ISOLDE installation: UnicodeDecodeError

[d.houldershaw@…]

The following bug report has been submitted:
Platform:        Linux-3.10.0-862.3.2.el7.x86_64-x86_64-with-centos-7.5.1804-Core
ChimeraX Version: 0.8 (2018-12-17)
Description
Installation of Isolde from toolshed fails with:-
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xa0 in position 44: invalid start byte

File "/opt/UCSF/ChimeraX/lib/python3.6/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 "/opt/UCSF/ChimeraX/lib/python3.6/site-  
packages/chimerax/core/toolshed/__init__.py", line 338, in __init__  
self.init_available_from_cache(logger)  
File "/opt/UCSF/ChimeraX/lib/python3.6/site-  
packages/chimerax/core/toolshed/__init__.py", line 445, in  
init_available_from_cache  
abc.load_from_cache()  
File "/opt/UCSF/ChimeraX/lib/python3.6/site-  
packages/chimerax/core/toolshed/available.py", line 61, in load_from_cache  
b = _build_bundle(d)  
File "/opt/UCSF/ChimeraX/lib/python3.6/site-  
packages/chimerax/core/toolshed/available.py", line 98, in _build_bundle  
bundle_d = d["bundle"][bundle_name]  
KeyError: 'ChimeraX_ISOLDE'  
  
UCSF ChimeraX version: 0.8 (2018-12-17)  
How to cite UCSF ChimeraX  
Updating list of available bundles failed: 'ChimeraX_ISOLDE'  
Downloading bundle ChimeraX_ISOLDE-1.0b2-cp36-cp36m-linux_x86_64.whl  
unloading module chimerax.isolde  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.6/site-
packages/chimerax/ui/widgets/htmlview.py", line 386, in download_finished  
session=self.session)  
File "/opt/UCSF/ChimeraX/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 548, in install_bundle  
results = self._pip_install(bundle, per_user=per_user, reinstall=reinstall)  
File "/opt/UCSF/ChimeraX/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 845, in _pip_install  
results = self._run_pip(command)  
File "/opt/UCSF/ChimeraX/lib/python3.6/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 44:
invalid start byte  
  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xa0 in position 44:
invalid start byte  
  
File "/opt/UCSF/ChimeraX/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 873, in _run_pip  
result = cp.stdout.decode("utf-8")  
  
See log for complete Python traceback.  
  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 2250, resource id:
29427117, major code: 40 (TranslateCoords), minor code: 0  

Downloading bundle ChimeraX_ISOLDE-1.0b2-cp36-cp36m-linux_x86_64.whl  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.6/site-
packages/chimerax/ui/widgets/htmlview.py", line 386, in download_finished  
session=self.session)  
File "/opt/UCSF/ChimeraX/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 548, in install_bundle  
results = self._pip_install(bundle, per_user=per_user, reinstall=reinstall)  
File "/opt/UCSF/ChimeraX/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 845, in _pip_install  
results = self._run_pip(command)  
File "/opt/UCSF/ChimeraX/lib/python3.6/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 44:
invalid start byte  
  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xa0 in position 44:
invalid start byte  
  
File "/opt/UCSF/ChimeraX/lib/python3.6/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 NVIDIA 390.48
OpenGL renderer: GeForce GTX 1050 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[Tristan Croll]

The Unicode error is a separate thing that is fixed in the ChimeraX development builds, but I think I have fixed the underlying error that was causing the installation to fail in the first place. It turns out devtoolset-3 in Fedora 24 isn't quite as backward-compatible as I thought, and built a Clipper module that won't run in CentOS 7. Could you try doing the following for me, please?

cd ~/.local/share/ChimeraX
rm -fr 0.8
cd ~/.cache/ChimeraX
rm -fr 0.8

... and then reinstall ISOLDE from the Tool Shed?

[Tristan Croll]

I've added instructions on how to work around the Unicode bug at ​https://isolde.cimr.cam.ac.uk/faq/#installation. Best that can be done for now, I think?

[d.houldershaw@…]

Hi,
   Many thanks, this fix plus others for chimerax 0.8 and Isolde have 
solved the problem.
   Many Thanks for such a quick response,
     Cheers, Dave H.

On 1/24/19 5:25 PM, ChimeraX wrote:

[tic20@…]

Wonderful! Please let me know (off-list, at tic20@cam.ac.uk) how you get 
on.

On 2019-01-25 11:16, ChimeraX wrote: