Opened 5 years ago
Closed 4 years ago
#3244 closed defect (fixed)
"toolshed uninstall" failure
Reported by: | Eric Pettersen | Owned by: | Greg Couch |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Tool Shed | Version: | |
Keywords: | Cc: | Conrad Huang | |
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Darwin-18.7.0-x86_64-i386-64bit ChimeraX Version: 1.0 (2020-05-09) Description Trying to uninstall Maestro bundle from release candidate. It shouldn't have been allowed to install in the first place AFAIK Log: UCSF ChimeraX version: 1.0rc202005091901 (2020-05-09) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > toolshed list List of installed bundles: AddH (1.0): Add hydrogens AlignmentAlgorithms (1.0): Sequence alignment algorithms AlignmentHdrs (1.0): Alignment header support AlignmentMatrices (1.0): Sequence alignment similarity matrices Alignments (1.0): Sequence alignment support Arrays (1.0): C++ library for parsing numpy arrays AtomSearch (1.0): 3D atom search Atomic (1.0): Atomic-structure functionality BILD (0.2): BILD file reader BasicActions (0.1): Basic actions for user- defined specifier names BlastProtein (0.2): Search PDB/NR using BLAST BondRot (1.0): Bond rotation support Bug-Reporter (1.0): Report bugs when an error occurs BuildStructure (1.0): Create/modify structures Bumps (1.0): Find protrusions in density maps ButtonPanel (1.0): Create custom user interface panels Cage-Builder (1.0): Build polygonal meshes for oligomeric molecular assemblies CellPack (1.0): Fetch cellPACK models from web ChemGroup (1.0): Detect chemically functional groups Clashes (1.0): Find clashes/contacts in structures ColorActions (1.0): Simple interface for coloring objects ColorGlobe (1.0): Show directional resolution colored sphere CommandLine (1.0): Command line support Connect-Structure (1.0): Add bonds to structures that lack them Contacts (1.0): Display chain contact maps Core (1.0rc202005091901): ChimeraX Core Package CoreFormats (1.0): ChimeraX session support Crosslinks (1.0): Analyze crosslinks Crystal (1.0): Crystal symmetries DataFormats (1.0): Data format management Dicom (1.0): Read medical imaging and segmentations in DICOM format Dist-Monitor (1.0): Interactive distance display Dist-UI (1.0): Distance measurement user interface Dssp (1.0): Compute/assign secondary structure ExperimentalCommands (1.0): Experimental commands FileHistory (1.0): File History Panel FunctionKey (1.0): Assign function keys to run commands Geometry (1.0): Vector and coordinate system routines Graphics (1.0): OpenGL graphics rendering HKCage (1.0): Create icosahedral mesh of hexagons and pentagons Hbonds (1.0): Identify hydrogen bonds in and among structures Help (0.9a1): Show ChimeraX Help IHM (1.0): Integrative Hybrid Models file reader IO (1.0): Python convenience input/output functions ImageFormats (1.0): Support for saving images Label (1.0): Add text labels to graphics List-Info (0.1): Report attributes for selected atomic data Log (1.0): Log support MD-crds (1.0): Molecular dynamics support MLP (1.0): Molecular lipophilicity calculation MMTF (1.0): MMTF format read/write Map (1.0): Density maps MapData (1.0): Volume data file formats MapEraser (1.0): Map eraser MapFilter (1.0): Operations on maps MapFit (1.0): Fit molecules into maps MapSeries (1.0): Volume series Markers (1.0): Place markers on density maps Mask (1.0): Mask a volume to a surface MatchMaker (1.0): Superimpose structures MedicalToolbar (1.0): Toolbar for medical image analysis Meeting (1.0): Shared interactive VR sessions. ModelPanel (1.0): ChimeraX Model Panel ModelSeries (1.0): Display sequences of models one by one Modeller (1.0): Interface to Modeller Mol2 (1.0): Mol2 reader/writer Morph (1.0): Morph atomic structures MouseModes (1.0): Provide right button mouse mode tool Movie (1.0): Commands to record movies Nucleotides (0.1): Create nucleotide-specific displays OpenCommand (1.0): Manages 'open' command extensibility PDB (1.0): PDB format read/write PickBlobs (1.0): Measure and color blobs Preset-Mgr (1.0): Preset management PubChem (1.0): PubChem fetch Read-Pbonds (1.0): Read in pseudobonds from a file Registration (0.1): Register ChimeraX RemoteControl (1.0): Control ChimeraX from other apps ResidueFit (1.0): Display fit of residues to density map RestServer (0.1): Starts REST server to execute commands from network requests Rotamer-Lib-Mgr (1.0): Manage rotamer libraries RotamerLibs-Dunbrack (1.0): Dunbrack rotamer library RotamerLibs-Dynameomics (1.0): Dynameomics rotamer library RotamerLibs-Richardson (1.0): Richardson rotamer libraries SDF (1.0): SDF file reader STL (1.0): STL file read/write SaveCommand (1.0): Manages 'save' command extensibility Scheme-Mgr (1.0): HTTP scheme management Segger (1.0): Segment map Segment (1.0): Watershed segment calculation SeqView (1.0): Sequence viewer Shape (1.0): Make models for geometric shapes Shell (1.0): Interactive Python shell Shortcuts (1.0): Button and keyboard shortcuts ShowAttr (1.0): Render/select by attribute ShowSequences (1.0): Choose/show structure sequences SideView (1.0): Side view of scene Smiles (1.0): SMILES fetch SmoothLines (1.0): Smooth network of lines SpaceNavigator (1.0): Space Navigator device support StdCommands (1.0): Standard commands Storm (1.0): STORM file reader Struts (1.0): struts for 3D printing Surface (1.0): Surface calculations SwapAA (1.0): Swap amino acid SwapRes (1.0): Swap residue side chains TapeMeasure (1.0): Tape measure mouse mode Test (1.0): simple regression test Texture (1.0): Apply images to surfaces Toolbar (0.1): Toolbar Tug (1.0): Tug on atoms with molecular dynamics UI (1.0): ChimeraX user interface VTK (1.0): Legacy VTK file reader and writer ViewDockX (0.1): Analyze ligand-receptor docking results Vive (1.1): Virtual reality headset support VolumeMenu (1.0): Volume menu WavefrontOBJ (1.0): Wavefront OBJ file read/write WebServices (1.0): Web service and HTTP request support Zone (1.0): Mouse mode to show atom and map zones gltf (1.0): Read/write glTF 3d scene files mmCIF (1.1): mmCIF format read/write uniprot (1.0): UniProt database support Downloading bundle ChimeraX_Maestro-1.5-py3-none-any.whl Successfully installed ChimeraX-Maestro-1.5 Installed ChimeraX-Maestro (1.5) > info Unknown command: toolshed info > info 0 models > help info > info path user user versioned cache directory: /Users/pett/Library/Caches/ChimeraX/1.0 user versioned config directory: /Users/pett/Library/Application Support/ChimeraX/1.0 user versioned data directory: /Users/pett/Library/Application Support/ChimeraX/1.0 user versioned log directory: /Users/pett/Library/Logs/ChimeraX/1.0 user versioned state directory: /Users/pett/Library/Application Support/ChimeraX/1.0 user unversioned cache directory: /Users/pett/Library/Caches/ChimeraX user unversioned config directory: /Users/pett/Library/Application Support/ChimeraX user unversioned data directory: /Users/pett/Library/Application Support/ChimeraX user unversioned log directory: /Users/pett/Library/Logs/ChimeraX user unversioned state directory: /Users/pett/Library/Application Support/ChimeraX > usage toolshed Subcommands are: * toolshed cache * toolshed hide * toolshed install * toolshed list * toolshed reload * toolshed show * toolshed uninstall * toolshed url > toolshed uninstall ChimeraX-Maestro Traceback (most recent call last): File "/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/distlib/metadata.py", line 732, in __init__ self._data = json.loads(data) File "/Applications/ChimeraX-1.0-rc-2020.05.09.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-1.0-rc-2020.05.09.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-1.0-rc-2020.05.09.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-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cmd_line/tool.py", line 258, in execute cmd.run(cmd_text) File "/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2849, in run result = ci.function(session, **kw_args) File "/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/toolshed.py", line 275, in toolshed_uninstall deps = bi.dependents(logger) File "/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/toolshed/info.py", line 661, in dependents for d in DistributionPath().get_distributions(): File "/Applications/ChimeraX-1.0-rc-2020.05.09.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-1.0-rc-2020.05.09.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-1.0-rc-2020.05.09.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-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/distlib/metadata.py", line 742, in __init__ scheme=scheme) File "/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/distlib/metadata.py", line 285, in __init__ self.read_file(fileobj) File "/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/distlib/metadata.py", line 383, in read_file self.set(field, value) File "/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/distlib/metadata.py", line 478, in set if not scheme.is_valid_constraint_list(value): File "/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/distlib/version.py", line 713, in is_valid_constraint_list return self.is_valid_matcher('dummy_name (%s)' % s) File "/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/distlib/version.py", line 703, in is_valid_matcher self.matcher(s) File "/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/distlib/version.py", line 104, in __init__ r = self.parse_requirement(s) File "/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/distlib/version.py", line 98, in parse_requirement return parse_requirement(s) File "/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/distlib/util.py", line 