#15376 closed defect (fixed)
Bundle 'ChimeraX-OpenCommand' custom initialization failed
Reported by: | Owned by: | Eric Pettersen | |
---|---|---|---|
Priority: | normal | Milestone: | 1.8 |
Component: | Input/Output | Version: | |
Keywords: | Cc: | Greg Couch | |
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: macOS-13.6.6-x86_64-i386-64bit ChimeraX Version: 1.8rc202406032355 (2024-06-03 23:55:07 UTC) Description Just started current 1.8 release candidate and clicked on a PDB file in the recent file history thumbnails and it gave this error. Log: Startup Errors --- error | Bundle 'ChimeraX-OpenCommand' custom initialization failed warning | Traceback (most recent call last): File "/Users/goddard/Desktop/ChimeraX-1.8-rc2024.06.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/open_command/manager.py", line 113, in add_provider data_format = self.session.data_formats[format_name] ~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^ File "/Users/goddard/Desktop/ChimeraX-1.8-rc2024.06.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/data_formats/manager.py", line 205, in __getitem__ raise KeyError("No known data format '%s'" % key) KeyError: "No known data format 'MTZ'" During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Users/goddard/Desktop/ChimeraX-1.8-rc2024.06.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py", line 387, in init_manager return api._api_caller.init_manager(api, session, self, name, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/goddard/Desktop/ChimeraX-1.8-rc2024.06.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/__init__.py", line 1302, in init_manager return cls._get_func(api, "init_manager")(session, bi, name, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/goddard/Desktop/ChimeraX-1.8-rc2024.06.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/open_command/__init__.py", line 135, in init_manager session.open_command = manager.OpenManager(session, name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/goddard/Desktop/ChimeraX-1.8-rc2024.06.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/open_command/manager.py", line 64, in __init__ super().__init__(name) File "/Users/goddard/Desktop/ChimeraX-1.8-rc2024.06.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/__init__.py", line 996, in __init__ ts._init_single_manager(self) File "/Users/goddard/Desktop/ChimeraX-1.8-rc2024.06.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/__init__.py", line 875, in _init_single_manager mgr.add_provider(pbi, pvdr, **kw) File "/Users/goddard/Desktop/ChimeraX-1.8-rc2024.06.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/open_command/manager.py", line 116, in add_provider raise ValueError("Database-fetch provider '%s' in bundle %s specified" ValueError: Database-fetch provider 'redo' in bundle Map specified unknown data format 'MTZ' UCSF ChimeraX version: 1.8rc202406032355 (2024-06-03) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 7evo format mmcif fromDatabase pdb Traceback (most recent call last): File "/Users/goddard/Desktop/ChimeraX-1.8-rc2024.06.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest self._callback(info) File "/Users/goddard/Desktop/ChimeraX-1.8-rc2024.06.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept return interceptor(request_info, *args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/goddard/Desktop/ChimeraX-1.8-rc2024.06.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/widgets/htmlview.py", line 353, in intercept chimerax_intercept(*args, view=view, session=session) File "/Users/goddard/Desktop/ChimeraX-1.8-rc2024.06.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/widgets/htmlview.py", line 455, in chimerax_intercept session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir) File "/Users/goddard/Desktop/ChimeraX-1.8-rc2024.06.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/gui.py", line 415, in thread_safe func(*args, **kw) File "/Users/goddard/Desktop/ChimeraX-1.8-rc2024.06.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/widgets/htmlview.py", line 446, in defer cxcmd(session, topic) File "/Users/goddard/Desktop/ChimeraX-1.8-rc2024.06.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/widgets/htmlview.py", line 464, in cxcmd run(session, cmd) File "/Users/goddard/Desktop/ChimeraX-1.8-rc2024.06.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/goddard/Desktop/ChimeraX-1.8-rc2024.06.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/goddard/Desktop/ChimeraX-1.8-rc2024.06.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/open_command/cmd.py", line 79, in cmd_open mgr = session.open_command ^^^^^^^^^^^^^^^^^^^^ AttributeError: 'Session' object has no attribute 'open_command' AttributeError: 'Session' object has no attribute 'open_command' File "/Users/goddard/Desktop/ChimeraX-1.8-rc2024.06.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/open_command/cmd.py", line 79, in cmd_open mgr = session.open_command ^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. OpenGL version: 4.1 ATI-4.14.1 OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine OpenGL vendor: ATI Technologies Inc. Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: iMac Model Identifier: iMac18,3 Processor Name: Quad-Core Intel Core i7 Processor Speed: 4.2 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 8 MB Hyper-Threading Technology: Enabled Memory: 32 GB System Firmware Version: 526.0.0.0.0 OS Loader Version: 577.140.2~22 SMC Version (system): 2.41f2 Software: System Software Overview: System Version: macOS 13.6.6 (22G630) Kernel Version: Darwin 22.6.0 Time since boot: 46 days, 2 hours, 6 minutes Graphics/Displays: Radeon Pro 580: Chipset Model: Radeon Pro 580 Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 8 GB Vendor: AMD (0x1002) Device ID: 0x67df Revision ID: 0x00c0 ROM Revision: 113-D000AA-931 VBIOS Version: 113-D0001A1X-025 EFI Driver Version: 01.00.931 Metal Support: Metal 2 Displays: iMac: Display Type: Built-In Retina LCD Resolution: Retina 5K (5120 x 2880) Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57 ChimeraX-AtomicLibrary: 14.0.5 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8rc202406032355 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.16 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.4 ChimeraX-PDB: 2.7.5 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.45 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4 traitlets: 5.14.2 typing-extensions: 4.12.1 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11
Attachments (1)
Change History (14)
comment:2 by , 17 months ago
Component: | Unassigned → Input/Output |
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Milestone: | → 1.8 |
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → assigned |
Summary: | ChimeraX bug report submission → Bundle 'ChimeraX-OpenCommand' custom initialization failed |
comment:3 by , 17 months ago
ChimeraX 1.9 June 4 daily build did not give this error on the same Intel Mac but also said "available bundle cache has not been initialized yet" which may be what is different. This is probably the first time a ChimeraX 1.9 was run on this Intel Mac.
comment:4 by , 17 months ago
Status: | assigned → accepted |
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comment:5 by , 17 months ago
Cc: | added |
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Is this reproducible? I just tried the current release candidate on my Intel Mac at home, both with and without removing the toolshed cache beforehand, and it worked every time. I'm imagining it could be a very rare race condition between the toolshed cache initializing and the manager/providers being executed, which is why I ask if it's reproducible.
comment:6 by , 17 months ago
Yes, it reproduces every time. I tried it about 10 times yesterday and just now today. Seems very likely it has something to do with installed user bundles or preferences.
comment:7 by , 17 months ago
This is on popper our build machine on my N453 desk. In fact there are no 1.8 user installed bundles. Let me move the setting directory and see if it starts correctly.
comment:8 by , 17 months ago
I also tried with todays June 4 candidate and get the same startup error.
comment:9 by , 17 months ago
Even moving ~/Library/Application Support/ChimeraX it still starts with the error. Maybe it is finding something on the build machine that confuses it.
comment:10 by , 17 months ago
I moved ~/Library/Caches/ChimeraX and then it starts correctly. So apparently the error has to do with the Toolshed cache. I'll attach that cache directory so you can debug.
by , 17 months ago
Attachment: | chimerax_cache.zip added |
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~/Library/Caches/ChimeraX folder that causes this error.
comment:11 by , 17 months ago
Resolution: | → fixed |
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Status: | accepted → closed |
I can see that your bundle_info.cache differ in size from mine:
(yours) -rw-r--r--@ 1 pett staff 192585 Jun 5 13:54 bundle_info.cache
(mine) -rw-r--r-- 1 pett staff 202696 Jun 5 13:44 bundle_info.cache
But using it works without error since it seems to immediately get updated to the "correct" size. I am simply going to downgrade to a warning, since there is also the possibility that (for instance) a bad version of Clipper gets uploaded to the Toolshed briefly that fails to declare MTZ, which would also cause the error (for everyone).
I don't know why the cache file on popper does not update on its own. Probably one of us should investigate tomorrow. Awkward that it's on your desk.
comment:12 by , 17 months ago
After the startup error, no files (PDB, mmCIF, maps, ...) can be opened because the open command didn't initialize. So if you downgrade to a warning, also need to make sure the initialization completes correctly so all the non-MTZ formats work.
Maybe the custom init failure somehow prevents the toolshed cache update?
I am often away from my desk if you want to use popper. Tomorrow I will meet at Dyche's lab 2 - 3 pm, and will go to talk 12-1 pm, and will probably be outside after 3 for lunch.
comment:13 by , 17 months ago
Unfortunately, it turns out I had only downgraded to a warning in one of two places that I needed to. I've updated the second location and we'll see if that works better on Monday.