Opened 5 years ago
Last modified 5 years ago
#4539 accepted defect
Permission denied setting timestamp
| Reported by: | Greg Couch | Owned by: | Greg Couch |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Tool Shed | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19041
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
Was uninstalling RMF bundle
Log:
Startup Messages
---
warning | Open-command provider in bundle RMF specified unknown data format
'RMF'; skipping
UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> toolshed list installed
List of installed bundles:
* AddH (2.1.1): Add hydrogens
* AlignmentAlgorithms (2.0): Sequence alignment algorithms
* AlignmentHdrs (3.2): Alignment header support
* AlignmentMatrices (2.0): Sequence alignment similarity matrices
* Alignments (2.1): Sequence alignment support
* Arrays (1.0): C++ library for parsing numpy arrays
* AtomSearch (2.0): 3D atom search
* Atomic (1.6.1): Atomic-structure functionality
* AxesPlanes (2.0): Depict axes or planes
* BILD (1.0): BILD file reader
* BasicActions (1.1): Basic actions for user-defined specifier names
* BlastProtein (1.1): Search PDB/NR using BLAST
* BondRot (2.0): Bond rotation support
* BugReporter (1.0): Report bugs when an error occurs
* BuildStructure (2.0): Create/modify structures
* Bumps (1.0): Find protrusions in density maps
* ButtonPanel (1.0): Create custom user interface panels
* CageBuilder (1.0): Build polygonal meshes for oligomeric molecular assemblies
* CellPack (1.0): Fetch cellPACK models from web
* Centroids (1.1): Depict centroid of atoms
* ChemGroup (2.0): Detect chemically functional groups
* Clashes (2.0): Find clashes/contacts in structures
* Clipper (0.15.0): Clipper: Efficient handling of volumetric data and symmetry
* ColorActions (1.0): Simple interface for coloring objects
* ColorGlobe (1.0): Show directional resolution colored sphere
* CommandLine (1.1.3): Command line support
* ConnectStructure (2.0): Add bonds to structures that lack them
* Contacts (1.0): Display chain contact maps
* Core (1.1): 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
* DistMonitor (1.1): Interactive distance display
* DistUI (1.0): Distance measurement user interface
* Dssp (2.0): Compute/assign secondary structure
* EMDB-SFF (1.0): EMDB SFF file reader
* ExperimentalCommands (1.0): Experimental commands
* FileHistory (1.0): File History Panel
* FunctionKey (1.0): Assign function keys to run commands
* Geometry (1.1): Vector and coordinate system routines
* Graphics (1.0): OpenGL graphics rendering
* HKCage (1.0): Create icosahedral mesh of hexagons and pentagons
* Hbonds (2.0): Identify hydrogen bonds in and among structures
* Help (1.0): Show ChimeraX Help
* IHM (1.0): Integrative Hybrid Models file reader
* IMOD (1.0): IMOD model file reader
* IO (1.0): Python convenience input/output functions
* ISOLDE (1.1.0): ISOLDE: Interactive Structure Optimisation by Local Direct Exploration
* ImageFormats (1.0): Support for saving images
* Label (1.0): Add text labels to graphics
* ListInfo (1.0): Report attributes for selected atomic data
* Log (1.1.1): Log support
* LookingGlass (1.1): LookingGlass holographic display
* MDcrds (2.0): Molecular dynamics support
* MLP (1.0): Molecular lipophilicity calculation
* MMTF (2.0): MMTF format read/write
* Maestro (1.0): Maestro reader
* Map (1.0.1): Density maps
* MapData (2.0): Volume data file formats
* MapEraser (1.0): Map eraser
* MapFilter (2.0): Operations on maps
* MapFit (2.0): Fit molecules into maps
* MapSeries (2.0): Volume series
* Markers (1.0): Place markers on density maps
* Mask (1.0): Mask a volume to a surface
* MatchMaker (1.1): Superimpose structures
* MedicalToolbar (1.0.1): 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 (2.0): 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
* Neuron (1.0): Read SWC neuron trace files
* Nucleotides (2.0): Create nucleotide-specific displays
* OpenCommand (1.2.1): Manages 'open' command extensibility
* PDB (2.1): PDB format read/write
* PDBBio (1.0): PDB biological assembly fetch
* PickBlobs (1.0): Measure and color blobs
* Positions (1.0): Read and write model position matrices
* PresetMgr (1.0): Preset management
* PubChem (2.0): PubChem fetch
* RMF (0.8): Support for the RMF file format
* RNALayout (1.0): Make RNA models
* Read-Pbonds (1.0): Read in pseudobonds from a file
* Registration (1.1): Register ChimeraX
* RemoteControl (1.0): Control ChimeraX from other apps
* ResidueFit (1.0): Display fit of residues to density map
* RestServer (1.0): Starts REST server to execute commands from network requests
* RotamerLibMgr (2.0): Manage rotamer libraries
* RotamerLibsDunbrack (2.0): Dunbrack rotamer library
* RotamerLibsDynameomics (2.0): Dynameomics rotamer library
* RotamerLibsRichardson (2.0): Richardson rotamer libraries
* SDF (2.0): SDF file reader
* STL (1.0): STL file read/write
