Opened 4 years ago
Closed 3 years ago
#5813 closed defect (can't reproduce)
Version conflict during ISOLDE initialization?!?
Reported by: | Owned by: | Tristan Croll | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Third Party | Version: | |
Keywords: | Cc: | Greg Couch | |
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Linux-5.11.0-43-generic-x86_64-with-glibc2.31 ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC) Description (Describe the actions that caused this problem to occur here) Log: Startup Errors --- error | Bundle 'ChimeraX-ISOLDE' custom initialization failed warning | Traceback (most recent call last): File "/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/core/toolshed/info.py", line 484, in get_module m = importlib.import_module(self.package_name) File "/usr/lib/ucsf-chimerax/lib/python3.9/importlib/__init__.py", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "<frozen importlib._bootstrap>", line 1030, in _gcd_import File "<frozen importlib._bootstrap>", line 1007, in _find_and_load File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked File "<frozen importlib._bootstrap>", line 680, in _load_unlocked File "<frozen importlib._bootstrap_external>", line 850, in exec_module File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed File "/home/jaemun/.local/share/ChimeraX/1.3/site- packages/chimerax/isolde/__init__.py", line 51, in <module> __version__ = _version() File "/home/jaemun/.local/share/ChimeraX/1.3/site- packages/chimerax/isolde/__init__.py", line 49, in _version return pkg_resources.require('ChimeraX-ISOLDE')[0].version File "/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/pkg_resources/__init__.py", line 886, in require needed = self.resolve(parse_requirements(requirements)) File "/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/pkg_resources/__init__.py", line 777, in resolve raise VersionConflict(dist, req).with_context(dependent_req) pkg_resources.ContextualVersionConflict: (ChimeraX-UI 1.2.1 (/home/jaemun/.local/share/ChimeraX/1.3/site-packages), Requirement.parse('ChimeraX-UI~=1.10'), {'ChimeraX-SaveCommand'}) During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/core/toolshed/info.py", line 359, in initialize api = self._get_api(session.logger) File "/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/core/toolshed/info.py", line 503, in _get_api m = self.get_module() File "/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/core/toolshed/info.py", line 486, in get_module raise ToolshedError("Error importing bundle %s's module: %s" % (self.name, str(e))) chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-ISOLDE's module: (ChimeraX-UI 1.2.1 (/home/jaemun/.local/share/ChimeraX/1.3/site- packages), Requirement.parse('ChimeraX-UI~=1.10'), {'ChimeraX-SaveCommand'}) UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > ui tool show Updates Errors may have occurred when running pip: pip standard error: \--- WARNING: Value for scheme.platlib does not match. Please report this to <https://github.com/pypa/pip/issues/10151> distutils: /home/jaemun/.local/share/ChimeraX/1.3/site-packages sysconfig: /home/jaemun/.local/lib/python3.9/site-packages WARNING: Value for scheme.purelib does not match. Please report this to <https://github.com/pypa/pip/issues/10151> distutils: /home/jaemun/.local/share/ChimeraX/1.3/site-packages sysconfig: /home/jaemun/.local/lib/python3.9/site-packages WARNING: Value for scheme.headers does not match. Please report this to <https://github.com/pypa/pip/issues/10151> distutils: /home/jaemun/.local/share/ChimeraX/include/python3.9/MolecularDynamicsViewer sysconfig: /home/jaemun/.local/include/python3.9/MolecularDynamicsViewer WARNING: Value for scheme.scripts does not match. Please report this to <https://github.com/pypa/pip/issues/10151> distutils: /home/jaemun/.local/share/ChimeraX/bin sysconfig: /home/jaemun/.local/bin WARNING: Value for scheme.data does not match. Please report this to <https://github.com/pypa/pip/issues/10151> distutils: /home/jaemun/.local/share/ChimeraX sysconfig: /home/jaemun/.local WARNING: Additional context: user = True home = None root = None prefix = None WARNING: Value for scheme.headers does not match. Please report this to <https://github.com/pypa/pip/issues/10151> distutils: /home/jaemun/.local/share/ChimeraX/include/python3.9/ChimeraX- Clipper sysconfig: /home/jaemun/.local/include/python3.9/ChimeraX-Clipper WARNING: Value for scheme.headers does