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Opened 2 years ago
Last modified 2 years ago
#10031 assigned defect
XMAS 1.1.2: this version of pandas is incompatible with numpy < 1.22.4
| Reported by: | Owned by: | Richard Scheltema | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | Eric Pettersen | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19045
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
When I tried to install XMAS, an error about Python appeared to me.
Log:
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> toolshed show
> ui tool show XMAS
Traceback (most recent call last):
File "C:\Users\lewis.abigail\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\pandas\\__init__.py", line 50, in <module>
from pandas.compat import (
File "C:\Users\lewis.abigail\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\pandas\compat\\__init__.py", line 26, in <module>
from pandas.compat.numpy import is_numpy_dev
File "C:\Users\lewis.abigail\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\pandas\compat\numpy\\__init__.py", line 17, in <module>
raise ImportError(
ImportError: this version of pandas is incompatible with numpy < 1.22.4
your numpy version is 1.22.1.
Please upgrade numpy to >= 1.22.4 to use this pandas version
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 559, in start_tool
ti = api._api_caller.start_tool(api, session, self, tool_info)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1325, in start_tool
return cls._get_func(api, "start_tool")(session, bi, ti)
File "C:\Users\lewis.abigail\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\xmas\\__init__.py", line 42, in start_tool
from . import tool
File "C:\Users\lewis.abigail\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\xmas\tool.py", line 16, in <module>
from .info_file import InfoFile
File "C:\Users\lewis.abigail\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\xmas\info_file.py", line 16, in <module>
import pandas as pd
File "C:\Users\lewis.abigail\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\pandas\\__init__.py", line 55, in <module>
raise ImportError(
ImportError: C extension: None not built. If you want to import pandas from
the source directory, you may need to run 'python setup.py build_ext' to build
the C extensions first.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-packages\chimerax\ui\gui.py",
line 1685, in <lambda>
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-packages\chimerax\ui\cmd.py",
line 219, in ui_tool_show
bi.start_tool(session, name)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 564, in start_tool
raise ToolshedError(
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool XMAS in
bundle ChimeraX-XMAS:
C extension: None not built. If you want to import pandas from the source
directory, you may need to run 'python setup.py build_ext' to build the C
extensions first.
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool XMAS in
bundle ChimeraX-XMAS:
C extension: None not built. If you want to import pandas from the source
directory, you may need to run 'python setup.py build_ext' to build the C
extensions first.
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 564, in start_tool
raise ToolshedError(
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 30.0.101.2079
OpenGL renderer: Intel(R) UHD Graphics 770
OpenGL vendor: Intel
Python: 3.9.11
Locale: en_US.cp1252
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: windows
Manufacturer: Dell Inc.
Model: OptiPlex 5000
OS: Microsoft Windows 10 Pro (Build 19045)
Memory: 16,853,479,424
MaxProcessMemory: 137,438,953,344
CPU: 20 12th Gen Intel(R) Core(TM) i7-12700
OSLanguage: en-US
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.10.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2022.5.18.1
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.4.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.39.1
ChimeraX-AtomicLibrary: 7.0
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.7
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: 2.2.4
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.2.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4
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: 1.1
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: 1.2
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: 1.1.1
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: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
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: 1.9
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
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: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.6
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: 1.8
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: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.18.3
