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Opened 7 years ago
Closed 7 years ago
#1676 closed defect (duplicate)
Library linking failure after ISOLDE install
| Reported by: | 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-4.15.0-36-generic-x86_64-with-debian-buster-sid
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 "/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
Downloading bundle ChimeraX_ISOLDE-1.0b2-cp36-cp36m-linux_x86_64.whl
Successfully installed ChimeraX-Clipper-0.3.1 ChimeraX-ISOLDE-1.0b2
Installed ChimeraX-Clipper (0.3.1)
Installed ChimeraX-ISOLDE (1.0b2)
> toolshed show ISOLDE
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/toolshed/info.py", line 579, in start_tool
ti = api._api_caller.start_tool(api, session, self, tool_info)
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 1188, in start_tool
return cls._get_func(api, "start_tool")(session, ti.name)
File "/home/ubuntu/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/__init__.py", line 31, in start_tool
return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=True)
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/tools.py", line 214, in get_singleton
tinst = tool_class(session, tool_name, **kw)
File "/home/ubuntu/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/tool.py", line 159, in __init__
self.isolde = isolde.Isolde(self)
File "/home/ubuntu/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/isolde.py", line 315, in __init__
self._start_gui(gui)
File "/home/ubuntu/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/isolde.py", line 443, in _start_gui
self._populate_menus_and_update_params()
File "/home/ubuntu/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/isolde.py", line 532, in
_populate_menus_and_update_params
self._update_model_list(None, None, force=True)
File "/home/ubuntu/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/isolde.py", line 919, in _update_model_list
from .restraints import MDFF_Mgr
File "/home/ubuntu/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/restraints/__init__.py", line 11, in <module>
from ..molobject import Restraint_Change_Tracker
File "/home/ubuntu/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/molobject.py", line 42, in <module>
_c_functions = CFunctions(os.path.splitext(libfile)[0])
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/atomic/molc.py", line 23, in __init__
self._c_lib = ctypes_open(library_path)
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/atomic/molc.py", line 261, in ctypes_open
lib = ctypes.PyDLL(lib_path)
File "/usr/lib/ucsf-chimerax/lib/python3.6/ctypes/__init__.py", line 348, in
__init__
self._handle = _dlopen(self._name, mode)
OSError: /home/ubuntu/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/libmolc.so: undefined symbol:
_ZNK10atomstruct7Residue9find_atomERKN6chutil7CStringILi5EILc65ELc116ELc111ELc109ELc32ELc78ELc97ELc109ELc101EEEE
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-packages/chimerax/ui/gui.py",
line 941, in <lambda>
run(ses, "toolshed show %s" % quote_if_necessary(tool_name)))
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/commands/run.py", line 31, in run
results = command.run(text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2587, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/commands/toolshed.py", line 337, in toolshed_show
bi.start_tool(session, tool_name)
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/toolshed/info.py", line 585, 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:
/home/ubuntu/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/libmolc.so: undefined symbol:
_ZNK10atomstruct7Residue9find_atomERKN6chutil7CStringILi5EILc65ELc116ELc111ELc109ELc32ELc78ELc97ELc109ELc101EEEE
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:
/home/ubuntu/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/libmolc.so: undefined symbol:
_ZNK10atomstruct7Residue9find_atomERKN6chutil7CStringILi5EILc65ELc116ELc111ELc109ELc32ELc78ELc97ELc109ELc101EEEE
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/toolshed/info.py", line 585, 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.