not match. Please report this to <https://github.com/pypa/pip/issues/10151> distutils: /home/jaemun/.local/share/ChimeraX/include/python3.9/UNKNOWN sysconfig: /home/jaemun/.local/include/python3.9/UNKNOWN WARNING: You are using pip version 21.2.4; however, version 21.3.1 is available. You should consider upgrading via the '/usr/bin/chimerax -m pip install --upgrade pip' command. \--- pip standard output: \--- Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Collecting ChimeraX-Clipper==0.17.0 Using cached https://cxtoolshed.rbvi.ucsf.edu/media/chimeraxclipper/releases/0.17.0/ChimeraX_Clipper-0.17.0-cp39-cp39-manylinux_2_17_x86_64.whl (44.5 MB) Collecting MolecularDynamicsViewer==1.2 Using cached https://cxtoolshed.rbvi.ucsf.edu/media/moleculardynamicsviewer/releases/1.2/MolecularDynamicsViewer-1.2-py3-none- any.whl (6.3 kB) Installing collected packages: MolecularDynamicsViewer, ChimeraX-Clipper Attempting uninstall: MolecularDynamicsViewer Found existing installation: MolecularDynamicsViewer 1.2 Uninstalling MolecularDynamicsViewer-1.2: Successfully uninstalled MolecularDynamicsViewer-1.2 Attempting uninstall: ChimeraX-Clipper Found existing installation: ChimeraX-Clipper 0.17.0 Uninstalling ChimeraX-Clipper-0.17.0: Successfully uninstalled ChimeraX-Clipper-0.17.0 Successfully installed ChimeraX-Clipper-0.17.0 MolecularDynamicsViewer-1.2 \--- Successfully installed ChimeraX-Clipper-0.17.0 MolecularDynamicsViewer-1.2 Installed ChimeraX-Clipper (0.17.0) Installed ChimeraX-ISOLDE (1.3) Installed MolecularDynamicsViewer (1.2) Replacing data format 'MTZ' as defined by ChimeraX-Clipper with definition from ChimeraX-Clipper Traceback (most recent call last): File "/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/core/toolshed/info.py", line 484, in get_module m = importlib.import_module(self.package_name) File "/usr/lib/ucsf-chimerax/lib/python3.9/importlib/__init__.py", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "<frozen importlib._bootstrap>", line 1030, in _gcd_import File "<frozen importlib._bootstrap>", line 1007, in _find_and_load File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked File "<frozen importlib._bootstrap>", line 680, in _load_unlocked File "<frozen importlib._bootstrap_external>", line 850, in exec_module File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed File "/home/jaemun/.local/share/ChimeraX/1.3/site- packages/chimerax/isolde/__init__.py", line 51, in <module> __version__ = _version() File "/home/jaemun/.local/share/ChimeraX/1.3/site- packages/chimerax/isolde/__init__.py", line 49, in _version return pkg_resources.require('ChimeraX-ISOLDE')[0].version File "/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/pkg_resources/__init__.py", line 886, in require needed = self.resolve(parse_requirements(requirements)) File "/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/pkg_resources/__init__.py", line 777, in resolve raise VersionConflict(dist, req).with_context(dependent_req) pkg_resources.ContextualVersionConflict: (ChimeraX-UI 1.2.1 (/home/jaemun/.local/share/ChimeraX/1.3/site-packages), Requirement.parse('ChimeraX-UI~=1.10'), {'ChimeraX-SaveCommand'}) During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/core/toolshed/info.py", line 359, in initialize api = self._get_api(session.logger) File "/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/core/toolshed/info.py", line 503, in _get_api m = self.get_module() File "/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/core/toolshed/info.py", line 486, in get_module raise ToolshedError("Error importing bundle %s's module: %s" % (self.name, str(e))) chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-ISOLDE's module: (ChimeraX-UI 1.2.1 (/home/jaemun/.local/share/ChimeraX/1.3/site- packages), Requirement.parse('ChimeraX-UI~=1.10'), {'ChimeraX-SaveCommand'}) ChimeraX-ISOLDE (installed) [version: 1.3] [api package: chimerax.isolde] [category: General] [tool: ISOLDE [categories: General] [synopsis: Interactive Molecular Dynamics Flexible Fitting (iMDFF)]] [command: isolde [categories: General] [synopsis: Command-line control of ISOLDE simulations]] [command: rama [categories: General] [synopsis: Live Ramachandran validation of models]] [command: rota [categories: General] [synopsis: Live rotamer validation of models]] [command: ~rama [categories: General] [synopsis: Turn off live Ramachandran validation of models]] [command: ~rota [categories: General] [synopsis: Turn off