ChimeraX bug report submission

[jaraque@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.17763
ChimeraX Version: 0.8 (2018-12-17)
Description
Downloading bundle ChimeraX_ISOLDE-1.0b2-cp36-cp36m-win_amd64.whl Traceback (most recent call last):   File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line 386, in download_finished     session=self.session)   File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\toolshed\__init__.py", line 548, in install_bundle     results = self._pip_install(bundle, per_user=per_user, reinstall=reinstall)   File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\toolshed\__init__.py", line 845, in _pip_install     results = self._run_pip(command)   File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\toolshed\__init__.py", line 873, in _run_pip     result = cp.stdout.decode("utf-8") UnicodeDecodeError: 'utf-8' codec can't decode byte 0xa0 in position 46: invalid start byte UnicodeDecodeError: 'utf-8' codec can't decode byte 0xa0 in position 46: invalid start byte File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\toolshed\__init__.py", line 873, in _run_pip result = cp.stdout.decode("utf-8")

Log:
Startup Messages  
---  
note | Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-  
packages\chimerax\core\toolshed\\\\__init__.py", line 338, in __init__  
self.init_available_from_cache(logger)  
File "C:\Program Files\ChimeraX\bin\lib\site-  
packages\chimerax\core\toolshed\\\\__init__.py", line 445, in  
init_available_from_cache  
abc.load_from_cache()  
File "C:\Program Files\ChimeraX\bin\lib\site-  
packages\chimerax\core\toolshed\available.py", line 61, in load_from_cache  
b = _build_bundle(d)  
File "C:\Program Files\ChimeraX\bin\lib\site-  
packages\chimerax\core\toolshed\available.py", line 242, in _build_bundle  
keywords = _extract_extra_keywords(keywords)  
File "C:\Program Files\ChimeraX\bin\lib\site-  
packages\chimerax\core\toolshed\installed.py", line 270, in  
_extract_extra_keywords  
all_kwds = [k.strip() for k in kwds.split(',')]  
AttributeError: 'list' object has no attribute 'split'  
  
UCSF ChimeraX version: 0.8 (2018-12-17)  
How to cite UCSF ChimeraX  
Downloading bundle ChimeraX_ISOLDE-1.0b2-cp36-cp36m-win_amd64.whl  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 386, in download_finished  
session=self.session)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 548, in install_bundle  
results = self._pip_install(bundle, per_user=per_user, reinstall=reinstall)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 845, in _pip_install  
results = self._run_pip(command)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 863, in _run_pip  
output = cp.stdout.decode("utf-8")  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xa0 in position 46:
invalid start byte  
  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xa0 in position 46:
invalid start byte  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 863, in _run_pip  
output = cp.stdout.decode("utf-8")  
  
See log for complete Python traceback.  
  
Downloading bundle ChimeraX_ISOLDE-1.0b2-cp36-cp36m-win_amd64.whl  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 386, in download_finished  
session=self.session)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 548, in install_bundle  
results = self._pip_install(bundle, per_user=per_user, reinstall=reinstall)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 845, in _pip_install  
results = self._run_pip(command)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 873, in _run_pip  
result = cp.stdout.decode("utf-8")  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xa0 in position 46:
invalid start byte  
  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xa0 in position 46:
invalid start byte  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 873, in _run_pip  
result = cp.stdout.decode("utf-8")  
  
See log for complete Python traceback.  
  
Downloading bundle ChimeraX_ISOLDE-1.0b2-cp36-cp36m-win_amd64.whl  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 386, in download_finished  
session=self.session)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 548, in install_bundle  
results = self._pip_install(bundle, per_user=per_user, reinstall=reinstall)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 845, in _pip_install  
results = self._run_pip(command)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 873, in _run_pip  
result = cp.stdout.decode("utf-8")  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xa0 in position 46:
invalid start byte  
  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xa0 in position 46:
invalid start byte  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 873, in _run_pip  
result = cp.stdout.decode("utf-8")  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 10.18.10.4885
OpenGL renderer: Intel(R) HD Graphics 4000
OpenGL vendor: Intel

[Tristan Croll]

This is a known bug affecting ChimeraX 0.8. You can find instructions to work around it at ​https://isolde.cimr.cam.ac.uk/faq/#installation.