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DrugBud-Suite / DockM8

All in one Structure-Based Virtual Screening workflow based on the concept of consensus docking.
https://drugbud-suite.github.io/dockm8-web/
GNU General Public License v3.0
32 stars 5 forks source link

ERROR: Failed building wheel for prody #63

Closed P4j45 closed 1 month ago

P4j45 commented 2 months ago

Hi,

I tried the setup script as well as manual installation but both fail at the same issue. See below the output from the manual install, the steps before this all went without issues reported. This is on Ubuntu 22.04. gcc is already the newest version (4:11.2.0-1ubuntu1). Please advise. Thank you,

BW/Evert


pip install pymesh espsim oddt biopandas redo MDAnalysis==2.0.0 prody==2.1.0 Pebble tensorflow==2.15 keras==2.15 meeko posebusters streamlit -q
  error: subprocess-exited-with-error

  × Building wheel for prody (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [338 lines of output]
      running bdist_wheel
      running build
      running build_py
      creating build
      creating build/lib.linux-x86_64-cpython-310
      creating build/lib.linux-x86_64-cpython-310/prody
      copying prody/__init__.py -> build/lib.linux-x86_64-cpython-310/prody
      creating build/lib.linux-x86_64-cpython-310/prody/atomic
      copying prody/atomic/hierview.py -> build/lib.linux-x86_64-cpython-310/prody/atomic
      copying prody/atomic/pointer.py -> build/lib.linux-x86_64-cpython-310/prody/atomic
      copying prody/atomic/atom.py -> build/lib.linux-x86_64-cpython-310/prody/atomic
      copying prody/atomic/residue.py -> build/lib.linux-x86_64-cpython-310/prody/atomic
      copying prody/atomic/__init__.py -> build/lib.linux-x86_64-cpython-310/prody/atomic
      copying prody/atomic/atommap.py -> build/lib.linux-x86_64-cpython-310/prody/atomic
      copying prody/atomic/crossterm.py -> build/lib.linux-x86_64-cpython-310/prody/atomic
      copying prody/atomic/dihedral.py -> build/lib.linux-x86_64-cpython-310/prody/atomic
      copying prody/atomic/improper.py -> build/lib.linux-x86_64-cpython-310/prody/atomic
      copying prody/atomic/subset.py -> build/lib.linux-x86_64-cpython-310/prody/atomic
      copying prody/atomic/acceptor.py -> build/lib.linux-x86_64-cpython-310/prody/atomic
      copying prody/atomic/nbexclusion.py -> build/lib.linux-x86_64-cpython-310/prody/atomic
      copying prody/atomic/fields.py -> build/lib.linux-x86_64-cpython-310/prody/atomic
      copying prody/atomic/atomgroup.py -> build/lib.linux-x86_64-cpython-310/prody/atomic
      copying prody/atomic/angle.py -> build/lib.linux-x86_64-cpython-310/prody/atomic
      copying prody/atomic/select.py -> build/lib.linux-x86_64-cpython-310/prody/atomic
      copying prody/atomic/donor.py -> build/lib.linux-x86_64-cpython-310/prody/atomic
      copying prody/atomic/flags.py -> build/lib.linux-x86_64-cpython-310/prody/atomic
      copying prody/atomic/selection.py -> build/lib.linux-x86_64-cpython-310/prody/atomic
      copying prody/atomic/chain.py -> build/lib.linux-x86_64-cpython-310/prody/atomic
      copying prody/atomic/atomic.py -> build/lib.linux-x86_64-cpython-310/prody/atomic
      copying prody/atomic/functions.py -> build/lib.linux-x86_64-cpython-310/prody/atomic
      copying prody/atomic/bond.py -> build/lib.linux-x86_64-cpython-310/prody/atomic
      copying prody/atomic/segment.py -> build/lib.linux-x86_64-cpython-310/prody/atomic
      creating build/lib.linux-x86_64-cpython-310/prody/database
      copying prody/database/__init__.py -> build/lib.linux-x86_64-cpython-310/prody/database
      copying prody/database/uniprot.py -> build/lib.linux-x86_64-cpython-310/prody/database
      copying prody/database/cath.py -> build/lib.linux-x86_64-cpython-310/prody/database
      copying prody/database/pfam.py -> build/lib.linux-x86_64-cpython-310/prody/database
      copying prody/database/quartataweb.py -> build/lib.linux-x86_64-cpython-310/prody/database
      copying prody/database/goa.py -> build/lib.linux-x86_64-cpython-310/prody/database
      copying prody/database/opm.py -> build/lib.linux-x86_64-cpython-310/prody/database
      copying prody/database/dali.py -> build/lib.linux-x86_64-cpython-310/prody/database
      creating build/lib.linux-x86_64-cpython-310/prody/dynamics
      copying prody/dynamics/nmdfile.py -> build/lib.linux-x86_64-cpython-310/prody/dynamics
      copying prody/dynamics/exgnm.py -> build/lib.linux-x86_64-cpython-310/prody/dynamics
      copying prody/dynamics/pca.py -> build/lib.linux-x86_64-cpython-310/prody/dynamics
