Opened 16 months ago

Closed 16 months ago

#15581 closed defect (limitation)

Restore new session in old ChimeraX

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Sessions Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-5.4.0-187-generic-x86_64-with-debian-bullseye-sid
ChimeraX Version: 1.0rc202005261745 (2020-05-26 17:45:19 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Errors  
---  
error | Bundle 'ChimeraX-Registration' custom initialization failed  
warning | Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 342, in initialize  
api._api_caller.initialize(api, session, self)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1571, in initialize  
return cls._get_func(api, "initialize")(session, bi)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/registration/__init__.py", line 41, in initialize  
nag(session)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/registration/nag.py", line 28, in nag  
if not check_registration(logger=session.logger):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/registration/nag.py", line 49, in check_registration  
return _check_expiration(param, logger)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/registration/nag.py", line 135, in _check_expiration  
logger.warning("Registration file %r has expired" % reg_file)  
NameError: name 'reg_file' is not defined  
  
UCSF ChimeraX version: 1.0rc202005261745 (2020-05-26)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /home/elin/Documentos/PsaMar/GT54/sequences/Consurf_Outputs_MGAT_ABD_CEFG/MGAT4A_HS_Ser107_consurf_chimerax_session

'/home/elin/Documentos/PsaMar/GT54/sequences/Consurf_Outputs_MGAT_ABD_CEFG/MGAT4A_HS_Ser107_consurf_chimerax_session'
has no suffix  

> open
> /home/elin/Documentos/PsaMar/GT54/sequences/Consurf_Outputs_MGAT_ABD_CEFG/MGAT4A_HS_Ser107_consurf_CBS_chimerax_session.cxs

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/dialog.py", line 150, in _qt_safe  
if data_format is None else " format " +
StringArg.unparse(data_format.nicknames[0])))  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2802, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 101, in cmd_open  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2802, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 152, in provider_open  
name or model_name_from_path(fi.file_name)), provider_kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 383, in collated_open  
return func(*func_args, **func_kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core_formats/__init__.py", line 26, in open  
return cxs_open(session, data, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 938, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 615, in restore  
version = serialize.pickle_deserialize(stream)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/serialize.py", line 57, in pickle_deserialize  
return unpickler.load()  
_pickle.UnpicklingError: invalid load key, '\x04'.  
  
_pickle.UnpicklingError: invalid load key, '\x04'.  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/serialize.py", line 57, in pickle_deserialize  
return unpickler.load()  
  
See log for complete Python traceback.  
  

> open
> /home/elin/Documentos/PsaMar/GT54/sequences/Consurf_Outputs_MGAT_ABD_CEFG/MGAT4A_HS_Ser107_consurf_chimerax_session.cxs

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/dialog.py", line 150, in _qt_safe  
if data_format is None else " format " +
StringArg.unparse(data_format.nicknames[0])))  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2802, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 101, in cmd_open  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2802, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 152, in provider_open  
name or model_name_from_path(fi.file_name)), provider_kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 383, in collated_open  
return func(*func_args, **func_kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core_formats/__init__.py", line 26, in open  
return cxs_open(session, data, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 938, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 615, in restore  
version = serialize.pickle_deserialize(stream)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/serialize.py", line 57, in pickle_deserialize  
return unpickler.load()  
_pickle.UnpicklingError: invalid load key, '\x04'.  
  
_pickle.UnpicklingError: invalid load key, '\x04'.  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/serialize.py", line 57, in pickle_deserialize  
return unpickler.load()  
  
See log for complete Python traceback.  
  

> open
> /home/elin/Documentos/PsaMar/GT54/sequences/Consurf_Outputs_MGAT_ABD_CEFG/MGAT4A_HS_Ser107_consurf_chimerax_session.cxs

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/dialog.py", line 150, in _qt_safe  
if data_format is None else " format " +
StringArg.unparse(data_format.nicknames[0])))  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2802, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 101, in cmd_open  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2802, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 152, in provider_open  
name or model_name_from_path(fi.file_name)), provider_kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 383, in collated_open  
return func(*func_args, **func_kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core_formats/__init__.py", line 26, in open  
return cxs_open(session, data, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 938, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 615, in restore  
version = serialize.pickle_deserialize(stream)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/serialize.py", line 57, in pickle_deserialize  
return unpickler.load()  
_pickle.UnpicklingError: invalid load key, '\x04'.  
  
_pickle.UnpicklingError: invalid load key, '\x04'.  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/serialize.py", line 57, in pickle_deserialize  
return unpickler.load()  
  
See log for complete Python traceback.  
  




OpenGL version: 4.6 (Core Profile) Mesa 21.2.6
OpenGL renderer: Mesa Intel(R) UHD Graphics 620 (KBL GT2)
OpenGL vendor: Intel
Manufacturer: Dell Inc.
Model: XPS 13 9370
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
CPU: 8 Intel(R) Core(TM) i7-8550U CPU @ 1.80GHz
Cache Size: 8192 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           15Gi       5.2Gi       2.9Gi       985Mi       7.3Gi       8.9Gi
	Swap:          31Gi       510Mi        30Gi

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation UHD Graphics 620 [8086:5917] (rev 07)	
	DeviceName:  Onboard IGD	
	Subsystem: Dell UHD Graphics 620 [1028:07e6]
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

Change History (2)

comment:1 by Eric Pettersen, 16 months ago

Component: Unassigned → Sessions
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Restore new session in old ChimeraX

comment:2 by Eric Pettersen, 16 months ago

Resolution: → limitation
Status: accepted → closed
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