live rotamer validation of models]]: custom initialization failed Traceback (most recent call last): File "/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/core/updateloop.py", line 129, in _redraw_timer_callback def _redraw_timer_callback(self): KeyboardInterrupt KeyboardInterrupt File "/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/core/updateloop.py", line 129, in _redraw_timer_callback def _redraw_timer_callback(self): See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 460.91.03 OpenGL renderer: GeForce GTX 1650/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: To Be Filled By O.E.M. Model: To Be Filled By O.E.M. OS: Ubuntu 20.04 focal Architecture: 64bit ELF Virutal Machine: none CPU: 16 Intel(R) Core(TM) i7-10700 CPU @ 2.90GHz Cache Size: 16384 KB Memory: total used free shared buff/cache available Mem: 31Gi 7.4Gi 16Gi 629Mi 7.7Gi 22Gi Swap: 2.0Gi 0B 2.0Gi Graphics: 01:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:2188] (rev a1) Subsystem: Micro-Star International Co., Ltd. [MSI] Device [1462:8d97] Kernel driver in use: nvidia Locale: ('en_US', 'UTF-8') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2021.10.8 cftime: 1.5.1.1 charset-normalizer: 2.0.9 ChimeraX-AddCharge: 1.2.2 ChimeraX-AddH: 2.1.3 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.31 ChimeraX-AtomicLibrary: 4.2 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.2 ChimeraX-Clipper: 0.17.0 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5 ChimeraX-CommandLine: 1.1.5 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-Cytoscape: 0.1 ChimeraX-DataFormats: 1.2.2 ChimeraX-DevelExtras: 0.4.0 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.5 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.3 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1 ChimeraX-LinuxSupport: 1.0 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.4 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.4 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.4 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.2.6 ChimeraX-ModelPanel: 1.2.1 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.7 ChimeraX-PDB: 2.6.5 ChimeraX-PDBBio: 1.0 ChimeraX-PDBImages: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-Phenix: 0.3 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RMF: 0.11 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.6.1 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-TestManager: 0.3 ChimeraX-Toolbar: 1.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.2.1 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.1 cycler: 0.11.0 Cython: 0.29.24 decorator: 5.1.0 distro: 1.6.0 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.21 imagecodecs: 2021.4.28 imagesize: 1.3.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 3.0.1 jupyter-client: 6.1.12 jupyter-core: 4.9.1 kiwisolver: 1.3.2 line-profiler: 3.3.0 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 2.0.1 matplotlib: 3.4.3 matplotlib-inline: 0.1.3 MolecularDynamicsViewer: 1.2 msgpack: 1.0.2 netCDF4: 1.5.7 networkx: 2.6.3 numexpr: 2.8.0 numpy: 1.21.2 openvr: 1.16.801 packaging: 21.3 ParmEd: 3.2.0 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 8.3.2 pip: 21.2.4 pkginfo: 1.7.1 prompt-toolkit: 3.0.23 psutil: 5.8.0 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.10.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.6 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.2 pytz: 2021.3 pyzmq: 22.3.0 qtconsole: 5.1.1 QtPy: 1.11.3 RandomWords: 0.3.0 requests: 2.26.0 scipy: 1.7.1 SEQCROW: 1.3 setuptools: 57.5.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.2.0 sphinx-autodoc-typehints: 1.12.0 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-jurko: 0.6 tables: 3.6.1 tifffile: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.7 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.0 wheel-filename: 1.3.0
Change History (3)
comment:1 by , 4 years ago
Cc: | added |
---|---|
Component: | Unassigned → Third Party |
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → assigned |
Summary: | ChimeraX bug report submission → Version conflict during ISOLDE initialization?!? |
comment:2 by , 4 years ago
comment:3 by , 3 years ago
Resolution: | → can't reproduce |
---|---|
Status: | assigned → closed |
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... huh?
I have no idea what's going on here. For the record, here is the collection of all ISOLDE's declared dependencies:
... and Clipper: