Opened 5 years ago

Closed 5 years ago

#4076 closed defect (fixed)

Bug report with bug-reporter failure(!)

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Infrastructure Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Darwin-19.6.0-x86_64-i386-64bit
ChimeraX Version: 1.1.1 (2020-10-07 08:32:49 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.1.1 (2020-10-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 2B9E format mmcif fromDatabase pdb

2b9e title:  
Human NSUN5 protein [more info...]  
  
Chain information for 2b9e #1  
---  
Chain | Description  
A | NOL1/NOP2/Sun domain family, member 5 isoform 2  
  
Non-standard residues in 2b9e #1  
---  
SAM — S-adenosylmethionine  
  

> coulombic

> toolshed show

Downloading bundle ChimeraX_AddH-2.1.3-py3-none-any.whl  
Traceback (most recent call last):  
File
"/private/var/folders/0s/vh7xxzmj0vx89d5_g5cljzgw0000gp/T/AppTranslocation/033EE131-A009-4172-9D81-95067A2CD68F/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/help_viewer/tool.py", line 389, in download_finished  
session=self.session)  
File
"/private/var/folders/0s/vh7xxzmj0vx89d5_g5cljzgw0000gp/T/AppTranslocation/033EE131-A009-4172-9D81-95067A2CD68F/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 903, in install_bundle  
_install_bundle(self, bundle, logger, per_user=per_user, reinstall=reinstall,
session=session, no_deps=no_deps)  
File
"/private/var/folders/0s/vh7xxzmj0vx89d5_g5cljzgw0000gp/T/AppTranslocation/033EE131-A009-4172-9D81-95067A2CD68F/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolshed_utils/__init__.py", line 213, in _install_bundle  
raise ToolshedInstalledError("bundle %r already installed" % bundle.name)  
AttributeError: 'str' object has no attribute 'name'  
  
AttributeError: 'str' object has no attribute 'name'  
  
File
"/private/var/folders/0s/vh7xxzmj0vx89d5_g5cljzgw0000gp/T/AppTranslocation/033EE131-A009-4172-9D81-95067A2CD68F/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolshed_utils/__init__.py", line 213, in _install_bundle  
raise ToolshedInstalledError("bundle %r already installed" % bundle.name)  
  
See log for complete Python traceback.  
  
Downloading bundle ChimeraX_AddH-2.1.3-py3-none-any.whl  
Traceback (most recent call last):  
File
"/private/var/folders/0s/vh7xxzmj0vx89d5_g5cljzgw0000gp/T/AppTranslocation/033EE131-A009-4172-9D81-95067A2CD68F/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/help_viewer/tool.py", line 389, in download_finished  
session=self.session)  
File
"/private/var/folders/0s/vh7xxzmj0vx89d5_g5cljzgw0000gp/T/AppTranslocation/033EE131-A009-4172-9D81-95067A2CD68F/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 903, in install_bundle  
_install_bundle(self, bundle, logger, per_user=per_user, reinstall=reinstall,
session=session, no_deps=no_deps)  
File
"/private/var/folders/0s/vh7xxzmj0vx89d5_g5cljzgw0000gp/T/AppTranslocation/033EE131-A009-4172-9D81-95067A2CD68F/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolshed_utils/__init__.py", line 213, in _install_bundle  
raise ToolshedInstalledError("bundle %r already installed" % bundle.name)  
AttributeError: 'str' object has no attribute 'name'  
  
AttributeError: 'str' object has no attribute 'name'  
  
File
"/private/var/folders/0s/vh7xxzmj0vx89d5_g5cljzgw0000gp/T/AppTranslocation/033EE131-A009-4172-9D81-95067A2CD68F/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolshed_utils/__init__.py", line 213, in _install_bundle  
raise ToolshedInstalledError("bundle %r already installed" % bundle.name)  
  
See log for complete Python traceback.  
  
Downloading bundle ChimeraX_AddH-2.1.3-py3-none-any.whl  
Traceback (most recent call last):  
File
"/private/var/folders/0s/vh7xxzmj0vx89d5_g5cljzgw0000gp/T/AppTranslocation/033EE131-A009-4172-9D81-95067A2CD68F/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/help_viewer/tool.py", line 389, in download_finished  
session=self.session)  
File
"/private/var/folders/0s/vh7xxzmj0vx89d5_g5cljzgw0000gp/T/AppTranslocation/033EE131-A009-4172-9D81-95067A2CD68F/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 903, in install_bundle  
_install_bundle(self, bundle, logger, per_user=per_user, reinstall=reinstall,
session=session, no_deps=no_deps)  
File
"/private/var/folders/0s/vh7xxzmj0vx89d5_g5cljzgw0000gp/T/AppTranslocation/033EE131-A009-4172-9D81-95067A2CD68F/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolshed_utils/__init__.py", line 213, in _install_bundle  
raise ToolshedInstalledError("bundle %r already installed" % bundle.name)  
AttributeError: 'str' object has no attribute 'name'  
  
AttributeError: 'str' object has no attribute 'name'  
  
File
"/private/var/folders/0s/vh7xxzmj0vx89d5_g5cljzgw0000gp/T/AppTranslocation/033EE131-A009-4172-9D81-95067A2CD68F/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolshed_utils/__init__.py", line 213, in _install_bundle  
raise ToolshedInstalledError("bundle %r already installed" % bundle.name)  
  
See log for complete Python traceback.  
  