      copying prody/dynamics/gnm.py -> build/lib.linux-x86_64-cpython-310/prody/dynamics
      copying prody/dynamics/analysis.py -> build/lib.linux-x86_64-cpython-310/prody/dynamics
      copying prody/dynamics/editing.py -> build/lib.linux-x86_64-cpython-310/prody/dynamics
      copying prody/dynamics/__init__.py -> build/lib.linux-x86_64-cpython-310/prody/dynamics
      copying prody/dynamics/exanm.py -> build/lib.linux-x86_64-cpython-310/prody/dynamics
      copying prody/dynamics/nma.py -> build/lib.linux-x86_64-cpython-310/prody/dynamics
      copying prody/dynamics/vmdfile.py -> build/lib.linux-x86_64-cpython-310/prody/dynamics
      copying prody/dynamics/mode.py -> build/lib.linux-x86_64-cpython-310/prody/dynamics
      copying prody/dynamics/sampling.py -> build/lib.linux-x86_64-cpython-310/prody/dynamics
      copying prody/dynamics/adaptive.py -> build/lib.linux-x86_64-cpython-310/prody/dynamics
      copying prody/dynamics/rtb.py -> build/lib.linux-x86_64-cpython-310/prody/dynamics
      copying prody/dynamics/anm.py -> build/lib.linux-x86_64-cpython-310/prody/dynamics
      copying prody/dynamics/bbenm.py -> build/lib.linux-x86_64-cpython-310/prody/dynamics
      copying prody/dynamics/essa.py -> build/lib.linux-x86_64-cpython-310/prody/dynamics
      copying prody/dynamics/perturb.py -> build/lib.linux-x86_64-cpython-310/prody/dynamics
      copying prody/dynamics/mechstiff.py -> build/lib.linux-x86_64-cpython-310/prody/dynamics
      copying prody/dynamics/clustenm.py -> build/lib.linux-x86_64-cpython-310/prody/dynamics
      copying prody/dynamics/plotting.py -> build/lib.linux-x86_64-cpython-310/prody/dynamics
      copying prody/dynamics/heatmapper.py -> build/lib.linux-x86_64-cpython-310/prody/dynamics
      copying prody/dynamics/signature.py -> build/lib.linux-x86_64-cpython-310/prody/dynamics
      copying prody/dynamics/gamma.py -> build/lib.linux-x86_64-cpython-310/prody/dynamics
      copying prody/dynamics/functions.py -> build/lib.linux-x86_64-cpython-310/prody/dynamics
      copying prody/dynamics/compare.py -> build/lib.linux-x86_64-cpython-310/prody/dynamics
      copying prody/dynamics/modeset.py -> build/lib.linux-x86_64-cpython-310/prody/dynamics
      copying prody/dynamics/entropy.py -> build/lib.linux-x86_64-cpython-310/prody/dynamics
      copying prody/dynamics/imanm.py -> build/lib.linux-x86_64-cpython-310/prody/dynamics
      creating build/lib.linux-x86_64-cpython-310/prody/ensemble
      copying prody/ensemble/__init__.py -> build/lib.linux-x86_64-cpython-310/prody/ensemble
      copying prody/ensemble/conformation.py -> build/lib.linux-x86_64-cpython-310/prody/ensemble
      copying prody/ensemble/ensemble.py -> build/lib.linux-x86_64-cpython-310/prody/ensemble
      copying prody/ensemble/functions.py -> build/lib.linux-x86_64-cpython-310/prody/ensemble
      copying prody/ensemble/pdbensemble.py -> build/lib.linux-x86_64-cpython-310/prody/ensemble
      creating build/lib.linux-x86_64-cpython-310/prody/kdtree
      copying prody/kdtree/kdtree.py -> build/lib.linux-x86_64-cpython-310/prody/kdtree
      copying prody/kdtree/__init__.py -> build/lib.linux-x86_64-cpython-310/prody/kdtree
      creating build/lib.linux-x86_64-cpython-310/prody/measure
      copying prody/measure/contacts.py -> build/lib.linux-x86_64-cpython-310/prody/measure
      copying prody/measure/__init__.py -> build/lib.linux-x86_64-cpython-310/prody/measure
      copying prody/measure/measure.py -> build/lib.linux-x86_64-cpython-310/prody/measure
      copying prody/measure/transform.py -> build/lib.linux-x86_64-cpython-310/prody/measure
      creating build/lib.linux-x86_64-cpython-310/prody/proteins
      copying prody/proteins/ciffile.py -> build/lib.linux-x86_64-cpython-310/prody/proteins
      copying prody/proteins/stride.py -> build/lib.linux-x86_64-cpython-310/prody/proteins
      copying prody/proteins/localpdb.py -> build/lib.linux-x86_64-cpython-310/prody/proteins
      copying prody/proteins/pdbclusters.py -> build/lib.linux-x86_64-cpython-310/prody/proteins
      copying prody/proteins/__init__.py -> build/lib.linux-x86_64-cpython-310/prody/proteins
      copying prody/proteins/emdfile.py -> build/lib.linux-x86_64-cpython-310/prody/proteins
      copying prody/proteins/starfile.py -> build/lib.linux-x86_64-cpython-310/prody/proteins
      copying prody/proteins/wwpdb.py -> build/lib.linux-x86_64-cpython-310/prody/proteins
      copying prody/proteins/pdbfile.py -> build/lib.linux-x86_64-cpython-310/prody/proteins