* SaveCommand (1.2): Manages 'save' command extensibility
* SchemeMgr (1.0): HTTP scheme management
* Segger (1.0): Segment map
* Segment (1.0): Watershed segment calculation
* SeqView (2.2): Sequence viewer
* Shape (1.0.1): 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
* SignalViewer (1.0): Display time varying signals at points in space
* Smiles (2.0): SMILES fetch
* SmoothLines (1.0): Smooth network of lines
* SpaceNavigator (1.0): Space Navigator device support
* StdCommands (1.0.4): Standard commands
* Storm (1.0): STORM file reader
* Struts (1.0): struts for 3D printing
* Surface (1.0): Surface calculations
* SwapAA (2.0): Swap amino acid
* SwapRes (2.0): Swap residue side chains
* TapeMeasure (1.0): Tape measure mouse mode
* Test (1.0): simple regression test
* Toolbar (1.0): Toolbar
* ToolshedUtils (1.0): Toolshed bundle utilities
* Tug (1.0): Tug on atoms with molecular dynamics
* UI (1.2.3): ChimeraX user interface
* VTK (1.0): Legacy VTK file reader and writer
* ViewDockX (1.0): 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
* WebCam (1.0): Combine camera video with graphics
* WebServices (1.0): Web service and HTTP request support
* Zone (1.0): Mouse mode to show atom and map zones
* coulombic (1.0.1): Compute/show electrostatic potential
* gltf (1.0): Read/write glTF 3d scene files
* mmCIF (2.2): mmCIF format read/write
* uniprot (2.0): UniProt database support
> toolshed uninstall rmf
unloading module chimerax.rmf
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 275, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\toolshed.py", line 328, in toolshed_uninstall
ts.uninstall_bundle(bundles, logger, session=session,
force_remove=force_remove)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 926, in uninstall_bundle
_uninstall_bundle(self, bundle, logger, session=session,
force_remove=force_remove)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\toolshed_utils\\__init__.py", line 422, in _uninstall_bundle
results = _pip_uninstall(uninstall_now, logger)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\toolshed_utils\\__init__.py", line 502, in _pip_uninstall
return _run_pip(command, logger)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\toolshed_utils\\__init__.py", line 538, in _run_pip
raise PermissionError(s)
PermissionError: Found existing installation: ChimeraX-RMF 0.8
Uninstalling ChimeraX-RMF-0.8:
Successfully uninstalled ChimeraX-RMF-0.8
Lock 2202222945672 acquired on
C:\Users\gregc\AppData\Local\UCSF\ChimeraX\Cache\1.1\toolshed\bundle_info.cache.lock
Lock 2202222945672 released on
C:\Users\gregc\AppData\Local\UCSF\ChimeraX\Cache\1.1\toolshed\bundle_info.cache.lock
ERROR:
Traceback (most recent call last):
\xa0\xa0File "C:\Program Files\ChimeraX 1.1\bin\lib\runpy.py", line 193, in
_run_module_as_main
\xa0\xa0\xa0\xa0"__main__", mod_spec)
\xa0\xa0File "C:\Program Files\ChimeraX 1.1\bin\lib\runpy.py", line 85, in
_run_code
\xa0\xa0\xa0\xa0exec(code, run_globals)
\xa0\xa0File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\ChimeraX_main.py",
line 919, in <module>
\xa0\xa0\xa0\xa0exit_code = init(sys.argv)
\xa0\xa0File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\ChimeraX_main.py",
line 711, in init
\xa0\xa0\xa0\xa0sess.toolshed.set_install_timestamp(per_user)
\xa0\xa0File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\toolshed\\\\__init__.py", line 580, in
set_install_timestamp
\xa0\xa0\xa0\xa0self._installed_bundle_info.set_install_timestamp(per_user=per_user)
\xa0\xa0File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\toolshed\installed.py", line 105, in
set_install_timestamp
\xa0\xa0\xa0\xa0with open(timestamp_file, 'w') as f:
PermissionError: [Errno 13] Permission denied: 'C:\\\\\Program
Files\\\\\ChimeraX
1.1\\\\\bin\\\\\share\\\\\install-timestamp'
PermissionError: Found existing installation: ChimeraX-RMF 0.8
Uninstalling ChimeraX-RMF-0.8:
Successfully uninstalled ChimeraX-RMF-0.8
Lock 2202222945672 acquired on
C:\Users\gregc\AppData\Local\UCSF\ChimeraX\Cache\1.1\toolshed\bundle_info.cache.lock
Lock 2202222945672 released on
C:\Users\gregc\AppData\Local\UCSF\ChimeraX\Cache\1.1\toolshed\bundle_info.cache.lock
ERROR:
Traceback (most recent call last):
\xa0\xa0File "C:\Program Files\ChimeraX 1.1\bin\lib\runpy.py", line 193, in
_run_module_as_main
\xa0\xa0\xa0\xa0"__main__", mod_spec)
\xa0\xa0File "C:\Program Files\ChimeraX 1.1\bin\lib\runpy.py", line 85, in
_run_code
\xa0\xa0\xa0\xa0exec(code, run_globals)
\xa0\xa0File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\ChimeraX_main.py",
line 919, in
\xa0\xa0\xa0\xa0exit_code = init(sys.argv)
\xa0\xa0File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\ChimeraX_main.py",
line 711, in init
\xa0\xa0\xa0\xa0sess.toolshed.set_install_timestamp(per_user)
\xa0\xa0File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\toolshed\\\\__init__.py", line 580, in
set_install_timestamp
