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Opened 4 years ago
Closed 4 years ago
#5177 closed defect (fixed)
Blast results: wrapped C/C++ object of type HtmlView has been deleted
| Reported by: | Owned by: | Zach Pearson | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sequence | Version: | |
| Keywords: | Cc: | Tom Goddard, Eric Pettersen | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-5.11.0-27-generic-x86_64-with-glibc2.14
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 1gux format mmcif fromDatabase pdb
1gux title:
Rb pocket bound to E7 lxcxe motif [more info...]
Chain information for 1gux #1
---
Chain | Description
A | retinoblastoma protein
B | retinoblastoma protein
E | oncoprotein
> toolshed show
> ui tool show "Blast Protein"
> blastprotein /A database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 name
> bp1
Web Service: BlastProtein2 is a Python wrapper that calls blastp to search nr
or pdb for sequences similar to the given protein sequence
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/BlastProtein2Service
Opal job id: appBlastProtein2Service16309462926421674082956
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appBlastProtein2Service16309462926421674082956
stdout.txt = standard output
stderr.txt = standard error
BlastProtein finished.
> blastprotein /A database nr cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 name bp1
Web Service: BlastProtein2 is a Python wrapper that calls blastp to search nr
or pdb for sequences similar to the given protein sequence
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/BlastProtein2Service
Opal job id: appBlastProtein2Service16309463197951098315932
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appBlastProtein2Service16309463197951098315932
stdout.txt = standard output
stderr.txt = standard error
> blastprotein /A database nr cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 name bp1
Web Service: BlastProtein2 is a Python wrapper that calls blastp to search nr
or pdb for sequences similar to the given protein sequence
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/BlastProtein2Service
Opal job id: appBlastProtein2Service1630946665546-959533203
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appBlastProtein2Service1630946665546-959533203
stdout.txt = standard output
stderr.txt = standard error
> ui tool show "Blast Protein"
> blastprotein /A database nr cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 name bp2
Web Service: BlastProtein2 is a Python wrapper that calls blastp to search nr
or pdb for sequences similar to the given protein sequence
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/BlastProtein2Service
Opal job id: appBlastProtein2Service1630946687712-1621393965
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appBlastProtein2Service1630946687712-1621393965
stdout.txt = standard output
stderr.txt = standard error
BlastProtein finished.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/ui/gui.py",
line 648, in customEvent
func(*args, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/blastprotein/job.py", line 92, in on_finish
self.tool.job_finished(self, p, self._params())
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/blastprotein/tool.py", line 279, in job_finished
self._show_params(params)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/blastprotein/tool.py", line 329, in _show_params
self.html_view.runJavaScript(js)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 291, in runJavaScript
self.page().runJavaScript(script, *args)
RuntimeError: wrapped C/C++ object of type HtmlView has been deleted
RuntimeError: wrapped C/C++ object of type HtmlView has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 291, in runJavaScript
self.page().runJavaScript(script, *args)
See log for complete Python traceback.
BlastProtein finished.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/ui/gui.py",
line 648, in customEvent
func(*args, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/blastprotein/job.py", line 92, in on_finish
self.tool.job_finished(self, p, self._params())
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/blastprotein/tool.py", line 279, in job_finished
self._show_params(params)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/blastprotein/tool.py", line 329, in _show_params
self.html_view.runJavaScript(js)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 291, in runJavaScript
self.page().runJavaScript(script, *args)
RuntimeError: wrapped C/C++ object of type HtmlView has been deleted
RuntimeError: wrapped C/C++ object of type HtmlView has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 291, in runJavaScript
self.page().runJavaScript(script, *args)
See log for complete Python traceback.
BlastProtein finished.
OpenGL version: 4.6 (Core Profile) Mesa 21.0.3
OpenGL renderer: AMD RENOIR (DRM 3.40.0, 5.11.0-27-generic, LLVM 12.0.0)
OpenGL vendor: AMD
Manufacturer: LENOVO
Model: 20UJS06300
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virutal Machine: none
CPU: 12 AMD Ryzen 5 PRO 4650U with Radeon Graphics
Cache Size: 512 KB
Memory:
total used free shared buff/cache available
Mem: 7.1Gi 5.4Gi 652Mi 158Mi 1.0Gi 1.3Gi
Swap: 7.4Gi 1.8Gi 5.6Gi
Graphics:
06:00.0 VGA compatible controller [0300]: Advanced Micro Devices, Inc. [AMD/ATI] Renoir [1002:1636] (rev d3)
Subsystem: Lenovo Renoir [17aa:5082]
Kernel driver in use: amdgpu
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: 2020.12.5
cftime: 1.5.0
chardet: 3.0.4
ChimeraX-AddCharge: 1.0.1
ChimeraX-AddH: 2.1.6
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.13.2
ChimeraX-AtomicLibrary: 3.1.3
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
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: 2.5.2
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.2.1
ChimeraX-CommandLine: 1.1.4
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.2.5
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.1.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.1
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.3
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: 2.1
ChimeraX-Help: 1.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.1
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-Label: 1.0
ChimeraX-LinuxSupport: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.0.2
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: 1.2.1
ChimeraX-MDcrds: 2.2
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.3
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.0.1
ChimeraX-ModelPanel: 1.0.1
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: 2.0.1
ChimeraX-OpenCommand: 1.5
ChimeraX-PDB: 2.4.1
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.1
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.0.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.4
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.3
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-Smiles: 2.0.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.3.1
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-Toolbar: 1.0.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.7.6
ChimeraX-uniprot: 2.1
ChimeraX-UnitCell: 1.0
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: 0.29.21
decorator: 5.0.9
distlib: 0.3.1
distro: 1.5.0
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.17
imagecodecs: 2020.5.30
imagesize: 1.2.0
ipykernel: 5.3.4
ipython: 7.18.1
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.7
jupyter-core: 4.7.1
kiwisolver: 1.3.1
line-profiler: 2.1.2
lxml: 4.6.2
lz4: 3.1.0
MarkupSafe: 2.0.1
matplotlib: 3.3.2
msgpack: 1.0.0
netCDF4: 1.5.4
networkx: 2.5
numexpr: 2.7.3
numpy: 1.19.2
numpydoc: 1.1.0
openvr: 1.14.1501
packaging: 20.9
ParmEd: 3.2.0
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.2.0
pip: 21.0.1
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.18
psutil: 5.7.2
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.7.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.1
pytz: 2021.1
pyzmq: 22.0.3
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.5.2
setuptools: 50.3.2
sfftk-rw: 0.6.7.dev1
six: 1.15.0
snowballstemmer: 2.1.0
sortedcontainers: 2.2.2
Sphinx: 3.2.1
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: 2020.9.3
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.0.5
urllib3: 1.25.11
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.36.0
wheel-filename: 1.2.0
Change History (3)
comment:1 by , 4 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Sequence |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Blast results: wrapped C/C++ object of type HtmlView has been deleted |
comment:2 by , 4 years ago
Should be obsolesced by tomorrow's daily build. Blastprotein switched to Qt GUI by https://github.com/RBVI/ChimeraX/commit/7615e3412aca6e25a2042623388ca24550ab2224
comment:3 by , 4 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
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Looks like the results window was somehow closed before it was finished. You can probably just close this since you are rewriting the UI in Qt.