      copying prody/proteins/header.py -> build/lib.linux-x86_64-cpython-310/prody/proteins
      copying prody/proteins/dssp.py -> build/lib.linux-x86_64-cpython-310/prody/proteins
      copying prody/proteins/cifheader.py -> build/lib.linux-x86_64-cpython-310/prody/proteins
      copying prody/proteins/functions.py -> build/lib.linux-x86_64-cpython-310/prody/proteins
      copying prody/proteins/compare.py -> build/lib.linux-x86_64-cpython-310/prody/proteins
      copying prody/proteins/blastpdb.py -> build/lib.linux-x86_64-cpython-310/prody/proteins
      creating build/lib.linux-x86_64-cpython-310/prody/sequence
      copying prody/sequence/analysis.py -> build/lib.linux-x86_64-cpython-310/prody/sequence
      copying prody/sequence/__init__.py -> build/lib.linux-x86_64-cpython-310/prody/sequence
      copying prody/sequence/msafile.py -> build/lib.linux-x86_64-cpython-310/prody/sequence
      copying prody/sequence/sequence.py -> build/lib.linux-x86_64-cpython-310/prody/sequence
      copying prody/sequence/msa.py -> build/lib.linux-x86_64-cpython-310/prody/sequence
      copying prody/sequence/plotting.py -> build/lib.linux-x86_64-cpython-310/prody/sequence
      creating build/lib.linux-x86_64-cpython-310/prody/trajectory
      copying prody/trajectory/dcdfile.py -> build/lib.linux-x86_64-cpython-310/prody/trajectory
      copying prody/trajectory/frame.py -> build/lib.linux-x86_64-cpython-310/prody/trajectory
      copying prody/trajectory/__init__.py -> build/lib.linux-x86_64-cpython-310/prody/trajectory
      copying prody/trajectory/trajectory.py -> build/lib.linux-x86_64-cpython-310/prody/trajectory
      copying prody/trajectory/psffile.py -> build/lib.linux-x86_64-cpython-310/prody/trajectory
      copying prody/trajectory/trajfile.py -> build/lib.linux-x86_64-cpython-310/prody/trajectory
      copying prody/trajectory/trajbase.py -> build/lib.linux-x86_64-cpython-310/prody/trajectory
      creating build/lib.linux-x86_64-cpython-310/prody/chromatin
      copying prody/chromatin/straw.py -> build/lib.linux-x86_64-cpython-310/prody/chromatin
      copying prody/chromatin/__init__.py -> build/lib.linux-x86_64-cpython-310/prody/chromatin
      copying prody/chromatin/cluster.py -> build/lib.linux-x86_64-cpython-310/prody/chromatin
      copying prody/chromatin/hic.py -> build/lib.linux-x86_64-cpython-310/prody/chromatin
      copying prody/chromatin/functions.py -> build/lib.linux-x86_64-cpython-310/prody/chromatin
      copying prody/chromatin/norm.py -> build/lib.linux-x86_64-cpython-310/prody/chromatin
      creating build/lib.linux-x86_64-cpython-310/prody/compounds
      copying prody/compounds/__init__.py -> build/lib.linux-x86_64-cpython-310/prody/compounds
      copying prody/compounds/bird.py -> build/lib.linux-x86_64-cpython-310/prody/compounds
      copying prody/compounds/pdbligands.py -> build/lib.linux-x86_64-cpython-310/prody/compounds
      copying prody/compounds/ccd.py -> build/lib.linux-x86_64-cpython-310/prody/compounds
      copying prody/compounds/functions.py -> build/lib.linux-x86_64-cpython-310/prody/compounds
      creating build/lib.linux-x86_64-cpython-310/prody/domain_decomposition
      copying prody/domain_decomposition/__init__.py -> build/lib.linux-x86_64-cpython-310/prody/domain_decomposition
      copying prody/domain_decomposition/spectrus.py -> build/lib.linux-x86_64-cpython-310/prody/domain_decomposition
      creating build/lib.linux-x86_64-cpython-310/prody/utilities
      copying prody/utilities/TreeConstruction.py -> build/lib.linux-x86_64-cpython-310/prody/utilities
      copying prody/utilities/checkers.py -> build/lib.linux-x86_64-cpython-310/prody/utilities
      copying prody/utilities/seqtools.py -> build/lib.linux-x86_64-cpython-310/prody/utilities
      copying prody/utilities/__init__.py -> build/lib.linux-x86_64-cpython-310/prody/utilities
      copying prody/utilities/legacy.py -> build/lib.linux-x86_64-cpython-310/prody/utilities
      copying prody/utilities/laptools.py -> build/lib.linux-x86_64-cpython-310/prody/utilities
      copying prody/utilities/misctools.py -> build/lib.linux-x86_64-cpython-310/prody/utilities
      copying prody/utilities/settings.py -> build/lib.linux-x86_64-cpython-310/prody/utilities
      copying prody/utilities/catchall.py -> build/lib.linux-x86_64-cpython-310/prody/utilities
      copying prody/utilities/pathtools.py -> build/lib.linux-x86_64-cpython-310/prody/utilities
      copying prody/utilities/drawtools.py -> build/lib.linux-x86_64-cpython-310/prody/utilities