\xa0\xa0\xa0\xa0self._installed_bundle_info.set_install_timestamp(per_user=per_user)
\xa0\xa0File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\toolshed\installed.py", line 105, in
set_install_timestamp
\xa0\xa0\xa0\xa0with open(timestamp_file, 'w') as f:
PermissionError: [Errno 13] Permission denied: 'C:\\\\\Program
Files\\\\\ChimeraX
1.1\\\\\bin\\\\\share\\\\\install-timestamp'
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\toolshed_utils\\__init__.py", line 538, in _run_pip
raise PermissionError(s)
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 461.72
OpenGL renderer: GeForce GTX 970/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: MSI
Model: MS-7885
OS: Microsoft Windows 10 Home (Build 19041)
Memory: 34,258,157,568
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.8.0
backcall: 0.2.0
biopython: 1.78
blockdiag: 2.0.1
certifi: 2020.6.20
chardet: 3.0.4
ChimeraX-AddH: 2.1.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.6.1
ChimeraX-AtomSearch: 2.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.0
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.0
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.0
ChimeraX-Clipper: 0.15.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.1
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.0.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-DataFormats: 1.0
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1
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: 1.0
ChimeraX-Hbonds: 2.0
ChimeraX-Help: 1.0
ChimeraX-HKCage: 1.0
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.0
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0
ChimeraX-ISOLDE: 1.1.0
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.0
ChimeraX-Log: 1.1.1
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.0
ChimeraX-Map: 1.0.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.1
ChimeraX-MDcrds: 2.0
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.0
ChimeraX-mmCIF: 2.2
ChimeraX-MMTF: 2.0
ChimeraX-Modeller: 1.0
ChimeraX-ModelPanel: 1.0
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.0
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0
ChimeraX-OpenCommand: 1.2.1
ChimeraX-PDB: 2.1
ChimeraX-PDBBio: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0
ChimeraX-PubChem: 2.0
ChimeraX-Read-Pbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.0
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.2
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-SignalViewer: 1.0
ChimeraX-Smiles: 2.0
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.0.4
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.0
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0
ChimeraX-ToolshedUtils: 1.0
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.2.3
ChimeraX-uniprot: 2.0
ChimeraX-ViewDockX: 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: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.20
decorator: 4.4.2
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
gdcm: 2.8.8
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.16
imagecodecs: 2020.5.30
imagecodecs-lite: 2020.1.31
imagesize: 1.2.0
ipykernel: 5.3.0
ipython: 7.15.0
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.3
jupyter-core: 4.6.3
kiwisolver: 1.2.0
line-profiler: 2.1.2
lxml: 4.5.1
MarkupSafe: 1.1.1
matplotlib: 3.2.1
msgpack: 1.0.0
netifaces: 0.10.9
networkx: 2.4
numexpr: 2.7.1
numpy: 1.18.5+mkl
numpydoc: 1.0.0
openvr: 1.12.501
packaging: 20.4
parso: 0.7.1
pickleshare: 0.7.5
Pillow: 7.1.2
pip: 20.2.2
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.7
psutil: 5.7.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.6.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.12.3
PyQt5-sip: 4.19.19
PyQtWebEngine-commercial: 5.12.1
python-dateutil: 2.8.1
pytz: 2020.1
pywin32: 228
pyzmq: 19.0.2
qtconsole: 4.7.4
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.4.1
setuptools: 49.4.0
sfftk-rw: 0.6.6.dev0
six: 1.15.0
snowballstemmer: 2.0.0
sortedcontainers: 2.2.2
Sphinx: 3.1.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 1.0.3
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.4
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.6.3
tinyarray: 1.2.2
tornado: 6.0.4
traitlets: 5.0.4
urllib3: 1.25.10
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.34.2
WMI: 1.5.1
Change History (2)
comment:1 by , 5 years ago
| Component: | Unassigned → Tool Shed |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Permission denied setting timestamp |
comment:2 by , 5 years ago
| Status: | assigned → accepted |
|---|
Note:
See TracTickets
for help on using tickets.
There is no --user argument to "pip uninstall", so the system timestamp was being incorrectly updated. Temporarily, changed it to always set the user timestamp when uninstalling. The correct solution will be to look at which bundles are being uninstalled, and set the appropriate timestamp.