Failed to send bug report. Error while sending follows:  

Traceback (most recent call last):  
File
"/private/var/folders/0s/vh7xxzmj0vx89d5_g5cljzgw0000gp/T/AppTranslocation/033EE131-A009-4172-9D81-95067A2CD68F/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/bug_reporter/bug_reporter_gui.py", line 241, in submit  
errcode, errmsg, headers, body = post_multipart_formdata(BUG_HOST,
BUG_SELECTOR, fields)  
File
"/private/var/folders/0s/vh7xxzmj0vx89d5_g5cljzgw0000gp/T/AppTranslocation/033EE131-A009-4172-9D81-95067A2CD68F/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/webservices/post_form.py", line 40, in
post_multipart_formdata  
h.request('POST', url, body=body, headers=headers)  
File
"/private/var/folders/0s/vh7xxzmj0vx89d5_g5cljzgw0000gp/T/AppTranslocation/033EE131-A009-4172-9D81-95067A2CD68F/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 1262, in request  
self._send_request(method, url, body, headers, encode_chunked)  
File
"/private/var/folders/0s/vh7xxzmj0vx89d5_g5cljzgw0000gp/T/AppTranslocation/033EE131-A009-4172-9D81-95067A2CD68F/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 1308, in _send_request  
self.endheaders(body, encode_chunked=encode_chunked)  
File
"/private/var/folders/0s/vh7xxzmj0vx89d5_g5cljzgw0000gp/T/AppTranslocation/033EE131-A009-4172-9D81-95067A2CD68F/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 1257, in endheaders  
self._send_output(message_body, encode_chunked=encode_chunked)  
File
"/private/var/folders/0s/vh7xxzmj0vx89d5_g5cljzgw0000gp/T/AppTranslocation/033EE131-A009-4172-9D81-95067A2CD68F/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 1028, in _send_output  
self.send(msg)  
File
"/private/var/folders/0s/vh7xxzmj0vx89d5_g5cljzgw0000gp/T/AppTranslocation/033EE131-A009-4172-9D81-95067A2CD68F/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 968, in send  
self.connect()  
File
"/private/var/folders/0s/vh7xxzmj0vx89d5_g5cljzgw0000gp/T/AppTranslocation/033EE131-A009-4172-9D81-95067A2CD68F/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 940, in connect  
(self.host,self.port), self.timeout, self.source_address)  
File
"/private/var/folders/0s/vh7xxzmj0vx89d5_g5cljzgw0000gp/T/AppTranslocation/033EE131-A009-4172-9D81-95067A2CD68F/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/socket.py",
line 707, in create_connection  
for res in getaddrinfo(host, port, 0, SOCK_STREAM):  
File
"/private/var/folders/0s/vh7xxzmj0vx89d5_g5cljzgw0000gp/T/AppTranslocation/033EE131-A009-4172-9D81-95067A2CD68F/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/socket.py",
line 752, in getaddrinfo  
for res in _socket.getaddrinfo(host, port, family, type, proto, flags):  
socket.gaierror: [Errno 8] nodename nor servname provided, or not known  




OpenGL version: 4.1 ATI-3.10.18
OpenGL renderer: AMD Radeon Pro 560X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,1
      Processor Name: 6-Core Intel Core i7
      Processor Speed: 2.6 GHz
      Number of Processors: 1
      Total Number of Cores: 6
      L2 Cache (per Core): 256 KB
      L3 Cache: 9 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: 1037.147.4.0.0 (iBridge: 17.16.16610.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H15)
      Kernel Version: Darwin 19.6.0
      Time since boot: 4:26

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0000
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1

    Radeon Pro 560X:

      Chipset Model: Radeon Pro 560X
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67ef
      Revision ID: 0x00c2
      ROM Revision: 113-C980AL-075
      VBIOS Version: 113-C97501U-005
      EFI Driver Version: 01.A1.075
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

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
    appnope: 0.1.0
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.3
    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: 1.0.1
    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-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-Cytoscape: 0.1
    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: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    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-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-Stringdb: 0.1
    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
    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
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pexpect: 4.8.0
    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
    ptyprocess: 0.6.0
    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
    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

Change History (2)

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → Infrastructure
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Bug report with bug-reporter failure(!)

Original error was an already fixed Toolshed problem.

comment:2 by Tom Goddard, 5 years ago

Resolution: → fixed
Status: assigned → closed

Fixed.

The bug reporter traceback was from submitting the bug with no internet connection. The user probably did not see the traceback since it was logged but no dialog was raised. Instead the bug report dialog said "Error while submitting feedback" and explained that might be from no internet connection. Probably better to say they have no internet connection, so I've made it do that. Also if www.rbvi.ucsf.edu is simply not responding, reduced timeout from 72 seconds to 10 seconds.

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