237, in parse_requirement versions, _ = get_versions(s) File "/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/distlib/util.py", line 220, in get_versions raise SyntaxError('invalid constraint: %s' % ver_remaining) File "<string>", line None SyntaxError: invalid constraint: File "", line None SyntaxError: invalid constraint: File "/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/distlib/util.py", line 220, in get_versions raise SyntaxError('invalid constraint: %s' % ver_remaining) See log for complete Python traceback. > toolshed uninstall ChimeraX-Maestro Traceback (most recent call last): File "/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/distlib/metadata.py", line 732, in __init__ self._data = json.loads(data) File "/Applications/ChimeraX-1.0-rc-2020.05.09.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-1.0-rc-2020.05.09.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-1.0-rc-2020.05.09.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-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cmd_line/tool.py", line 258, in execute cmd.run(cmd_text) File "/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2849, in run result = ci.function(session, **kw_args) File "/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/toolshed.py", line 275, in toolshed_uninstall deps = bi.dependents(logger) File "/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/toolshed/info.py", line 661, in dependents for d in DistributionPath().get_distributions(): File "/Applications/ChimeraX-1.0-rc-2020.05.09.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-1.0-rc-2020.05.09.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-1.0-rc-2020.05.09.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-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/distlib/metadata.py", line 742, in __init__ scheme=scheme) File "/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/distlib/metadata.py", line 285, in __init__ self.read_file(fileobj) File "/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/distlib/metadata.py", line 383, in read_file self.set(field, value) File "/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/distlib/metadata.py", line 478, in set if not scheme.is_valid_constraint_list(value): File "/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/distlib/version.py", line 713, in is_valid_constraint_list return self.is_valid_matcher('dummy_name (%s)' % s) File "/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/distlib/version.py", line 703, in is_valid_matcher self.matcher(s) File "/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/distlib/version.py", line 104, in __init__ r = self.parse_requirement(s) File "/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/distlib/version.py", line 98, in parse_requirement return parse_requirement(s) File "/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/distlib/util.py", line 237, in parse_requirement versions, _ = get_versions(s) File "/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/distlib/util.py", line 220, in get_versions raise SyntaxError('invalid constraint: %s' % ver_remaining) File "<string>", line None SyntaxError: invalid constraint: File "", line None SyntaxError: invalid constraint: File "/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/distlib/util.py", line 220, in get_versions raise SyntaxError('invalid constraint: %s' % ver_remaining) See log for complete Python traceback. OpenGL version: 4.1 INTEL-12.10.16 OpenGL renderer: Intel(R) Iris(TM) Pro Graphics 6200 OpenGL vendor: Intel Inc.Hardware: Hardware Overview: Model Name: iMac Model Identifier: iMac16,2 Processor Name: Intel Core i5 Processor Speed: 2.8 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 4 MB Memory: 16 GB Boot ROM Version: 232.0.0.0.0 SMC Version (system): 2.32f20 Software: System Software Overview: System Version: macOS 10.14.6 (18G3020) Kernel Version: Darwin 18.7.0 Time since boot: 5:38 Graphics/Displays: Intel Iris Pro Graphics 6200: Chipset Model: Intel Iris Pro Graphics 6200 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x1622 Revision ID: 0x000a Metal: Supported, feature set macOS GPUFamily1 v4 Displays: iMac: Display Type: LCD Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: No Connection Type: DisplayPort
Change History (2)
comment:1 by , 5 years ago
Cc: | added |
---|---|
Component: | Unassigned → Tool Shed |
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → assigned |
Summary: | ChimeraX bug report submission → "toolshed uninstall" failure |
comment:2 by , 4 years ago
Resolution: | → fixed |
---|---|
Status: | assigned → closed |
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This error should be no more. Much better compatibility testing before installing. Don't use distlib anymore. Newer version of setuptools. Etc.