Opened 6 years ago

Closed 3 years ago

#2798 closed defect (fixed)

Arcane version-conflict reporting

Reported by: john.kelly@… Owned by: Tristan Croll
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-8.1-6.3.9600
ChimeraX Version: 0.9 (2019-06-06)
Description
Trying to load ISOLDE with a map and model in windows ChimeraX0.90

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 0.9 (2019-06-06)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
"W:\\\XX01TRICA\\\04-i003-postproc\\\modelbuilding\\\c1_closedmodel_rsr_notub-
coot-53_noligands.pdb"

Summary of feedback from opening
W:\XX01TRICA\04-i003-postproc\modelbuilding\c1_closedmodel_rsr_notub-
coot-53_noligands.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 301 301 GLY T
13 HIS T 28 1 16  
Start residue of secondary structure not found: HELIX 302 302 LEU T 44 VAL T
51 1 6  
Start residue of secondary structure not found: HELIX 303 303 PRO T 72 ARG T
79 1 8  
Start residue of secondary structure not found: HELIX 304 304 TRP T 103 TYR T
108 1 6  
Start residue of secondary structure not found: HELIX 305 305 GLY T 111 GLU T
127 1 17  
13 messages similar to the above omitted  
  
Chain information for c1_closedmodel_rsr_notub-coot-53_noligands.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
D | No description available  
E | No description available  
G | No description available  
H h | No description available  
N n | No description available  
Q | No description available  
Z | No description available  
a | No description available  
b | No description available  
d | No description available  
e | No description available  
g | No description available  
q | No description available  
z | No description available  
  

> toolshed show ISOLDE

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX09\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 627, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File "C:\Program Files\ChimeraX09\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1435, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
File "C:\Users\jkelly\AppData\Local\UCSF\ChimeraX\0.9\site-
packages\chimerax\isolde\\__init__.py", line 31, in start_tool  
return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=True)  
File "C:\Program Files\ChimeraX09\bin\lib\site-
packages\chimerax\core\tools.py", line 214, in get_singleton  
tinst = tool_class(session, tool_name, **kw)  
File "C:\Users\jkelly\AppData\Local\UCSF\ChimeraX\0.9\site-
packages\chimerax\isolde\tool.py", line 167, in __init__  
from . import isolde  
File "C:\Users\jkelly\AppData\Local\UCSF\ChimeraX\0.9\site-
packages\chimerax\isolde\isolde.py", line 35, in <module>  
from chimerax import clipper  
File "C:\Users\jkelly\AppData\Local\UCSF\ChimeraX\0.9\site-
packages\chimerax\clipper\\__init__.py", line 26, in <module>  
__version__ = _version()  
File "C:\Users\jkelly\AppData\Local\UCSF\ChimeraX\0.9\site-
packages\chimerax\clipper\\__init__.py", line 24, in _version  
return pkg_resources.require('ChimeraX-Clipper')[0].version  
File "C:\Program Files\ChimeraX09\bin\lib\site-
packages\pkg_resources\\__init__.py", line 900, in require  
needed = self.resolve(parse_requirements(requirements))  
File "C:\Program Files\ChimeraX09\bin\lib\site-
packages\pkg_resources\\__init__.py", line 791, in resolve  
raise VersionConflict(dist, req).with_context(dependent_req)  
pkg_resources.ContextualVersionConflict: (ChimeraX-Core 0.9 (c:\program
files\chimerax09\bin\lib\site-packages), Requirement.parse('ChimeraX-
Core==0.92'), {'ChimeraX-Clipper'})  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX09\bin\lib\site-packages\chimerax\ui\gui.py",
line 1137, in <lambda>  
run(ses, "toolshed show %s" % quote_if_necessary(tool_name)))  
File "C:\Program Files\ChimeraX09\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX09\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2632, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX09\bin\lib\site-
packages\chimerax\core\commands\toolshed.py", line 337, in toolshed_show  
bi.start_tool(session, tool_name)  
File "C:\Program Files\ChimeraX09\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 633, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
(ChimeraX-Core 0.9 (c:\program files\chimerax09\bin\lib\site-packages),
Requirement.parse('ChimeraX-Core==0.92'), {'ChimeraX-Clipper'})  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
(ChimeraX-Core 0.9 (c:\program files\chimerax09\bin\lib\site-packages),
Requirement.parse('ChimeraX-Core==0.92'), {'ChimeraX-Clipper'})  
  
File "C:\Program Files\ChimeraX09\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 633, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
  
See log for complete Python traceback.  
  

> style selAtoms stick

Changed 65801 atom styles  

> ~select #1

Nothing selected  

> close

> toolshed show ISOLDE

> open
"W:\\\XX01TRICA\\\04-i003-postproc\\\modelbuilding\\\c1_closedmodel_rsr_notub-
coot-53_noligands.pdb"

Summary of feedback from opening
W:\XX01TRICA\04-i003-postproc\modelbuilding\c1_closedmodel_rsr_notub-
coot-53_noligands.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 301 301 GLY T
13 HIS T 28 1 16  
Start residue of secondary structure not found: HELIX 302 302 LEU T 44 VAL T
51 1 6  
Start residue of secondary structure not found: HELIX 303 303 PRO T 72 ARG T
79 1 8  
Start residue of secondary structure not found: HELIX 304 304 TRP T 103 TYR T
108 1 6  
Start residue of secondary structure not found: HELIX 305 305 GLY T 111 GLU T
127 1 17  
13 messages similar to the above omitted  
  
Chain information for c1_closedmodel_rsr_notub-coot-53_noligands.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
D | No description available  
E | No description available  
G | No description available  
H h | No description available  
N n | No description available  
Q | No description available  
Z | No description available  
a | No description available  
b | No description available  
d | No description available  
e | No description available  
g | No description available  
q | No description available  
z | No description available  
  