      copying prody/utilities/doctools.py -> build/lib.linux-x86_64-cpython-310/prody/utilities
      copying prody/utilities/eigtools.py -> build/lib.linux-x86_64-cpython-310/prody/utilities
      copying prody/utilities/logger.py -> build/lib.linux-x86_64-cpython-310/prody/utilities
      creating build/lib.linux-x86_64-cpython-310/prody/apps
      copying prody/apps/__init__.py -> build/lib.linux-x86_64-cpython-310/prody/apps
      copying prody/apps/apptools.py -> build/lib.linux-x86_64-cpython-310/prody/apps
      creating build/lib.linux-x86_64-cpython-310/prody/apps/prody_apps
      copying prody/apps/prody_apps/prody_gnm.py -> build/lib.linux-x86_64-cpython-310/prody/apps/prody_apps
      copying prody/apps/prody_apps/__init__.py -> build/lib.linux-x86_64-cpython-310/prody/apps/prody_apps
      copying prody/apps/prody_apps/prody_catdcd.py -> build/lib.linux-x86_64-cpython-310/prody/apps/prody_apps
      copying prody/apps/prody_apps/prody_align.py -> build/lib.linux-x86_64-cpython-310/prody/apps/prody_apps
      copying prody/apps/prody_apps/prody_pca.py -> build/lib.linux-x86_64-cpython-310/prody/apps/prody_apps
      copying prody/apps/prody_apps/prody_select.py -> build/lib.linux-x86_64-cpython-310/prody/apps/prody_apps
      copying prody/apps/prody_apps/prody_anm.py -> build/lib.linux-x86_64-cpython-310/prody/apps/prody_apps
      copying prody/apps/prody_apps/prody_contacts.py -> build/lib.linux-x86_64-cpython-310/prody/apps/prody_apps
      copying prody/apps/prody_apps/prody_blast.py -> build/lib.linux-x86_64-cpython-310/prody/apps/prody_apps
      copying prody/apps/prody_apps/nmaoptions.py -> build/lib.linux-x86_64-cpython-310/prody/apps/prody_apps
      copying prody/apps/prody_apps/prody_eda.py -> build/lib.linux-x86_64-cpython-310/prody/apps/prody_apps
      copying prody/apps/prody_apps/prody_fetch.py -> build/lib.linux-x86_64-cpython-310/prody/apps/prody_apps
      copying prody/apps/prody_apps/prody_biomol.py -> build/lib.linux-x86_64-cpython-310/prody/apps/prody_apps
      creating build/lib.linux-x86_64-cpython-310/prody/apps/evol_apps
      copying prody/apps/evol_apps/evol_coevol.py -> build/lib.linux-x86_64-cpython-310/prody/apps/evol_apps
      copying prody/apps/evol_apps/evol_fetch.py -> build/lib.linux-x86_64-cpython-310/prody/apps/evol_apps
      copying prody/apps/evol_apps/__init__.py -> build/lib.linux-x86_64-cpython-310/prody/apps/evol_apps
      copying prody/apps/evol_apps/evol_occupancy.py -> build/lib.linux-x86_64-cpython-310/prody/apps/evol_apps
      copying prody/apps/evol_apps/evol_conserv.py -> build/lib.linux-x86_64-cpython-310/prody/apps/evol_apps
      copying prody/apps/evol_apps/evol_filter.py -> build/lib.linux-x86_64-cpython-310/prody/apps/evol_apps
      copying prody/apps/evol_apps/evol_rankorder.py -> build/lib.linux-x86_64-cpython-310/prody/apps/evol_apps
      copying prody/apps/evol_apps/evol_merge.py -> build/lib.linux-x86_64-cpython-310/prody/apps/evol_apps
      copying prody/apps/evol_apps/evol_search.py -> build/lib.linux-x86_64-cpython-310/prody/apps/evol_apps
      copying prody/apps/evol_apps/evol_refine.py -> build/lib.linux-x86_64-cpython-310/prody/apps/evol_apps
      creating build/lib.linux-x86_64-cpython-310/prody/tests
      copying prody/tests/__init__.py -> build/lib.linux-x86_64-cpython-310/prody/tests
      creating build/lib.linux-x86_64-cpython-310/prody/tests/apps
      copying prody/tests/apps/__init__.py -> build/lib.linux-x86_64-cpython-310/prody/tests/apps
      copying prody/tests/apps/test_prody_examples.py -> build/lib.linux-x86_64-cpython-310/prody/tests/apps
      copying prody/tests/apps/test_prody_gnm.py -> build/lib.linux-x86_64-cpython-310/prody/tests/apps
      copying prody/tests/apps/test_prody_pca.py -> build/lib.linux-x86_64-cpython-310/prody/tests/apps
      copying prody/tests/apps/test_prody_catdcd.py -> build/lib.linux-x86_64-cpython-310/prody/tests/apps
      copying prody/tests/apps/test_prody_anm.py -> build/lib.linux-x86_64-cpython-310/prody/tests/apps
      creating build/lib.linux-x86_64-cpython-310/prody/tests/atomic
      copying prody/tests/atomic/test_subset.py -> build/lib.linux-x86_64-cpython-310/prody/tests/atomic
      copying prody/tests/atomic/test_fragment.py -> build/lib.linux-x86_64-cpython-310/prody/tests/atomic
      copying prody/tests/atomic/__init__.py -> build/lib.linux-x86_64-cpython-310/prody/tests/atomic
      copying prody/tests/atomic/test_atomic.py -> build/lib.linux-x86_64-cpython-310/prody/tests/atomic
      copying prody/tests/atomic/test_hierview.py -> build/lib.linux-x86_64-cpython-310/prody/tests/atomic