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
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: 1.1.0
ChimeraX-XMAS: 1.1.2
ChimeraX-Zone: 1.0
colorama: 0.4.4
comtypes: 1.1.10
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.6.0
decorator: 5.1.1
docutils: 0.17.1
entrypoints: 0.4
et-xmlfile: 1.1.0
filelock: 3.4.2
fonttools: 4.33.3
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.10.0
kiwisolver: 1.4.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.5
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.26.1
openpyxl: 3.1.2
openvr: 1.16.802
packaging: 21.3
pandas: 2.1.1
ParmEd: 3.4.3
parso: 0.8.3
pickleshare: 0.7.5
Pillow: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.29
psutil: 5.9.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.0
PyQt6-Qt6: 6.3.0
PyQt6-sip: 13.3.1
PyQt6-WebEngine-commercial: 6.3.0
PyQt6-WebEngine-Qt6: 6.3.0
python-dateutil: 2.8.2
pytz: 2022.1
pywin32: 303
pyzmq: 23.1.0
qtconsole: 5.3.0
QtPy: 2.1.0
QtRangeSlider: 0.1.5
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
seaborn: 0.13.0
setuptools: 59.8.0
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
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-community: 1.0.0
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.1.1
tzdata: 2023.3
urllib3: 1.26.9
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
WMI: 1.5.1
Attachments (2)
Change History (6)
comment:1 by , 2 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Third Party |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → XMAS 1.1.3: this version of pandas is incompatible with numpy < 1.22.4 |
comment:2 by , 2 years ago
| Summary: | XMAS 1.1.3: this version of pandas is incompatible with numpy < 1.22.4 → XMAS 1.1.2: this version of pandas is incompatible with numpy < 1.22.4 |
|---|
comment:3 by , 2 years ago
Thank you Erik for your prompt reply. Best, Diogo _____________________________________ *Diogo Borges Lima* About me: @diogobor <http://twitter.com/diogobor> | diogobor <https://www.linkedin.com/in/diogobor/> URL: diogobor <http://diogobor.droppages.com/> Le ven. 20 oct. 2023 à 19:09, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> a écrit : > > > > > >
comment:4 by , 2 years ago
Hi Diogo,
Let me know whether it works 🙂.
Cheers, Richard
-
Dr. Richard Scheltema
Utrecht University / Pharmaceutical Sciences
Biomolecular Mass Spectrometry and Proteomics
Padualaan 8 , 3584 CH Utrecht
Kruyt-building, room O604
(+31) 30 253 6804
https://scheltemalab.com<https://scheltemalab.com/>
https://www.uu.nl/medewerkers/RAScheltema
[image001]
Treasurer - Dutch Society for Mass Spectrometry
www.nvms.nl<http://www.nvms.nl/>
[cid:36de2982-17b8-4818-ba3f-cce6579dea38]
Mark your agenda for the NVMS-BSMS Rolduc
meeting happening 28 – 30 April, 2024! Great science
in a lovely environment in the former abbey Rolduc.
________________________________
From: Diogo Borges <diogobor@gmail.com>
Sent: Friday, October 20, 2023 7:25 PM
To: ChimeraX-bugs@cgl.ucsf.edu <ChimeraX-bugs@cgl.ucsf.edu>
Cc: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; Scheltema, R.A. (Richard) <R.A.Scheltema@uu.nl>
Subject: Re: [ChimeraX] #10031: XMAS 1.1.2: this version of pandas is incompatible with numpy < 1.22.4 (was: XMAS 1.1.3: this version of pandas is incompatible with numpy < 1.22.4)
CAUTION: This email originated from outside of Utrecht University. Do not click links or open attachments unless you recognize the sender and know the content is safe.
Thank you Erik for your prompt reply.
Best,
Diogo
_____________________________________
Diogo Borges Lima
About me: @diogobor<http://twitter.com/diogobor> | diogobor<https://www.linkedin.com/in/diogobor/>
URL: diogobor<http://diogobor.droppages.com/>
Le ven. 20 oct. 2023 à 19:09, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu<mailto:ChimeraX-bugs-admin@cgl.ucsf.edu>> a écrit :
#10031: XMAS 1.1.2: this version of pandas is incompatible with numpy < 1.22.4
----------------------------------+-------------------------------
Reporter: diogobor@… | Owner: Richard Scheltema
Type: defect | Status: assigned
Priority: normal | Milestone:
Component: Third Party | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
----------------------------------+-------------------------------
Changes (by pett):
* summary: XMAS 1.1.3: this version of pandas is incompatible with numpy <
1.22.4 => XMAS 1.1.2: this version of pandas is incompatible with
numpy < 1.22.4
Comment:
Hi Diogo,
I would suggest using the newest version of XMAS (1.1.3) which has
several bug fixes. This would also require you to upgrade to a newer
version of ChimeraX (at least 1.6.1), which also has many bug fixes and
new features.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/10031#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
Note:
See TracTickets
for help on using tickets.
Hi Diogo,
--Eric