> open
W:/XX01TRICA/04-i003-postproc/phenix_workspace/MapBox_33/c2closed_mapbox.ccp4

Opened c2closed_mapbox.ccp4, grid size 169,159,176, pixel 1.06, shown at level
16.6, step 1, values float32  

> show #2 target m

> view #2 clip false

> view #2 clip false

'ISOLDE_ToolUI' object has no attribute 'isolde'  
File "C:\Program Files\ChimeraX09\bin\lib\runpy.py", line 193, in
_run_module_as_main  
"__main__", mod_spec)  
File "C:\Program Files\ChimeraX09\bin\lib\runpy.py", line 85, in _run_code  
exec(code, run_globals)  
File "C:\Program Files\ChimeraX09\bin\lib\site-packages\ChimeraX_main.py",
line 874, in <module>  
exit_code = init(sys.argv)  
File "C:\Program Files\ChimeraX09\bin\lib\site-packages\ChimeraX_main.py",
line 750, in init  
sess.ui.event_loop()  
File "C:\Program Files\ChimeraX09\bin\lib\site-packages\chimerax\ui\gui.py",
line 248, in event_loop  
self.exec_()  
File "C:\Program Files\ChimeraX09\bin\lib\site-packages\chimerax\ui\gui.py",
line 1579, in <lambda>  
dw.closeEvent = lambda e, tw=tool_window, mw=mw: mw.close_request(tw, e)  
File "C:\Program Files\ChimeraX09\bin\lib\site-packages\chimerax\ui\gui.py",
line 537, in close_request  
tool_instance.delete()  
File "C:\Users\jkelly\AppData\Local\UCSF\ChimeraX\0.9\site-
packages\chimerax\isolde\tool.py", line 179, in delete  
traceback.print_stack(file=sys.__stderr__)  

> toolshed show ISOLDE

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX09\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 627, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File "C:\Program Files\ChimeraX09\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1435, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
File "C:\Users\jkelly\AppData\Local\UCSF\ChimeraX\0.9\site-
packages\chimerax\isolde\\__init__.py", line 31, in start_tool  
return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=True)  
File "C:\Program Files\ChimeraX09\bin\lib\site-
packages\chimerax\core\tools.py", line 214, in get_singleton  
tinst = tool_class(session, tool_name, **kw)  
File "C:\Users\jkelly\AppData\Local\UCSF\ChimeraX\0.9\site-
packages\chimerax\isolde\tool.py", line 167, in __init__  
from . import isolde  
File "C:\Users\jkelly\AppData\Local\UCSF\ChimeraX\0.9\site-
packages\chimerax\isolde\isolde.py", line 35, in <module>  
from chimerax import clipper  
File "C:\Users\jkelly\AppData\Local\UCSF\ChimeraX\0.9\site-
packages\chimerax\clipper\\__init__.py", line 26, in <module>  
__version__ = _version()  
File "C:\Users\jkelly\AppData\Local\UCSF\ChimeraX\0.9\site-
packages\chimerax\clipper\\__init__.py", line 24, in _version  
return pkg_resources.require('ChimeraX-Clipper')[0].version  
File "C:\Program Files\ChimeraX09\bin\lib\site-
packages\pkg_resources\\__init__.py", line 900, in require  
needed = self.resolve(parse_requirements(requirements))  
File "C:\Program Files\ChimeraX09\bin\lib\site-
packages\pkg_resources\\__init__.py", line 791, in resolve  
raise VersionConflict(dist, req).with_context(dependent_req)  
pkg_resources.ContextualVersionConflict: (ChimeraX-Core 0.9 (c:\program
files\chimerax09\bin\lib\site-packages), Requirement.parse('ChimeraX-
Core==0.92'), {'ChimeraX-Clipper'})  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX09\bin\lib\site-packages\chimerax\ui\gui.py",
line 1137, in <lambda>  
run(ses, "toolshed show %s" % quote_if_necessary(tool_name)))  
File "C:\Program Files\ChimeraX09\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX09\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2632, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX09\bin\lib\site-
packages\chimerax\core\commands\toolshed.py", line 337, in toolshed_show  
bi.start_tool(session, tool_name)  
File "C:\Program Files\ChimeraX09\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 633, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
(ChimeraX-Core 0.9 (c:\program files\chimerax09\bin\lib\site-packages),
Requirement.parse('ChimeraX-Core==0.92'), {'ChimeraX-Clipper'})  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
(ChimeraX-Core 0.9 (c:\program files\chimerax09\bin\lib\site-packages),
Requirement.parse('ChimeraX-Core==0.92'), {'ChimeraX-Clipper'})  
  
File "C:\Program Files\ChimeraX09\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 633, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.13474 Core Profile Forward-Compatible Context 22.19.162.4
OpenGL renderer: AMD Radeon(TM) R5 240
OpenGL vendor: ATI Technologies Inc.

Change History (3)

comment:1 by Tristan Croll, 6 years ago

Platform: → all
Project: → ChimeraX

I'm afraid that due to a bug in Pip's version handling that support for ISOLDE in ChimeraX 0.9 is a bit broken unless you go the the ToolShed and explicitly choose Clipper 0.9.4 to install. A much better idea would be to update to ChimeraX 0.91 (or the 0.92 daily build) and use that to install the latest ISOLDE. There are a great many bug fixes and improvements in the newest versions of all packages involved.

comment:2 by Eric Pettersen, 6 years ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Status: new → assigned
Summary: ChimeraX bug report submission → Arcane version-conflict reporting

comment:3 by Tristan Croll, 3 years ago

Resolution: → fixed
Status: assigned → closed
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