Could not install ISOLDE/Clipper: EnvironmentError

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.17134
ChimeraX Version: 0.8 (2018-12-17)
Description
(Describe the actions that caused this problem to occur here)

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  

> open "D:\SAMSON docking\HMG-reductase.pdb"

Summary of feedback from opening D:\SAMSON docking\HMG-reductase.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Accelrys Discovery Studio PDB file  
  
Ignored bad PDB record found on line 2  
REMARK Created: 2019-07-04T20:22:41Z  
  
Chain information for HMG-reductase.pdb #1  
---  
Chain | Description  
A | No description available  
  
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 872, in _run_pip  
raise RuntimeError(s)  
RuntimeError: ERROR:  
Traceback (most recent call last):  
\xa0\xa0File "C:\Program Files\ChimeraX\bin\lib\site-  
packages\chimerax\core\toolshed\\\\__init__.py", line 338, in __init__  
\xa0\xa0\xa0\xa0self.init_available_from_cache(logger)  
\xa0\xa0File "C:\Program Files\ChimeraX\bin\lib\site-  
packages\chimerax\core\toolshed\\\\__init__.py", line 445, in  
init_available_from_cache  
\xa0\xa0\xa0\xa0abc.load_from_cache()  
\xa0\xa0File "C:\Program Files\ChimeraX\bin\lib\site-  
packages\chimerax\core\toolshed\available.py", line 61, in load_from_cache  
\xa0\xa0\xa0\xa0b = _build_bundle(d)  
\xa0\xa0File "C:\Program Files\ChimeraX\bin\lib\site-  
packages\chimerax\core\toolshed\available.py", line 242, in _build_bundle  
\xa0\xa0\xa0\xa0keywords = _extract_extra_keywords(keywords)  
\xa0\xa0File "C:\Program Files\ChimeraX\bin\lib\site-  
packages\chimerax\core\toolshed\installed.py", line 270, in  
_extract_extra_keywords  
\xa0\xa0\xa0\xa0all_kwds = [k.strip() for k in kwds.split(',')]  
AttributeError: 'list' object has no attribute 'split'  
  
  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing
c:\users\acer\downloads\chimerax_isolde-1.0b2-cp36-cp36m-win_amd64.whl  
Requirement already satisfied, skipping upgrade: ChimeraX-Core==0.8 in
c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.0b2)
(0.8)  
Collecting ChimeraX-Clipper>=0.3 (from ChimeraX-ISOLDE==1.0b2)  
Using cached
https://cxtoolshed.rbvi.ucsf.edu/media/chimeraxclipper/releases/0.3/ChimeraX_Clipper-0.3-cp36-cp36m-win_amd64.whl  
Requirement already satisfied, skipping upgrade: ChimeraX-Atomic>=0.7 in
c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.0b2)
(1.0)  
Requirement already satisfied, skipping upgrade: ChimeraX-UI>=1.0 in
c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-
Atomic>=0.7->ChimeraX-ISOLDE==1.0b2) (1.0)  
Installing collected packages: ChimeraX-Clipper, ChimeraX-ISOLDE  
Could not install packages due to an EnvironmentError: [WinError 5] Acc\xe8s
refus\xe9: 'C:\\\Program Files\\\ChimeraX\\\bin\\\Lib\\\site-
packages\\\chimerax\\\clipper'  
Consider using the `--user` option or check the permissions.  
  
You are using pip version 18.1, however version 19.1.1 is available.  
You should consider upgrading via the 'python -m pip install --upgrade pip'
command.  
  
  
RuntimeError: ERROR:  
Traceback (most recent call last):  
\xa0\xa0File "C:\Program Files\ChimeraX\bin\lib\site-  
packages\chimerax\core\toolshed\\\\__init__.py", line 338, in __init__  
\xa0\xa0\xa0\xa0self.init_available_from_cache(logger)  
\xa0\xa0File "C:\Program Files\ChimeraX\bin\lib\site-  
packages\chimerax\core\toolshed\\\\__init__.py", line 445, in  
init_available_from_cache  
\xa0\xa0\xa0\xa0abc.load_from_cache()  
\xa0\xa0File "C:\Program Files\ChimeraX\bin\lib\site-  
packages\chimerax\core\toolshed\available.py", line 61, in load_from_cache  
\xa0\xa0\xa0\xa0b = _build_bundle(d)  
\xa0\xa0File "C:\Program Files\ChimeraX\bin\lib\site-  
packages\chimerax\core\toolshed\available.py", line 242, in _build_bundle  
\xa0\xa0\xa0\xa0keywords = _extract_extra_keywords(keywords)  
\xa0\xa0File "C:\Program Files\ChimeraX\bin\lib\site-  
packages\chimerax\core\toolshed\installed.py", line 270, in  
_extract_extra_keywords  
\xa0\xa0\xa0\xa0all_kwds = [k.strip() for k in kwds.split(',')]  
AttributeError: 'list' object has no attribute 'split'  
  
  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing
c:\users\acer\downloads\chimerax_isolde-1.0b2-cp36-cp36m-win_amd64.whl  
Requirement already satisfied, skipping upgrade: ChimeraX-Core==0.8 in
c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.0b2)
(0.8)  
Collecting ChimeraX-Clipper>=0.3 (from ChimeraX-ISOLDE==1.0b2)  
Using cached
https://cxtoolshed.rbvi.ucsf.edu/media/chimeraxclipper/releases/0.3/ChimeraX_Clipper-0.3-cp36-cp36m-win_amd64.whl  
Requirement already satisfied, skipping upgrade: ChimeraX-Atomic>=0.7 in
c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.0b2)
(1.0)  
Requirement already satisfied, skipping upgrade: ChimeraX-UI>=1.0 in
c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-
Atomic>=0.7->ChimeraX-ISOLDE==1.0b2) (1.0)  
Installing collected packages: ChimeraX-Clipper, ChimeraX-ISOLDE  
Could not install packages due to an EnvironmentError: [WinError 5] Acc\xe8s
refus\xe9: 'C:\\\Program Files\\\ChimeraX\\\bin\\\Lib\\\site-
packages\\\chimerax\\\clipper'  
Consider using the `--user` option or check the permissions.  
  
You are using pip version 18.1, however version 19.1.1 is available.  
You should consider upgrading via the 'python -m pip install --upgrade pip'
command.  
  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 872, in _run_pip  
raise RuntimeError(s)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 20.19.15.4390
OpenGL renderer: Intel(R) HD Graphics 520
OpenGL vendor: Intel

[Tristan Croll]

Would be great if that one could be caught and converted to a warning saying the user needs to be running as administrator/root to install a bundle for everybody.

[Greg Couch]

Can't install globally anymore.