Opened 5 years ago

Last modified 5 years ago

#3705 assigned enhancement

Bundle builder opaque error message

Reported by: chimerax-bug-report@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Build System Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.17763
ChimeraX Version: 1.1rc202009092222 (2020-09-09 22:22:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.1rc202009092222 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> help help:user

> devel build E:/MorphOT/otmorph-bundle

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1rc202009092222\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 275, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.1rc202009092222\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1rc202009092222\bin\lib\site-
packages\chimerax\core\commands\devel.py", line 98, in devel_build  
_run(path, session.logger, exit, BundleBuilder.make_wheel, debug=debug)  
File "C:\Program Files\ChimeraX 1.1rc202009092222\bin\lib\site-
packages\chimerax\core\commands\devel.py", line 157, in _run  
bb = _get_builder(path, logger)  
File "C:\Program Files\ChimeraX 1.1rc202009092222\bin\lib\site-
packages\chimerax\core\commands\devel.py", line 201, in _get_builder  
bb = BundleBuilder(logger, bundle_path=path)  
File "C:\Program Files\ChimeraX 1.1rc202009092222\bin\lib\site-
packages\chimerax\bundle_builder\bundle_builder.py", line 54, in __init__  
self._read_bundle_info(info_file)  
File "C:\Program Files\ChimeraX 1.1rc202009092222\bin\lib\site-
packages\chimerax\bundle_builder\bundle_builder.py", line 157, in
_read_bundle_info  
doc = parse(bundle_info)  
File "src\lxml\etree.pyx", line 3521, in lxml.etree.parse  
File "src\lxml\parser.pxi", line 1839, in lxml.etree._parseDocument  
File "src\lxml\parser.pxi", line 1865, in lxml.etree._parseDocumentFromURL  
File "src\lxml\parser.pxi", line 1769, in lxml.etree._parseDocFromFile  
File "src\lxml\parser.pxi", line 1163, in
lxml.etree._BaseParser._parseDocFromFile  
File "src\lxml\parser.pxi", line 601, in
lxml.etree._ParserContext._handleParseResultDoc  
File "src\lxml\parser.pxi", line 711, in lxml.etree._handleParseResult  
File "src\lxml\parser.pxi", line 640, in lxml.etree._raiseParseError  
File "file:/E:/MorphOT/otmorph-bundle/bundle_info.xml", line 1  
lxml.etree.XMLSyntaxError: Start tag expected, '<' not found, line 1, column 1  
  
File "file:/E:/MorphOT/otmorph-bundle/bundle_info.xml", line 1  
lxml.etree.XMLSyntaxError: Start tag expected, '  
File "src\lxml\parser.pxi", line 640, in lxml.etree._raiseParseError  
  
See log for complete Python traceback.  
  

> devel build E:\MorphOT\otmorph-bundle

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1rc202009092222\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 275, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.1rc202009092222\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1rc202009092222\bin\lib\site-
packages\chimerax\core\commands\devel.py", line 98, in devel_build  
_run(path, session.logger, exit, BundleBuilder.make_wheel, debug=debug)  
File "C:\Program Files\ChimeraX 1.1rc202009092222\bin\lib\site-
packages\chimerax\core\commands\devel.py", line 157, in _run  
bb = _get_builder(path, logger)  
File "C:\Program Files\ChimeraX 1.1rc202009092222\bin\lib\site-
packages\chimerax\core\commands\devel.py", line 201, in _get_builder  
bb = BundleBuilder(logger, bundle_path=path)  
File "C:\Program Files\ChimeraX 1.1rc202009092222\bin\lib\site-
packages\chimerax\bundle_builder\bundle_builder.py", line 54, in __init__  
self._read_bundle_info(info_file)  
File "C:\Program Files\ChimeraX 1.1rc202009092222\bin\lib\site-
packages\chimerax\bundle_builder\bundle_builder.py", line 157, in
_read_bundle_info  
doc = parse(bundle_info)  
File "src\lxml\etree.pyx", line 3521, in lxml.etree.parse  
File "src\lxml\parser.pxi", line 1839, in lxml.etree._parseDocument  
File "src\lxml\parser.pxi", line 1865, in lxml.etree._parseDocumentFromURL  
File "src\lxml\parser.pxi", line 1769, in lxml.etree._parseDocFromFile  
File "src\lxml\parser.pxi", line 1163, in
lxml.etree._BaseParser._parseDocFromFile  
File "src\lxml\parser.pxi", line 601, in
lxml.etree._ParserContext._handleParseResultDoc  
File "src\lxml\parser.pxi", line 711, in lxml.etree._handleParseResult  
File "src\lxml\parser.pxi", line 640, in lxml.etree._raiseParseError  
File "file:/E:/MorphOT/otmorph-bundle/bundle_info.xml", line 1  
lxml.etree.XMLSyntaxError: Start tag expected, '<' not found, line 1, column 1  
  
File "file:/E:/MorphOT/otmorph-bundle/bundle_info.xml", line 1  
lxml.etree.XMLSyntaxError: Start tag expected, '  
File "src\lxml\parser.pxi", line 640, in lxml.etree._raiseParseError  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 430.86
OpenGL renderer: Quadro P620/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: OptiPlex 7070
OS: Microsoft Windows 10 企业版 LTSC (Build 17763)
Memory: 16,951,214,080
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-9700 CPU @ 3.00GHz"
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
    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: 1.0.1
    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: 1.1rc202009092222
    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-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-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 (1)

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → Build System
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Bundle builder opaque error message
Type: defect → enhancement

Perhaps bundle builder could produce a better error message when a bundle_info.xml file fails to parse?

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