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#5344 closed defect

Logger: RuntimeError: wrapped C/C++ object of type QTimer has been deleted — at Initial Version

Reported by:	guillaume.gaullier@…	Owned by:	Tom Goddard
Priority:	moderate	Milestone:
Component:	Logging	Version:
Keywords:		Cc:	Eric Pettersen
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

Begin forwarded message:

From: Guillaume Gaullier via ChimeraX-users <chimerax-users@…>
Subject: [chimerax-users] Error messages when executing command file with chimerax --exit
Date: October 5, 2021 at 2:01:02 AM PDT
To: ChimeraX Users Help <chimerax-users@…>
Reply-To: Guillaume Gaullier

Hello,

When I run the attached command file from within ChimeraX 1.2.5 on macOS 10.15.7 (open 7otq_figure-2-supplement-2.cxc), it completes without any error. However, when I run it from the shell with 'chimerax --exit 7otq_figure-2-supplement-2.cxc', I get the attached errors in the terminal. In both cases, the figures are generated correctly, so as far as I am concerned it seems I can simply ignore these errors. But I thought you (ChimeraX developers) might need to know that this happens.

This does not happen with other command files (I have been happily making movies without ever seeing these error messages), which makes me think maybe the problem is specific to this particular one?

Cheers,

Guillaume

Error in sys.excepthook:
Traceback (most recent call last):

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/logger.py", line 297, in ehook

self.session.ui.thread_safe(self.report_exception, exc_info=exc_info)

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/ui/gui.py", line 366, in thread_safe

func(*args, kw)

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/logger.py", line 443, in report_exception

self.info(tb_msg, is_html=True)

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/logger.py", line 388, in info

self._log(Log.LEVEL_INFO, msg, add_newline, image, is_html,

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/logger.py", line 498, in _log

if log.log(*args):

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/log/tool.py", line 340, in log

self.show_page_source()

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/log/tool.py", line 344, in show_page_source

self.session.ui.thread_safe(self._show)

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/ui/gui.py", line 366, in thread_safe

func(*args, kw)

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/log/tool.py", line 348, in _show

self.regulating_timer.start(100)

RuntimeError: wrapped C/C++ object of type QTimer has been deleted

Original exception was:
Traceback (most recent call last):

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/ui/gui.py", line 202, in cx_qt_msg_handler

self.session.logger.method_map[log_level](msg_string)

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/logger.py", line 465, in warning

self._log(Log.LEVEL_WARNING, msg, add_newline, image, is_html,

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/logger.py", line 498, in _log

if log.log(*args):

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/log/tool.py", line 340, in log

self.show_page_source()

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/log/tool.py", line 344, in show_page_source

self.session.ui.thread_safe(self._show)

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/ui/gui.py", line 366, in thread_safe

func(*args, kw)

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/log/tool.py", line 348, in _show

self.regulating_timer.start(100)

RuntimeError: wrapped C/C++ object of type QTimer has been deleted
Error in sys.excepthook:
Traceback (most recent call last):

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/logger.py", line 297, in ehook

self.session.ui.thread_safe(self.report_exception, exc_info=exc_info)

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/ui/gui.py", line 366, in thread_safe

func(*args, kw)

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/logger.py", line 443, in report_exception

self.info(tb_msg, is_html=True)

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/logger.py", line 388, in info

self._log(Log.LEVEL_INFO, msg, add_newline, image, is_html,

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/logger.py", line 498, in _log

if log.log(*args):

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/log/tool.py", line 340, in log

self.show_page_source()

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/log/tool.py", line 344, in show_page_source

self.session.ui.thread_safe(self._show)

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/ui/gui.py", line 366, in thread_safe

func(*args, kw)

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/log/tool.py", line 348, in _show

self.regulating_timer.start(100)

RuntimeError: wrapped C/C++ object of type QTimer has been deleted

Original exception was:
Traceback (most recent call last):

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/ui/gui.py", line 202, in cx_qt_msg_handler

self.session.logger.method_map[log_level](msg_string)

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/logger.py", line 465, in warning

self._log(Log.LEVEL_WARNING, msg, add_newline, image, is_html,

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/logger.py", line 498, in _log

if log.log(*args):

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/log/tool.py", line 340, in log

self.show_page_source()

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/log/tool.py", line 344, in show_page_source

self.session.ui.thread_safe(self._show)

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/ui/gui.py", line 366, in thread_safe

func(*args, kw)

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/log/tool.py", line 348, in _show

self.regulating_timer.start(100)

RuntimeError: wrapped C/C++ object of type QTimer has been deleted
Error in sys.excepthook:
Traceback (most recent call last):

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/logger.py", line 297, in ehook

self.session.ui.thread_safe(self.report_exception, exc_info=exc_info)

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/ui/gui.py", line 366, in thread_safe

func(*args, kw)

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/logger.py", line 443, in report_exception

self.info(tb_msg, is_html=True)

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/logger.py", line 388, in info

self._log(Log.LEVEL_INFO, msg, add_newline, image, is_html,

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/logger.py", line 498, in _log

if log.log(*args):

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/log/tool.py", line 340, in log

self.show_page_source()

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/log/tool.py", line 344, in show_page_source

self.session.ui.thread_safe(self._show)

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/ui/gui.py", line 366, in thread_safe

func(*args, kw)

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/log/tool.py", line 348, in _show

self.regulating_timer.start(100)

RuntimeError: wrapped C/C++ object of type QTimer has been deleted

Original exception was:
Traceback (most recent call last):

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/ui/gui.py", line 202, in cx_qt_msg_handler

self.session.logger.method_map[log_level](msg_string)

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/logger.py", line 465, in warning

self._log(Log.LEVEL_WARNING, msg, add_newline, image, is_html,

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/logger.py", line 498, in _log

if log.log(*args):

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/log/tool.py", line 340, in log

self.show_page_source()

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/log/tool.py", line 344, in show_page_source

self.session.ui.thread_safe(self._show)

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/ui/gui.py", line 366, in thread_safe

func(*args, kw)

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/log/tool.py", line 348, in _show

self.regulating_timer.start(100)

RuntimeError: wrapped C/C++ object of type QTimer has been deleted

Change History (1)

by Tom Goddard, 4 years ago

Attachment:	7otq_figure-2-supplement-2.cxc added

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