id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2061 Uninstall Clipper: JSONDecodeError Scooter Morris Conrad Huang "{{{ The following bug report has been submitted: Platform: Darwin-18.2.0-x86_64-i386-64bit ChimeraX Version: 0.9 (2019-06-06) Description Since ISOLDE wasn't working, I tried to uninstall it and got this... Log: Startup Messages --- warning | 'clip' is a prefix of an existing command 'clipper' UCSF ChimeraX version: 0.9 (2019-06-06) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > toolshed uninstall ISOLDE Traceback (most recent call last): File ""/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/distlib/metadata.py"", line 730, in __init__ self._data = json.loads(data) File ""/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/json/__init__.py"", line 348, in loads return _default_decoder.decode(s) File ""/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/json/decoder.py"", line 337, in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) File ""/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/json/decoder.py"", line 355, in raw_decode raise JSONDecodeError(""Expecting value"", s, err.value) from None json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0) During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cmd_line/tool.py"", line 254, in execute cmd.run(cmd_text) File ""/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2632, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/toolshed.py"", line 254, in toolshed_uninstall deps = bi.dependents(logger) File ""/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/toolshed/info.py"", line 667, in dependents for d in DistributionPath().get_distributions(): File ""/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/distlib/database.py"", line 213, in get_distributions self._generate_cache() File ""/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/distlib/database.py"", line 167, in _generate_cache for dist in self._yield_distributions(): File ""/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/distlib/database.py"", line 148, in _yield_distributions metadata = Metadata(fileobj=stream, scheme='legacy') File ""/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/distlib/metadata.py"", line 741, in __init__ self.validate() File ""/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/distlib/metadata.py"", line 958, in validate missing, warnings = self._legacy.check(True) File ""/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/distlib/metadata.py"", line 522, in check self.set_metadata_version() File ""/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/distlib/metadata.py"", line 289, in set_metadata_version self._fields['Metadata-Version'] = _best_version(self._fields) File ""/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/distlib/metadata.py"", line 167, in _best_version raise MetadataConflictError('Unknown metadata set') distlib.metadata.MetadataConflictError: Unknown metadata set distlib.metadata.MetadataConflictError: Unknown metadata set File ""/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/distlib/metadata.py"", line 167, in _best_version raise MetadataConflictError('Unknown metadata set') See log for complete Python traceback. OpenGL version: 4.1 ATI-2.4.10 OpenGL renderer: AMD Radeon Pro 555X OpenGL Engine OpenGL vendor: ATI Technologies Inc. }}} " defect closed normal Tool Shed duplicate Tristan Croll all ChimeraX