Opened 7 years ago

Closed 7 years ago

#1685 closed defect (not a bug)

Core requirement mismatch

Reported by: pgleiman@… Owned by: Conrad
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-4.15.0-43-generic-x86_64-with-debian-stretch-sid
ChimeraX Version: 0.9 (2019-01-15)
Description
Started ChimeraX. Got this error message:
NOTE: Traceback (most recent call last):  
  File "/usr/local/lbbs/chimerax/current/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 338, in __init__  
    self.init_available_from_cache(logger)  
  File "/usr/local/lbbs/chimerax/current/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 449, in
init_available_from_cache  
    abc.load_from_cache()  
  File "/usr/local/lbbs/chimerax/current/lib/python3.6/site-
packages/chimerax/core/toolshed/available.py", line 64, in load_from_cache  
    b = _build_bundle(d)  
  File "/usr/local/lbbs/chimerax/current/lib/python3.6/site-
packages/chimerax/core/toolshed/available.py", line 249, in _build_bundle  
    keywords = _extract_extra_keywords(keywords)  
  File "/usr/local/lbbs/chimerax/current/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'  
  

BUG: Error preloading available bundles:  
AttributeError: 'list' object has no attribute 'split'  
  
File "/usr/local/lbbs/chimerax/current/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(',')]  
  
 _See log for complete Python traceback._  


Log:
Startup Messages  
---  
note | Traceback (most recent call last):  
  
File "/usr/local/lbbs/chimerax/current/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 338, in __init__  
  
self.init_available_from_cache(logger)  
  
File "/usr/local/lbbs/chimerax/current/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 449, in
init_available_from_cache  
  
abc.load_from_cache()  
  
File "/usr/local/lbbs/chimerax/current/lib/python3.6/site-
packages/chimerax/core/toolshed/available.py", line 64, in load_from_cache  
  
b = _build_bundle(d)  
  
File "/usr/local/lbbs/chimerax/current/lib/python3.6/site-
packages/chimerax/core/toolshed/available.py", line 249, in _build_bundle  
  
keywords = _extract_extra_keywords(keywords)  
  
File "/usr/local/lbbs/chimerax/current/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: 0.9 (2019-01-15)  
How to cite UCSF ChimeraX  

> help help:credits.html

Downloading bundle ChimeraX_Clipper-0.3.1-cp36-cp36m-linux_x86_64.whl  
Traceback (most recent call last):  
File "/usr/local/lbbs/chimerax/current/lib/python3.6/site-
packages/chimerax/ui/widgets/htmlview.py", line 384, in download_finished  
session=self.session)  
File "/usr/local/lbbs/chimerax/current/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 605, in install_bundle  
results = self._pip_install(bundle, per_user=per_user, reinstall=reinstall)  
File "/usr/local/lbbs/chimerax/current/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 901, in _pip_install  
results = self._run_pip(command)  
File "/usr/local/lbbs/chimerax/current/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 928, in _run_pip  
raise RuntimeError(s)  
RuntimeError: ERROR:  
Traceback (most recent call last):  
File "/usr/local/lbbs/chimerax/current/lib/python3.6/site-  
packages/chimerax/core/toolshed/__init__.py", line 338, in __init__  
self.init_available_from_cache(logger)  
File "/usr/local/lbbs/chimerax/current/lib/python3.6/site-  
packages/chimerax/core/toolshed/__init__.py", line 449, in  
init_available_from_cache  
abc.load_from_cache()  
File "/usr/local/lbbs/chimerax/current/lib/python3.6/site-  
packages/chimerax/core/toolshed/available.py", line 64, in load_from_cache  
b = _build_bundle(d)  
File "/usr/local/lbbs/chimerax/current/lib/python3.6/site-  
packages/chimerax/core/toolshed/available.py", line 249, in _build_bundle  
keywords = _extract_extra_keywords(keywords)  
File "/usr/local/lbbs/chimerax/current/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
/home/leiman/Downloads/ChimeraX_Clipper-0.3.1-cp36-cp36m-linux_x86_64.whl  
Collecting ChimeraX-Core==0.8 (from ChimeraX-Clipper==0.3.1)  
Could not find a version that satisfies the requirement ChimeraX-Core==0.8
(from ChimeraX-Clipper==0.3.1) (from versions: )  
No matching distribution found for ChimeraX-Core==0.8 (from ChimeraX-
Clipper==0.3.1)  
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/local/lbbs/chimerax/current/lib/python3.6/site-  
packages/chimerax/core/toolshed/__init__.py", line 338, in __init__  
self.init_available_from_cache(logger)  
File "/usr/local/lbbs/chimerax/current/lib/python3.6/site-  
packages/chimerax/core/toolshed/__init__.py", line 449, in  
init_available_from_cache  
abc.load_from_cache()  
File "/usr/local/lbbs/chimerax/current/lib/python3.6/site-  
packages/chimerax/core/toolshed/available.py", line 64, in load_from_cache  
b = _build_bundle(d)  
File "/usr/local/lbbs/chimerax/current/lib/python3.6/site-  
packages/chimerax/core/toolshed/available.py", line 249, in _build_bundle  
keywords = _extract_extra_keywords(keywords)  
File "/usr/local/lbbs/chimerax/current/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
/home/leiman/Downloads/ChimeraX_Clipper-0.3.1-cp36-cp36m-linux_x86_64.whl  
Collecting ChimeraX-Core==0.8 (from ChimeraX-Clipper==0.3.1)  
Could not find a version that satisfies the requirement ChimeraX-Core==0.8
(from ChimeraX-Clipper==0.3.1) (from versions: )  
No matching distribution found for ChimeraX-Core==0.8 (from ChimeraX-
Clipper==0.3.1)  
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/local/lbbs/chimerax/current/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 928, in _run_pip  
raise RuntimeError(s)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 410.79
OpenGL renderer: GeForce GTX 780/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Change History (3)

comment:1 by Tristan Croll, 7 years ago

Cc: Tristan Croll added
Platform: → all
Project: → ChimeraX

The Clipper and ISOLDE plugins currently require the ChimeraX 0.8 release build, not the 0.9 daily builds.

comment:2 by Eric Pettersen, 7 years ago

Component: Unassigned → Tool Shed
Owner: set to Conrad
Status: new → assigned

comment:3 by Eric Pettersen, 7 years ago

Resolution: → not a bug
Status: assigned → closed
Summary: ChimeraX bug report submission → Core requirement mismatch
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