atomic copying prody/tests/atomic/init.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/atomic copying prody/tests/atomic/test_atommap.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/atomic copying prody/tests/atomic/test_hierview.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/atomic copying prody/tests/atomic/test_fragment.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/atomic creating build/lib.macosx-10.14-x86_64-3.7/prody/tests/datafiles copying prody/tests/datafiles/init.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/datafiles creating build/lib.macosx-10.14-x86_64-3.7/prody/tests/dynamics copying prody/tests/dynamics/test_editing.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/dynamics copying prody/tests/dynamics/init.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/dynamics copying prody/tests/dynamics/test_signature.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/dynamics copying prody/tests/dynamics/test_enms.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/dynamics creating build/lib.macosx-10.14-x86_64-3.7/prody/tests/ensemble copying prody/tests/ensemble/test_pdbensemble.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/ensemble copying prody/tests/ensemble/test_conformation.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/ensemble copying prody/tests/ensemble/init.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/ensemble copying prody/tests/ensemble/test_functions.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/ensemble copying prody/tests/ensemble/test_ensemble.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/ensemble creating build/lib.macosx-10.14-x86_64-3.7/prody/tests/kdtree copying prody/tests/kdtree/test_kdtree.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/kdtree copying prody/tests/kdtree/init.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/kdtree creating build/lib.macosx-10.14-x86_64-3.7/prody/tests/measure copying prody/tests/measure/test_transform.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/measure copying prody/tests/measure/test_measure.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/measure copying prody/tests/measure/init.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/measure copying prody/tests/measure/test_contacts.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/measure creating build/lib.macosx-10.14-x86_64-3.7/prody/tests/proteins copying prody/tests/proteins/test_wwpdb.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/proteins copying prody/tests/proteins/test_dssp.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/proteins copying prody/tests/proteins/init.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/proteins copying prody/tests/proteins/test_header.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/proteins copying prody/tests/proteins/test_pdbfile.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/proteins copying prody/tests/proteins/test_localpdb.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/proteins creating build/lib.macosx-10.14-x86_64-3.7/prody/tests/sequence copying prody/tests/sequence/test_sequence.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/sequence copying prody/tests/sequence/test_msa.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/sequence copying prody/tests/sequence/test_analysis.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/sequence copying prody/tests/sequence/init.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/sequence copying prody/tests/sequence/test_msafile.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/sequence creating build/lib.macosx-10.14-x86_64-3.7/prody/tests/trajectory copying prody/tests/trajectory/test_frame.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/trajectory copying prody/tests/trajectory/test_dcdfile.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/trajectory copying prody/tests/trajectory/init.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/trajectory creating build/lib.macosx-10.14-x86_64-3.7/prody/tests/utilities copying prody/tests/utilities/init.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/utilities copying prody/tests/utilities/test_pathtools.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/utilities copying prody/tests/utilities/test_misctools.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/utilities copying prody/tests/utilities/test_checkers.py -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/utilities creating build/lib.macosx-10.14-x86_64-3.7/prody/utilities/datafiles copying prody/utilities/datafiles/saxs_water.dat -> build/lib.macosx-10.14-x86_64-3.7/prody/utilities/datafiles copying prody/utilities/datafiles/mod_res_map.dat -> build/lib.macosx-10.14-x86_64-3.7/prody/utilities/datafiles copying prody/tests/datafiles/pdb1r19_dssp.pdb -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/datafiles copying prody/tests/datafiles/pdb1ubi_ca.pdb -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/datafiles copying prody/tests/datafiles/pdb3mht.pdb -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/datafiles copying prody/tests/datafiles/pdb1ejg.pdb -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/datafiles copying prody/tests/datafiles/pdb1ejg_oneatom.pdb -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/datafiles copying prody/tests/datafiles/pdb2k39_truncated.pdb -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/datafiles copying prody/tests/datafiles/pdb1ubi.pdb -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/datafiles copying prody/tests/datafiles/pdb2gb1_truncated.pdb -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/datafiles copying prody/tests/datafiles/pdbRTER.pdb -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/datafiles copying prody/tests/datafiles/anm1ubi_evalues.dat -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/datafiles copying prody/tests/datafiles/gnm1ubi_evalues.dat -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/datafiles copying prody/tests/datafiles/msa_Cys_knot_di.dat -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/datafiles copying prody/tests/datafiles/anm1ubi_vectors.dat -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/datafiles copying prody/tests/datafiles/msa_Cys_knot_sca.dat -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/datafiles copying prody/tests/datafiles/gnm1ubi_vectors.dat -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/datafiles copying prody/tests/datafiles/anm1ubi_hessian.coo -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/datafiles copying prody/tests/datafiles/rtb2gb1_project.coo -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/datafiles copying prody/tests/datafiles/gnm1ubi_kirchhoff.coo -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/datafiles copying prody/tests/datafiles/rtb2gb1_hessian.coo -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/datafiles copying prody/tests/datafiles/dcd2k39_truncated.dcd -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/datafiles copying prody/tests/datafiles/xmlSTI.xml -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/datafiles copying prody/tests/datafiles/msa_Cys_knot.sth -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/datafiles copying prody/tests/datafiles/msa_Cys_knot.fasta -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/datafiles copying prody/tests/datafiles/msa_Cys_knot.slx -> build/lib.macosx-10.14-x86_64-3.7/prody/tests/datafiles running build_ext building 'prody.dynamics.rtbtools' extension creating build/temp.macosx-10.14-x86_64-3.7 creating build/temp.macosx-10.14-x86_64-3.7/prody creating build/temp.macosx-10.14-x86_64-3.7/prody/dynamics /usr/bin/clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -pipe -Os -isysroot/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk -I/private/tmp/pip-build-env-7atbnf9h/overlay/lib/python3.7/site-packages/numpy/core/include -I/opt/local/Library/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c prody/dynamics/rtbtools.c -o build/temp.macosx-10.14-x86_64-3.7/prody/dynamics/rtbtools.o error: $MACOSX_DEPLOYMENT_TARGET mismatch: now "10.9" but "10.14" during configure

ERROR: Failed building wheel for ProDy Running setup.py clean for ProDy Failed to build ProDy ERROR: Could not build wheels for ProDy which use PEP 517 and cannot be installed directly

jamesmkrieger commented 4 years ago

Please install ProDy from github instead for now. To do that, run the following commands:

git clone https://github.com/prody/ProDy.git (This make a new directory called ProDy) cd ProDy pip install --upgrade . (You can do the other bit at the beginning if you want/need to. I haven't seen that before and other users probably don't need it).

We are aware of this problem and will release a new version with a fix for it soon.

MooersLab commented 4 years ago

That worked.

A recent upgrade of Xcode may have been the cause of my trouble.