Permission denied installing Clipper

[rinku.jain@…]

The following bug report has been submitted:
Platform:        Darwin-18.2.0-x86_64-i386-64bit
ChimeraX Version: 0.8 (2018-12-17)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 0.8 (2018-12-17)  
How to cite UCSF ChimeraX  
Downloading bundle ChimeraX_ISOLDE-1.0b2-cp36-cp36m-macosx_10_9_x86_64.whl  
Traceback (most recent call last):  
File
"/private/var/folders/mq/23gvl9rx03q6x282wq8c_9cw0000gn/T/AppTranslocation/D16C4160-224E-4198-BC8C-AC1D75BA81C4/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/ui/widgets/htmlview.py", line 386, in download_finished  
session=self.session)  
File
"/private/var/folders/mq/23gvl9rx03q6x282wq8c_9cw0000gn/T/AppTranslocation/D16C4160-224E-4198-BC8C-AC1D75BA81C4/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/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
"/private/var/folders/mq/23gvl9rx03q6x282wq8c_9cw0000gn/T/AppTranslocation/D16C4160-224E-4198-BC8C-AC1D75BA81C4/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 845, in _pip_install  
results = self._run_pip(command)  
File
"/private/var/folders/mq/23gvl9rx03q6x282wq8c_9cw0000gn/T/AppTranslocation/D16C4160-224E-4198-BC8C-AC1D75BA81C4/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 872, in _run_pip  
raise RuntimeError(s)  
RuntimeError: Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing
/Users/rinkujain/Downloads/ChimeraX_ISOLDE-1.0b2-cp36-cp36m-macosx_10_9_x86_64.whl  
Requirement already satisfied, skipping upgrade: ChimeraX-Atomic>=0.7 in
/private/var/folders/mq/23gvl9rx03q6x282wq8c_9cw0000gn/T/AppTranslocation/D16C4160-224E-4198-BC8C-AC1D75BA81C4/d/ChimeraX.app/Contents/lib/python3.6/site-
packages (from ChimeraX-ISOLDE==1.0b2) (1.0)  
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-macosx_10_9_x86_64.whl  
Requirement already satisfied, skipping upgrade: ChimeraX-Core==0.8 in
/private/var/folders/mq/23gvl9rx03q6x282wq8c_9cw0000gn/T/AppTranslocation/D16C4160-224E-4198-BC8C-AC1D75BA81C4/d/ChimeraX.app/Contents/lib/python3.6/site-
packages (from ChimeraX-ISOLDE==1.0b2) (0.8)  
Requirement already satisfied, skipping upgrade: ChimeraX-UI>=1.0 in
/private/var/folders/mq/23gvl9rx03q6x282wq8c_9cw0000gn/T/AppTranslocation/D16C4160-224E-4198-BC8C-AC1D75BA81C4/d/ChimeraX.app/Contents/lib/python3.6/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: [Errno 30] Read-only
file system:
'/private/var/folders/mq/23gvl9rx03q6x282wq8c_9cw0000gn/T/AppTranslocation/D16C4160-224E-4198-BC8C-AC1D75BA81C4/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages'  
  
You are using pip version 18.1, however version 19.0.3 is available.  
You should consider upgrading via the 'pip install --upgrade pip' command.  
  
  
RuntimeError: Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing
/Users/rinkujain/Downloads/ChimeraX_ISOLDE-1.0b2-cp36-cp36m-macosx_10_9_x86_64.whl  
Requirement already satisfied, skipping upgrade: ChimeraX-Atomic>=0.7 in
/private/var/folders/mq/23gvl9rx03q6x282wq8c_9cw0000gn/T/AppTranslocation/D16C4160-224E-4198-BC8C-AC1D75BA81C4/d/ChimeraX.app/Contents/lib/python3.6/site-
packages (from ChimeraX-ISOLDE==1.0b2) (1.0)  
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-macosx_10_9_x86_64.whl  
Requirement already satisfied, skipping upgrade: ChimeraX-Core==0.8 in
/private/var/folders/mq/23gvl9rx03q6x282wq8c_9cw0000gn/T/AppTranslocation/D16C4160-224E-4198-BC8C-AC1D75BA81C4/d/ChimeraX.app/Contents/lib/python3.6/site-
packages (from ChimeraX-ISOLDE==1.0b2) (0.8)  
Requirement already satisfied, skipping upgrade: ChimeraX-UI>=1.0 in
/private/var/folders/mq/23gvl9rx03q6x282wq8c_9cw0000gn/T/AppTranslocation/D16C4160-224E-4198-BC8C-AC1D75BA81C4/d/ChimeraX.app/Contents/lib/python3.6/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: [Errno 30] Read-only
file system:
'/private/var/folders/mq/23gvl9rx03q6x282wq8c_9cw0000gn/T/AppTranslocation/D16C4160-224E-4198-BC8C-AC1D75BA81C4/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages'  
  
You are using pip version 18.1, however version 19.0.3 is available.  
You should consider upgrading via the 'pip install --upgrade pip' command.  
  
  
File
"/private/var/folders/mq/23gvl9rx03q6x282wq8c_9cw0000gn/T/AppTranslocation/D16C4160-224E-4198-BC8C-AC1D75BA81C4/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 872, in _run_pip  
raise RuntimeError(s)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-2.4.10
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

[Conrad Huang]

Are you running ChimeraX from the disk image? If so, trying copying the app to a local folder and run the copy instead. Also, before trying to install ISOLDE, see ​https://isolde.cimr.cam.ac.uk/faq/#installation for a workaround for a known ChimeraX 0.8 issue.

[Greg Couch]

No response.