id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 5344 Logger: RuntimeError: wrapped C/C++ object of type QTimer has been deleted guillaume.gaullier@… Tom Goddard " Begin forwarded message: From: Guillaume Gaullier via 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 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 }}} " defect assigned moderate Logging all ChimeraX