      copying prody/tests/atomic/test_select.py -> build/lib.linux-x86_64-cpython-310/prody/tests/atomic
      copying prody/tests/atomic/test_atommap.py -> build/lib.linux-x86_64-cpython-310/prody/tests/atomic
      creating build/lib.linux-x86_64-cpython-310/prody/tests/datafiles
      copying prody/tests/datafiles/__init__.py -> build/lib.linux-x86_64-cpython-310/prody/tests/datafiles
      creating build/lib.linux-x86_64-cpython-310/prody/tests/dynamics
      copying prody/tests/dynamics/test_signature.py -> build/lib.linux-x86_64-cpython-310/prody/tests/dynamics
      copying prody/tests/dynamics/__init__.py -> build/lib.linux-x86_64-cpython-310/prody/tests/dynamics
      copying prody/tests/dynamics/test_enms.py -> build/lib.linux-x86_64-cpython-310/prody/tests/dynamics
      copying prody/tests/dynamics/test_editing.py -> build/lib.linux-x86_64-cpython-310/prody/tests/dynamics
      copying prody/tests/dynamics/test_pca.py -> build/lib.linux-x86_64-cpython-310/prody/tests/dynamics
      creating build/lib.linux-x86_64-cpython-310/prody/tests/ensemble
      copying prody/tests/ensemble/test_functions.py -> build/lib.linux-x86_64-cpython-310/prody/tests/ensemble
      copying prody/tests/ensemble/__init__.py -> build/lib.linux-x86_64-cpython-310/prody/tests/ensemble
      copying prody/tests/ensemble/test_ensemble.py -> build/lib.linux-x86_64-cpython-310/prody/tests/ensemble
      copying prody/tests/ensemble/test_conformation.py -> build/lib.linux-x86_64-cpython-310/prody/tests/ensemble
      copying prody/tests/ensemble/test_pdbensemble.py -> build/lib.linux-x86_64-cpython-310/prody/tests/ensemble
      creating build/lib.linux-x86_64-cpython-310/prody/tests/kdtree
      copying prody/tests/kdtree/__init__.py -> build/lib.linux-x86_64-cpython-310/prody/tests/kdtree
      copying prody/tests/kdtree/test_kdtree.py -> build/lib.linux-x86_64-cpython-310/prody/tests/kdtree
      creating build/lib.linux-x86_64-cpython-310/prody/tests/measure
      copying prody/tests/measure/test_measure.py -> build/lib.linux-x86_64-cpython-310/prody/tests/measure
      copying prody/tests/measure/__init__.py -> build/lib.linux-x86_64-cpython-310/prody/tests/measure
      copying prody/tests/measure/test_transform.py -> build/lib.linux-x86_64-cpython-310/prody/tests/measure
      copying prody/tests/measure/test_contacts.py -> build/lib.linux-x86_64-cpython-310/prody/tests/measure
      creating build/lib.linux-x86_64-cpython-310/prody/tests/proteins
      copying prody/tests/proteins/test_localpdb.py -> build/lib.linux-x86_64-cpython-310/prody/tests/proteins
      copying prody/tests/proteins/test_wwpdb.py -> build/lib.linux-x86_64-cpython-310/prody/tests/proteins
      copying prody/tests/proteins/__init__.py -> build/lib.linux-x86_64-cpython-310/prody/tests/proteins
      copying prody/tests/proteins/test_header.py -> build/lib.linux-x86_64-cpython-310/prody/tests/proteins
      copying prody/tests/proteins/test_dssp.py -> build/lib.linux-x86_64-cpython-310/prody/tests/proteins
      copying prody/tests/proteins/test_pdbfile.py -> build/lib.linux-x86_64-cpython-310/prody/tests/proteins
      creating build/lib.linux-x86_64-cpython-310/prody/tests/sequence
      copying prody/tests/sequence/test_msafile.py -> build/lib.linux-x86_64-cpython-310/prody/tests/sequence
      copying prody/tests/sequence/__init__.py -> build/lib.linux-x86_64-cpython-310/prody/tests/sequence
      copying prody/tests/sequence/test_sequence.py -> build/lib.linux-x86_64-cpython-310/prody/tests/sequence
      copying prody/tests/sequence/test_msa.py -> build/lib.linux-x86_64-cpython-310/prody/tests/sequence
      copying prody/tests/sequence/test_analysis.py -> build/lib.linux-x86_64-cpython-310/prody/tests/sequence
      creating build/lib.linux-x86_64-cpython-310/prody/tests/trajectory
      copying prody/tests/trajectory/test_frame.py -> build/lib.linux-x86_64-cpython-310/prody/tests/trajectory
      copying prody/tests/trajectory/__init__.py -> build/lib.linux-x86_64-cpython-310/prody/tests/trajectory
      copying prody/tests/trajectory/test_dcdfile.py -> build/lib.linux-x86_64-cpython-310/prody/tests/trajectory
      creating build/lib.linux-x86_64-cpython-310/prody/tests/utilities
      copying prody/tests/utilities/test_pathtools.py -> build/lib.linux-x86_64-cpython-310/prody/tests/utilities
      copying prody/tests/utilities/__init__.py -> build/lib.linux-x86_64-cpython-310/prody/tests/utilities
      copying prody/tests/utilities/test_misctools.py -> build/lib.linux-x86_64-cpython-310/prody/tests/utilities
