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.