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Opened 4 years ago
Closed 3 years ago
#5866 closed defect (fixed)
Registration time-format error
| Reported by: | pett | Owned by: | Greg Couch |
|---|---|---|---|
| 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: Linux-4.15.0-163-generic-x86_64-with-glibc2.27
ChimeraX Version: 1.4.dev202201020113 (2022-01-02 01:13:47 UTC)
Description
At startup after initial install
Log:
Startup Errors
---
error | Bundle 'ChimeraX-Registration' custom initialization failed
warning | Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/registration/nag.py", line 278, in _strptime
month = _months.index(month_name)
ValueError: tuple.index(x): x not in tuple
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/registration/nag.py", line 289, in _strptime
return datetime.strptime(TimeFormat, value)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/_strptime.py", line 568, in
_strptime_datetime
tt, fraction, gmtoff_fraction = _strptime(data_string, format)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/_strptime.py", line 349, in
_strptime
raise ValueError("time data %r does not match format %r" %
ValueError: time data '%a %b %d %H:%M:%S %Y' does not match format 'sze febr
14 20:32:46 2018'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 360, in initialize
api._api_caller.initialize(api, session, self)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1276, in initialize
return cls._get_func(api, "initialize")(session, bi)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/registration/__init__.py", line 41, in initialize
nag(session)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/registration/nag.py", line 38, in nag
_check_usage(session)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/registration/nag.py", line 192, in _check_usage
usage = _get_usage()
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/registration/nag.py", line 240, in _get_usage
usage["dates"].append(_strptime(value))
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/registration/nag.py", line 291, in _strptime
raise ValueError("time data does not match format")
ValueError: time data does not match format
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.4.dev202201020113 (2022-01-02)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/urllib3/connectionpool.py", line 699, in urlopen
httplib_response = self._make_request(
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/urllib3/connectionpool.py", line 382, in _make_request
self._validate_conn(conn)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/urllib3/connectionpool.py", line 1010, in _validate_conn
conn.connect()
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/urllib3/connection.py", line 416, in connect
self.sock = ssl_wrap_socket(
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/urllib3/util/ssl_.py", line 449, in ssl_wrap_socket
ssl_sock = _ssl_wrap_socket_impl(
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/urllib3/util/ssl_.py", line 493, in _ssl_wrap_socket_impl
return ssl_context.wrap_socket(sock, server_hostname=server_hostname)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/ssl.py", line 500, in
wrap_socket
return self.sslsocket_class._create(
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/ssl.py", line 1040, in
_create
self.do_handshake()
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/ssl.py", line 1309, in
do_handshake
self._sslobj.do_handshake()
ssl.SSLCertVerificationError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate
verify failed: unable to get local issuer certificate (_ssl.c:1129)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 691, in customEvent
func(*args, **kw)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1502, in on_finish
versions = self.result.get()
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/multiprocessing/pool.py",
line 771, in get
raise self._value
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/multiprocessing/pool.py",
line 125, in worker
result = (True, func(*args, **kwds))
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/cxservices/api_client.py", line 148, in __call_api
response_data = self.request(
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/cxservices/api_client.py", line 338, in request
return self.rest_client.GET(url,
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/cxservices/rest.py", line 233, in GET
return self.request("GET", url,
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/cxservices/rest.py", line 206, in request
r = self.pool_manager.request(method, url,
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/urllib3/request.py", line 74, in request
return self.request_encode_url(
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/urllib3/request.py", line 96, in request_encode_url
return self.urlopen(method, url, **extra_kw)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/urllib3/poolmanager.py", line 375, in urlopen
response = conn.urlopen(method, u.request_uri, **kw)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/urllib3/connectionpool.py", line 783, in urlopen
return self.urlopen(
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/urllib3/connectionpool.py", line 783, in urlopen
return self.urlopen(
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/urllib3/connectionpool.py", line 783, in urlopen
return self.urlopen(
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/urllib3/connectionpool.py", line 755, in urlopen
retries = retries.increment(
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/urllib3/util/retry.py", line 574, in increment
raise MaxRetryError(_pool, url, error or ResponseError(cause))
urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='webservices-
test.rbvi.ucsf.edu', port=443): Max retries exceeded with url:
/cxservices/api/v1/chimerax/newer?uuid=085bdfd8-c56c-599b-b8c5-650029dd90f0&OS=ubuntu+debian&OSVersion=18.04.6&ChimeraXVersion=1.4.dev202201020113
(Caused by SSLError(SSLCertVerificationError(1, '[SSL:
CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local
issuer certificate (_ssl.c:1129)')))
urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='webservices-
test.rbvi.ucsf.edu', port=443): Max retries exceeded with url:
/cxservices/api/v1/chimerax/newer?uuid=085bdfd8-c56c-599b-b8c5-650029dd90f0&OS=ubuntu+debian&OSVersion=18.04.6&ChimeraXVersion=1.4.dev202201020113
(Caused by SSLError(SSLCertVerificationError(1, '[SSL:
CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local
issuer certificate (_ssl.c:1129)')))
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/urllib3/util/retry.py", line 574, in increment
raise MaxRetryError(_pool, url, error or ResponseError(cause))
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 340.108
OpenGL renderer: GeForce GT 320/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Hewlett-Packard
Model: HPE-380t
OS: Ubuntu 18.04 bionic
Architecture: 64bit ELF
Virutal Machine: none
CPU: 8 Intel(R) Core(TM) i7 CPU 930 @ 2.80GHz
Cache Size: 8192 KB
Memory:
total used free shared buff/cache available
Mem: 5.8G 1.7G 902M 41M 3.2G 3.8G
Swap: 2.0G 0B 2.0G
Graphics:
06:00.0 VGA compatible controller [0300]: NVIDIA Corporation GT215 [GeForce GT 320] [10de:0ca2] (rev a2)
Subsystem: Micro-Star International Co., Ltd. [MSI] GT215 [GeForce GT 320] [1462:1917]
Kernel driver in use: nvidia
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: 2021.10.8
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.32.1
ChimeraX-AtomicLibrary: 5.0
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4.dev202201020113
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
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: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
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
ChimeraX-Label: 1.1
ChimeraX-LinuxSupport: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.5
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.1
ChimeraX-ModelPanel: 1.3.1
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: 2.0.2
ChimeraX-OpenCommand: 1.8
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.7.4
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.15.2
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 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: 0.4.4
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.5.1
decorator: 5.1.0
distro: 1.6.0
docutils: 0.17.1
entrypoints: 0.3
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 6.6.0
ipython: 7.30.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.1
jupyter-client: 7.1.0
jupyter-core: 4.9.1
kiwisolver: 1.3.2
line-profiler: 3.3.0
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
nest-asyncio: 1.5.4
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.24
psutil: 5.8.0
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pyzmq: 22.3.0
qtconsole: 5.2.2
QtPy: 2.0.0
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
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: 3.7.0
tifffile: 2021.4.8
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 4 years ago
| Component: | Unassigned → Infrastructure |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Registration time-format error |
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