      copying prody/tests/utilities/test_checkers.py -> build/lib.linux-x86_64-cpython-310/prody/tests/utilities
      creating build/lib.linux-x86_64-cpython-310/prody/utilities/datafiles
      copying prody/utilities/datafiles/mod_res_map.dat -> build/lib.linux-x86_64-cpython-310/prody/utilities/datafiles
      copying prody/utilities/datafiles/saxs_water.dat -> build/lib.linux-x86_64-cpython-310/prody/utilities/datafiles
      copying prody/tests/datafiles/pdb1tw7_step3_charmm2namd.pdb -> build/lib.linux-x86_64-cpython-310/prody/tests/datafiles
      copying prody/tests/datafiles/pdbRTER.pdb -> build/lib.linux-x86_64-cpython-310/prody/tests/datafiles
      copying prody/tests/datafiles/pdb1ejg.pdb -> build/lib.linux-x86_64-cpython-310/prody/tests/datafiles
      copying prody/tests/datafiles/pdb1tw7_step3_charmm2namd_doubled_h36.pdb -> build/lib.linux-x86_64-cpython-310/prody/tests/datafiles
      copying prody/tests/datafiles/pdb1r19_dssp.pdb -> build/lib.linux-x86_64-cpython-310/prody/tests/datafiles
      copying prody/tests/datafiles/pdb1ejg_oneatom.pdb -> build/lib.linux-x86_64-cpython-310/prody/tests/datafiles
      copying prody/tests/datafiles/pdb2k39_ca.pdb -> build/lib.linux-x86_64-cpython-310/prody/tests/datafiles
      copying prody/tests/datafiles/pdb2gb1_truncated.pdb -> build/lib.linux-x86_64-cpython-310/prody/tests/datafiles
      copying prody/tests/datafiles/pdb1ubi.pdb -> build/lib.linux-x86_64-cpython-310/prody/tests/datafiles
      copying prody/tests/datafiles/pdb1tw7_step3_charmm2namd_doubled_hex.pdb -> build/lib.linux-x86_64-cpython-310/prody/tests/datafiles
      copying prody/tests/datafiles/pdb2nwl-opm.pdb -> build/lib.linux-x86_64-cpython-310/prody/tests/datafiles
      copying prody/tests/datafiles/pdb3mht.pdb -> build/lib.linux-x86_64-cpython-310/prody/tests/datafiles
      copying prody/tests/datafiles/pdb2k39_truncated.pdb -> build/lib.linux-x86_64-cpython-310/prody/tests/datafiles
      copying prody/tests/datafiles/pdb1ubi_ca.pdb -> build/lib.linux-x86_64-cpython-310/prody/tests/datafiles
      copying prody/tests/datafiles/commute1ubi.dat -> build/lib.linux-x86_64-cpython-310/prody/tests/datafiles
      copying prody/tests/datafiles/gnm1ubi_vectors.dat -> build/lib.linux-x86_64-cpython-310/prody/tests/datafiles
      copying prody/tests/datafiles/exanm2nwl_evalues.dat -> build/lib.linux-x86_64-cpython-310/prody/tests/datafiles
      copying prody/tests/datafiles/pca2k39_vectors.dat -> build/lib.linux-x86_64-cpython-310/prody/tests/datafiles
      copying prody/tests/datafiles/hit1ubi.dat -> build/lib.linux-x86_64-cpython-310/prody/tests/datafiles
      copying prody/tests/datafiles/gnm1ubi_evalues.dat -> build/lib.linux-x86_64-cpython-310/prody/tests/datafiles
      copying prody/tests/datafiles/msa_Cys_knot_di.dat -> build/lib.linux-x86_64-cpython-310/prody/tests/datafiles
      copying prody/tests/datafiles/anm1ubi_evalues.dat -> build/lib.linux-x86_64-cpython-310/prody/tests/datafiles
      copying prody/tests/datafiles/msa_Cys_knot_sca.dat -> build/lib.linux-x86_64-cpython-310/prody/tests/datafiles
      copying prody/tests/datafiles/anm1ubi_vectors.dat -> build/lib.linux-x86_64-cpython-310/prody/tests/datafiles
      copying prody/tests/datafiles/exanm2nwl_vectors.dat -> build/lib.linux-x86_64-cpython-310/prody/tests/datafiles
      copying prody/tests/datafiles/pca2k39_evalues.dat -> build/lib.linux-x86_64-cpython-310/prody/tests/datafiles
      copying prody/tests/datafiles/pca2k39_cov.coo -> build/lib.linux-x86_64-cpython-310/prody/tests/datafiles
      copying prody/tests/datafiles/rtb2gb1_hessian.coo -> build/lib.linux-x86_64-cpython-310/prody/tests/datafiles
      copying prody/tests/datafiles/exanm2nwl_hessian.coo -> build/lib.linux-x86_64-cpython-310/prody/tests/datafiles
      copying prody/tests/datafiles/anm1ubi_hessian.coo -> build/lib.linux-x86_64-cpython-310/prody/tests/datafiles
      copying prody/tests/datafiles/rtb2gb1_project.coo -> build/lib.linux-x86_64-cpython-310/prody/tests/datafiles
      copying prody/tests/datafiles/gnm1ubi_kirchhoff.coo -> build/lib.linux-x86_64-cpython-310/prody/tests/datafiles
      copying prody/tests/datafiles/dcd2k39_truncated.dcd -> build/lib.linux-x86_64-cpython-310/prody/tests/datafiles
      copying prody/tests/datafiles/xmlSTI.xml -> build/lib.linux-x86_64-cpython-310/prody/tests/datafiles
      copying prody/tests/datafiles/msa_Cys_knot.fasta -> build/lib.linux-x86_64-cpython-310/prody/tests/datafiles
      copying prody/tests/datafiles/msa_Cys_knot.slx -> build/lib.linux-x86_64-cpython-310/prody/tests/datafiles