> open /home/ubuntu/img-data/SAGA/map/cryosparc_P22_J22__localfilter.mrc
Opened cryosparc_P22_J22__localfilter.mrc, grid size 512,512,512, pixel 1.09,
shown at level -0.000942, step 2, values float32
> open /home/ubuntu/img-
data/SAGA/Phenix/RealSpaceRefine_2/Taf12_432-474_real_space_refined.pdb
Summary of feedback from opening /home/ubuntu/img-
data/SAGA/Phenix/RealSpaceRefine_2/Taf12_432-474_real_space_refined.pdb
---
warnings | Ignored bad PDB record found on line 20
Ignored bad PDB record found on line 21
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 22
BOND : 0.013 0.089 346
Ignored bad PDB record found on line 23
ANGLE : 2.220 9.823 476
Ignored bad PDB record found on line 24
CHIRALITY : 0.093 0.381 57
17 messages similar to the above omitted
Chain information for Taf12_432-474_real_space_refined.pdb #2
---
Chain | Description
| No description available
> select #2
336 atoms, 346 bonds selected
'ISOLDE_ToolUI' object has no attribute 'isolde'
> toolshed show ISOLDE
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/toolshed/info.py", line 579, in start_tool
ti = api._api_caller.start_tool(api, session, self, tool_info)
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 1188, in start_tool
return cls._get_func(api, "start_tool")(session, ti.name)
File "/home/ubuntu/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/__init__.py", line 31, in start_tool
return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=True)
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/tools.py", line 214, in get_singleton
tinst = tool_class(session, tool_name, **kw)
File "/home/ubuntu/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/tool.py", line 159, in __init__
self.isolde = isolde.Isolde(self)
File "/home/ubuntu/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/isolde.py", line 315, in __init__
self._start_gui(gui)
File "/home/ubuntu/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/isolde.py", line 443, in _start_gui
self._populate_menus_and_update_params()
File "/home/ubuntu/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/isolde.py", line 532, in
_populate_menus_and_update_params
self._update_model_list(None, None, force=True)
File "/home/ubuntu/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/isolde.py", line 919, in _update_model_list
from .restraints import MDFF_Mgr
File "/home/ubuntu/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/restraints/__init__.py", line 11, in <module>
from ..molobject import Restraint_Change_Tracker
File "/home/ubuntu/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/molobject.py", line 42, in <module>
_c_functions = CFunctions(os.path.splitext(libfile)[0])
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/atomic/molc.py", line 23, in __init__
self._c_lib = ctypes_open(library_path)
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/atomic/molc.py", line 261, in ctypes_open
lib = ctypes.PyDLL(lib_path)
File "/usr/lib/ucsf-chimerax/lib/python3.6/ctypes/__init__.py", line 348, in
__init__
self._handle = _dlopen(self._name, mode)
OSError: /home/ubuntu/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/libmolc.so: undefined symbol:
_ZNK10atomstruct7Residue9find_atomERKN6chutil7CStringILi5EILc65ELc116ELc111ELc109ELc32ELc78ELc97ELc109ELc101EEEE
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-packages/chimerax/ui/gui.py",
line 941, in <lambda>
run(ses, "toolshed show %s" % quote_if_necessary(tool_name)))
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/commands/run.py", line 31, in run
results = command.run(text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2587, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/commands/toolshed.py", line 337, in toolshed_show
bi.start_tool(session, tool_name)
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/toolshed/info.py", line 585, 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:
/home/ubuntu/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/libmolc.so: undefined symbol:
_ZNK10atomstruct7Residue9find_atomERKN6chutil7CStringILi5EILc65ELc116ELc111ELc109ELc32ELc78ELc97ELc109ELc101EEEE
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:
/home/ubuntu/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/libmolc.so: undefined symbol:
_ZNK10atomstruct7Residue9find_atomERKN6chutil7CStringILi5EILc65ELc116ELc111ELc109ELc32ELc78ELc97ELc109ELc101EEEE
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/toolshed/info.py", line 585, 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: 4.2 (Core Profile) Mesa 18.0.5
OpenGL renderer: Mesa DRI Intel(R) Ivybridge Desktop
OpenGL vendor: Intel Open Source Technology Center
Change History (2)
comment:1 by , 7 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Tool Shed |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Library linking failure after ISOLDE install |
comment:2 by , 7 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Duplicate of #1672