Opened 7 years ago

Closed 6 years ago

#1671 closed defect (fixed)

Permission denied installing Clipper

Reported by: arnaud.basle@… Owned by: Conrad Huang
Priority: normal Milestone:
Component: Tool Shed Version:
Keywords: Cc: Tristan Croll
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-4.15.0-20-generic-x86_64-with-debian-buster-sid
ChimeraX Version: 0.8 (2018-12-17)
Description
trying to install ISOLDE plugin for all users but get an error

Log:
Startup Messages  
---  
note | Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/__init__.py", line 338, in __init__  
self.init_available_from_cache(logger)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/__init__.py", line 445, in  
init_available_from_cache  
abc.load_from_cache()  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/available.py", line 61, in load_from_cache  
b = _build_bundle(d)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/available.py", line 242, in _build_bundle  
keywords = _extract_extra_keywords(keywords)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/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  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-packages/chimerax/ui/gui.py",
line 706, in _about  
with open(fn) as f:  
FileNotFoundError: [Errno 2] No such file or directory: '/usr/lib/ucsf-
chimerax/lib/python3.6/site-packages/chimerax/ui/about.html'  
  
FileNotFoundError: [Errno 2] No such file or directory: '/usr/lib/ucsf-
chimerax/lib/python3.6/site-packages/chimerax/ui/about.html'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-packages/chimerax/ui/gui.py",
line 706, in _about  
with open(fn) as f:  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-packages/chimerax/ui/gui.py",
line 706, in _about  
with open(fn) as f:  
FileNotFoundError: [Errno 2] No such file or directory: '/usr/lib/ucsf-
chimerax/lib/python3.6/site-packages/chimerax/ui/about.html'  
  
FileNotFoundError: [Errno 2] No such file or directory: '/usr/lib/ucsf-
chimerax/lib/python3.6/site-packages/chimerax/ui/about.html'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-packages/chimerax/ui/gui.py",
line 706, in _about  
with open(fn) as f:  
  
See log for complete Python traceback.  
  
Downloading bundle ChimeraX_ISOLDE-1.0b2-cp36-cp36m-linux_x86_64.whl  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/ui/widgets/htmlview.py", line 386, in download_finished  
session=self.session)  
File "/usr/lib/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 "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 845, in _pip_install  
results = self._run_pip(command)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 872, in _run_pip  
raise RuntimeError(s)  
RuntimeError: ERROR:  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/__init__.py", line 338, in __init__  
self.init_available_from_cache(logger)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/__init__.py", line 445, in  
init_available_from_cache  
abc.load_from_cache()  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/available.py", line 61, in load_from_cache  
b = _build_bundle(d)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/available.py", line 242, in _build_bundle  
keywords = _extract_extra_keywords(keywords)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/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'  
  
  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing ./Downloads/ChimeraX_ISOLDE-1.0b2-cp36-cp36m-linux_x86_64.whl  
Requirement already satisfied, skipping upgrade: ChimeraX-Atomic>=0.7 in
/usr/lib/ucsf-chimerax/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/0.3.1/ChimeraX_Clipper-0.3.1-cp36-cp36m-linux_x86_64.whl  
Requirement already satisfied, skipping upgrade: ChimeraX-Core==0.8 in
/usr/lib/ucsf-chimerax/lib/python3.6/site-packages (from ChimeraX-
ISOLDE==1.0b2) (0.8)  
Requirement already satisfied, skipping upgrade: ChimeraX-UI>=1.0 in
/usr/lib/ucsf-chimerax/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 13] Permission
denied: '/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/ChimeraX_Clipper-0.3.1.dist-info'  
Consider using the `--user` option or check the permissions.  
  
You are using pip version 18.1, however version 19.0.1 is available.  
You should consider upgrading via the 'pip install --upgrade pip' command.  
  
  
RuntimeError: ERROR:  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/__init__.py", line 338, in __init__  
self.init_available_from_cache(logger)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/__init__.py", line 445, in  
init_available_from_cache  
abc.load_from_cache()  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/available.py", line 61, in load_from_cache  
b = _build_bundle(d)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/available.py", line 242, in _build_bundle  
keywords = _extract_extra_keywords(keywords)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/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'  
  
  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing ./Downloads/ChimeraX_ISOLDE-1.0b2-cp36-cp36m-linux_x86_64.whl  
Requirement already satisfied, skipping upgrade: ChimeraX-Atomic>=0.7 in
/usr/lib/ucsf-chimerax/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/0.3.1/ChimeraX_Clipper-0.3.1-cp36-cp36m-linux_x86_64.whl  
Requirement already satisfied, skipping upgrade: ChimeraX-Core==0.8 in
/usr/lib/ucsf-chimerax/lib/python3.6/site-packages (from ChimeraX-
ISOLDE==1.0b2) (0.8)  
Requirement already satisfied, skipping upgrade: ChimeraX-UI>=1.0 in
/usr/lib/ucsf-chimerax/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 13] Permission
denied: '/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/ChimeraX_Clipper-0.3.1.dist-info'  
Consider using the `--user` option or check the permissions.  
  
You are using pip version 18.1, however version 19.0.1 is available.  
You should consider upgrading via the 'pip install --upgrade pip' command.  
  
  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 872, in _run_pip  
raise RuntimeError(s)  
  
See log for complete Python traceback.  
  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 6613, resource id:
11480320, major code: 40 (TranslateCoords), minor code: 0  




OpenGL version: 3.3.0 NVIDIA 340.107
OpenGL renderer: Quadro FX 580/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Change History (3)

comment:1 by Tristan Croll, 7 years ago

Platform: → all
Project: → ChimeraX

To install for all users, you'll need to be running ChimeraX with administrator privileges.

comment:2 by Eric Pettersen, 7 years ago

Cc: Tristan Croll added
Component: Unassigned → Tool Shed
Owner: set to Conrad Huang
Status: new → assigned
Summary: ChimeraX bug report submission → Permission denied installing Clipper

comment:3 by Conrad Huang, 6 years ago

Resolution: → fixed
Status: assigned → closed

Permission errors are now reported as user errors rather than tracebacks.

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