      copying prody/tests/datafiles/msa_Cys_knot.sth -> build/lib.linux-x86_64-cpython-310/prody/tests/datafiles
      running build_ext
      building 'prody.dynamics.rtbtools' extension
      creating build/temp.linux-x86_64-cpython-310
      creating build/temp.linux-x86_64-cpython-310/prody
      creating build/temp.linux-x86_64-cpython-310/prody/dynamics
      gcc -pthread -B /home/evehom/miniconda3/envs/dockm8/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/evehom/miniconda3/envs/dockm8/include -fPIC -O2 -isystem /home/evehom/miniconda3/envs/dockm8/include -fPIC -I/tmp/pip-build-env-sn15fqlu/overlay/lib/python3.10/site-packages/numpy/_core/include -I/home/evehom/miniconda3/envs/dockm8/include/python3.10 -c prody/dynamics/rtbtools.c -o build/temp.linux-x86_64-cpython-310/prody/dynamics/rtbtools.o
      In file included from /tmp/pip-build-env-sn15fqlu/overlay/lib/python3.10/site-packages/numpy/_core/include/numpy/npy_common.h:380,
                       from /tmp/pip-build-env-sn15fqlu/overlay/lib/python3.10/site-packages/numpy/_core/include/numpy/ndarraytypes.h:4,
                       from /tmp/pip-build-env-sn15fqlu/overlay/lib/python3.10/site-packages/numpy/_core/include/numpy/ndarrayobject.h:12,
                       from /tmp/pip-build-env-sn15fqlu/overlay/lib/python3.10/site-packages/numpy/_core/include/numpy/arrayobject.h:5,
                       from prody/dynamics/rtbtools.c:9:
      prody/dynamics/rtbtools.c: In function ‘dblock_projections2’:
      prody/dynamics/rtbtools.c:422:17: error: expected identifier or ‘(’ before ‘__extension__’
        422 |   double **X, **I, **IC, *CM, *W, **A, **ISQT;
            |                 ^
      prody/dynamics/rtbtools.c:431:3: error: ‘CM’ undeclared (first use in this function)
        431 |   CM = dvector(1, 3);
            |   ^~
      prody/dynamics/rtbtools.c:431:3: note: each undeclared identifier is reported only once for each function it appears in
      prody/dynamics/rtbtools.c:432:5: error: lvalue required as left operand of assignment
        432 |   I = dmatrix(1, 3, 1, 3);
            |     ^
      prody/dynamics/rtbtools.c:433:3: error: ‘IC’ undeclared (first use in this function); did you mean ‘I’?
        433 |   IC = dmatrix(1, 3, 1, 3);
            |   ^~
            |   I
      prody/dynamics/rtbtools.c:434:3: error: ‘W’ undeclared (first use in this function)
        434 |   W = dvector(1, 3);
            |   ^
      prody/dynamics/rtbtools.c:435:3: error: ‘A’ undeclared (first use in this function)
        435 |   A = dmatrix(1, 3, 1, 3);
            |   ^
      prody/dynamics/rtbtools.c:436:3: error: ‘ISQT’ undeclared (first use in this function)
        436 |   ISQT = dmatrix(1, 3, 1, 3);
            |   ^~~~
      prody/dynamics/rtbtools.c:445:28: error: subscripted value is neither array nor pointer nor vector
        445 |       for(i=1; i<=3; i++) I[i][j] = 0.0;
            |                            ^
      prody/dynamics/rtbtools.c:481:10: error: subscripted value is neither array nor pointer nor vector
        481 |         I[i][i] += (dd - X[k][i] * X[k][i]);
            |          ^
      prody/dynamics/rtbtools.c:484:12: error: subscripted value is neither array nor pointer nor vector
        484 |           I[i][j] -= X[k][i]*X[k][j];
            |            ^
      prody/dynamics/rtbtools.c:485:12: error: subscripted value is neither array nor pointer nor vector
        485 |           I[j][i] = I[i][j];
            |            ^
      prody/dynamics/rtbtools.c:485:22: error: subscripted value is neither array nor pointer nor vector
        485 |           I[j][i] = I[i][j];
            |                      ^
      prody/dynamics/rtbtools.c:493:25: error: subscripted value is neither array nor pointer nor vector
        493 |               IC[i][j]=I[i][j];
            |                         ^
      prody/dynamics/rtbtools.c:548:16: error: incompatible type for argument 1 of ‘free_dmatrix’
        548 |   free_dmatrix(I, 1, 3, 1, 3);
            |                ^
            |                |
            |                complex float
      prody/dynamics/rtbtools.c:72:28: note: expected ‘double **’ but argument is of type ‘complex float’
         72 | void free_dmatrix(double **m, long nrl, long nrh, long ncl, long nch);
            |                   ~~~~~~~~~^
      error: command '/usr/bin/gcc' failed with exit code 1
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for prody
Tonylac77 commented 2 months ago

