Error messages when executing command file with chimerax --exit
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
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Hi Guillame In general, when you have problems like this, instead of sending e-mail here, it is better to use ChimeraX menu: Help... Report a Bug.
That bug-reporting form automatically includes the log (with any error messages) and other information like what version and type of computer you are using, and allows attaching a file. You should also include a short description of how to reproduce the problem, and your e-mail address on the bug report. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 5, 2021, at 2:01 AM, Guillaume Gaullier via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
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
När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy <7otq_figure-2-supplement-2.cxc><chimerax-errors.txt>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Elaine,
Sorry about that. I thought it would only work when prompted upon the bug triggering (which, in this case, was not triggering in an interactive session, only from the shell), and I didn’t realize one can use the bug report tool in a session that didn’t error out. I will submit the bug report this way by the end of the week (unless one of you already opened a ticket for it? let me know).
Thank you for the reminder,
Guillaume
On 5 Oct 2021, at 17:32, Elaine Meng <meng@cgl.ucsf.edumailto:meng@cgl.ucsf.edu> wrote:
Hi Guillame In general, when you have problems like this, instead of sending e-mail here, it is better to use ChimeraX menu: Help... Report a Bug.
That bug-reporting form automatically includes the log (with any error messages) and other information like what version and type of computer you are using, and allows attaching a file. You should also include a short description of how to reproduce the problem, and your e-mail address on the bug report. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 5, 2021, at 2:01 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> wrote:
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
När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy <7otq_figure-2-supplement-2.cxc><chimerax-errors.txt>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edumailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users
Hi Guillaume,
I made a ChimeraX bug report for you
https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5344 https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5344
I do not get the error you get with ChimeraX 1.2.5 and macOS 11.6 but I can see from the Python traceback what caused it.
Tom
On Oct 5, 2021, at 9:09 AM, Guillaume Gaullier via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Elaine,
Sorry about that. I thought it would only work when prompted upon the bug triggering (which, in this case, was not triggering in an interactive session, only from the shell), and I didn’t realize one can use the bug report tool in a session that didn’t error out. I will submit the bug report this way by the end of the week (unless one of you already opened a ticket for it? let me know).
Thank you for the reminder,
Guillaume
On 5 Oct 2021, at 17:32, Elaine Meng <meng@cgl.ucsf.edu mailto:meng@cgl.ucsf.edu> wrote:
Hi Guillame In general, when you have problems like this, instead of sending e-mail here, it is better to use ChimeraX menu: Help... Report a Bug.
That bug-reporting form automatically includes the log (with any error messages) and other information like what version and type of computer you are using, and allows attaching a file. You should also include a short description of how to reproduce the problem, and your e-mail address on the bug report. Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 5, 2021, at 2:01 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:
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
När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ http://www.uu.se/om-uu/dataskydd-personuppgifter/
E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy http://www.uu.se/en/about-uu/data-protection-policy <7otq_figure-2-supplement-2.cxc><chimerax-errors.txt>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (3)
-
Elaine Meng -
Guillaume Gaullier -
Tom Goddard