Hi, thanks for highlighting this. I could not reproduce the issue on a clean python 3.10 environment. Can you please ensure build-essential is installed on Ubuntu or install it using : sudo apt-get install build-essential This is the most likely culprit, if the issue keeps occurring you can try installing prody from the source distribution using pip install prody==2.1.0 --no-binary=prody. If that still doesn't work I will check if v2.1 is actually required or if you can downgrade to v2.0.

Tonylac77 commented 2 months ago

It also seems the issue may be arising from numpy, I am using numpy 1.26.4 for reference.

P4j45 commented 2 months ago 
sudo apt-get install build-essential
[sudo] password for evehom: 
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
build-essential is already the newest version (12.9ubuntu3).
0 upgraded, 0 newly installed, 0 to remove and 208 not upgraded.
P4j45 commented 2 months ago

Changing prody==2.1.0 to prody==2.0.0. in the setup script does not seem to fix this

Tonylac77 commented 2 months ago

You can also try ensuring the python 3 dev headers are installed (sudo apt-get install python3-dev), beyond that, you can try ensuring that the following packages are up to date : pip install --upgrade pip setuptools wheel Beyond that, I would suggest raising the issue with the prody team. (https://github.com/prody/ProDy) Sorry if I can't be of more help than that. The packages are required to run the RTMScore scoring function (although there could be more obscure dependencies), if you don't plan on using RTMScore you can proceed with the manual installation without those. If an issue arises in that case please let me know.

Evert-Homan commented 2 months ago

Please explain what this ZIP file contains, I am not going to polute my PC with something unknown

Tonylac77 commented 2 months ago

I'm not sure what zip file you are referring to.

Evert-Homan commented 2 months ago

There were 2 comments from different users referring to the same ZIP file related to gcc. They seem to have been deleted.

Tonylac77 commented 1 month ago

@Evert-Homan Quick update, I could replicate the issue on a clean install of DockM8 (new WSL install, latest build-essentials etc.). However, running pip install prody (which installed prody 2.4.1) after all other dependencies were installed seemed to work. I will update the docs and installer to reflect this. If you still have the issue and want to try this I would love to know if that works for you.

Evert-Homan commented 1 month ago

Still the same problem. What did you change? Am I meant to run the setup script directly in my home directory? I see a lot of error messages along the lines of

mkdir: cannot create directory ‘/home/evehom/DockM8/software’: No such file or directory
./setup.sh: line 188: cd: /home/evehom/DockM8/software: No such file or directory
Tonylac77 commented 1 month ago

Hi, Sorry for the continued issues. The installer now installs the prody package last. I would recommend deleting any previous DockM8 installation (remove the DockM8 folder and conda env remove -n dockm8 to remove the environment) and downloading the latest release (1.0.5). When running the installer, it should be run from the installer location :

  1. cd /path/to/setup_py310.sh
  2. chmod +x ./setup_py310.sh
  3. ./setup_py310.sh

Please let me know if you still encounter issues

Evert-Homan commented 1 month ago

Hi,

No error messages this time, so progress. I see there is a conda environment called dockm8_test now after running the setup script. But how do I run the GUI? I activate dockm8_test and then invoke

streamlit run gui.py

(dockm8_test) evehom@everthodell:~/dockm8/DockM8/software$ streamlit run gui.py
Usage: streamlit run [OPTIONS] TARGET [ARGS]...
Try 'streamlit run --help' for help.

Error: Invalid value: File does not exist: gui.py

Where should this file be located? Thanks for your patience,

Evert

Evert-Homan commented 1 month ago

After a fresh install:

evehom@everthodell:~$ cd DockM8/
evehom@everthodell:~/DockM8$ conda activate dockm8

EnvironmentNameNotFound: Could not find conda environment: dockm8
You can list all discoverable environments with `conda info --envs`.

evehom@everthodell:~/DockM8$ conda info --envs
# conda environments:
#
base                     /home/evehom/miniconda3
admet_ai                 /home/evehom/miniconda3/envs/admet_ai
chemprop_v1              /home/evehom/miniconda3/envs/chemprop_v1
dockm8_test              /home/evehom/miniconda3/envs/dockm8_test
gypsum_dl                /home/evehom/miniconda3/envs/gypsum_dl

evehom@everthodell:~/DockM8$ conda activate dockm8_test
(dockm8_test) evehom@everthodell:~/DockM8$ streamlit run gui.py
Usage: streamlit run [OPTIONS] TARGET [ARGS]...
Try 'streamlit run --help' for help.

Error: Invalid value: File does not exist: gui.py
(dockm8_test) evehom@everthodell:~/DockM8$
Tonylac77 commented 1 month ago

Hi, the dockm8_test naming was a mistake. I've edited the file now, you can either rerun the installer to get the correct environment name (in that case, delete the DockM8 folder and environment as before) or you can keep running with the dockm8_test environment, only the name changes. Not finding the gui.py is odd, it should have been downloaded at the same time as the rest of dockm8 during the installation. When running the installer (if only downloading the installer from the release page 1.0.5 ensure no DockM8 folder or dockm8.py is present in the folder from which you running the installer. I will work on an improved version of the installer right now so you will have less trouble in the future.

Evert-Homan commented 1 month ago

Tried this today on Ubuntu 22.04. The latest setup script doesn't even find my miniconda, tries to install it. Since I don't want to screw up my environment I broke off the installation. I'm sorry but I am giving up on this, am getting very tired of open source code that doesn't work. Schrödinger may be expensive but at least it works.

Good luck and thanks for your support/Evert