Created attachment 389175 [details] gdb backtrace from an octave segfault Description of problem: After starting qtoctave various windows open an the followin output shows up: warning: mark_as_command is obsolete and will be removed from a future version of Octave >>>panic: Segmentation fault -- stopping myself... attempting to save variables to `octave-core'... save to `octave-core' complete After the above octave is restarted and this time it pretends that nothing really happened. A backtrace with octave-debug loaded from a core generated by the above is attached. Version-Release number of selected component (if applicable): octave-3.2.3-1.fc11.x86_64 qtoctave-0.8.2-2.fc11.x86_64 How reproducible: every time when qtoctave starts Expected results: Not a segfault - regardless of any weird things qtoctave is possibly doing. Additional info: I did not try qtoctave before so I cannot tell if this is something new or not.
Created attachment 389177 [details] octave-core file produced in this bomb
With the following packages on F-12: # rpm -q octave qtoctave octave-3.2.3-4.fc12.x86_64 qtoctave-0.8.2-2.fc12.x86_64 I get "warning: mark_as_command is obsolete and will be removed from a future version of Octave" in the window but no segfault. I will try to reproduce on F-11. It's possible that this is an issue with the older version of octave on F-11, there were some changes in the package that fixed certain issues on F-12. Can you reproduce this with the command-line version of octave only (i.e. without using qtoctave)?
(In reply to comment #2) > Can you reproduce this with the command-line > version of octave only (i.e. without using qtoctave)? No, I cannot. OTOH qtoctave is not running just "octave". As a backtrace makes clear this comes from: Core was generated by `octave --eval PS1('octave:\#>');PS2('octave:\#+>');addpath('/usr/share/qtoctave'. It looks like that an octave startup command was shortened here (to a width of a buffer or something like that) and it appears that this "eval" is what really is causing problems. Trying on a command line just octave --eval "PS1('octave:\#>');PS2('octave:\#+>');" simply prints an introductory information, "warning: mark_as_command is obsolete ..." and exits. Like I already mentioned - after this segfault qtoctave restarts octave and continues. No idea what startup is used on that retry. Quite possibly the real error is burried in File "/usr/lib64/python2.6/encodings/utf_8.py", line 16, in decode return codecs.utf_8_decode(input, errors, True) UnicodeDecodeError: 'utf8' codec can't decode bytes in position 0-1: invalid data , idx=std::list = {...}, nargout=-1581871475) at ov.cc:1061 which you can find in a backtrace. Maybe data are really invalid or maybe 'nargout' value is shot on 64 bits? It does not look healthy but this may be an illusion.
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I've experienced this bug a number of times under Fedora 12. It seems related to the variables saved on closure of QtOctave. I attempted to load the variables saved by QtOctave using vanilla console Octave and encountered the same segmentation fault.This may be why the new save of variables to octave core on fault allows QtOctave to recover.This fault does not occur every time QtOctave starts up under Fedora 12, though the size of the variables files seems to affect the likelihood of experiencing the fault.
(In reply to comment #5) > I've experienced this bug a number of times under Fedora 12. In that case beside a comment you should bump a "Version" or this will be automatically closed pretty soon as bug in an unmaintained release.
*** Bug 590268 has been marked as a duplicate of this bug. ***
This might be related to this: If you have both octave and octave-forge installed than doing: octave:1> save A octave:2> quit ... octave:> load A would crash octave with segfault. Removing package ann (with extreme prejudice) seams to solve this problem.
*** Bug 594916 has been marked as a duplicate of this bug. ***
After upgrading to Fedora Core 13, qtoctave is still crashing on startup with the mark_as_command warning and the segmentation fault restart. From the command-line, the same segmentation fault is obtained as Dmitri commented by simply using load on a saved variable (no need to quit after saving). octave:1> save A octave:2> load A gives the segfault crash. Dmitri's workaround worked for me. uninstalling octave-forge stopped both the qtoctave and the command-line segmentation faults, even the mark_as_command warning. Hope this will help to figure out the bug source.
*** Bug 593484 has been marked as a duplicate of this bug. ***
Me again... ;-) I'm afraid that I missread last lines in Comment 8. To avoid the segfault crash, there is no need to uninstall the whole octave-forge, just the ANN package.
I can duplicate the bug as described in comment #10. I suspect the ANN package may have been mis-compiled, there were some issues with it compiling a while back, I'll have a look into it.
*** Bug 603476 has been marked as a duplicate of this bug. ***
I think the short-term fix to this is to disable the "ann" package in octave-forge. I will also report to upstream. I already backported a fix from upstream SVN to fix the ann build and there is nothing more recent than that fix in upstream ann. I don't know how often this package is used in practice and how big a loss this would be. I think the issue is something to do with old SWIG wrappers being used. Hopefully upstream will know more.
Reported on upstream mailing list: http://thread.gmane.org/gmane.comp.gnu.octave.devel/4215
(In reply to comment #16) > Reported on upstream mailing list: > > http://thread.gmane.org/gmane.comp.gnu.octave.devel/4215 OK, based on discussions on upstream list, the short-term workaround is to disable the autoloading of 'ann' by default. I have adapted some patches from Debian to do this, see: http://article.gmane.org/gmane.comp.gnu.octave.devel/4221 and I am making new builds now that I'll be pushing to updates-testing in active branches ASAP.
octave-forge-20090607-16.fc13 has been submitted as an update for Fedora 13. http://admin.fedoraproject.org/updates/octave-forge-20090607-16.fc13
octave-forge-20090607-16.fc12 has been submitted as an update for Fedora 12. http://admin.fedoraproject.org/updates/octave-forge-20090607-16.fc12
octave-forge-20090607-16.fc11 has been submitted as an update for Fedora 11. http://admin.fedoraproject.org/updates/octave-forge-20090607-16.fc11
octave-forge-20090607-16.fc11 has been pushed to the Fedora 11 testing repository. If problems still persist, please make note of it in this bug report. If you want to test the update, you can install it with su -c 'yum --enablerepo=updates-testing update octave-forge'. You can provide feedback for this update here: http://admin.fedoraproject.org/updates/octave-forge-20090607-16.fc11
octave-forge-20090607-16.fc12 has been pushed to the Fedora 12 testing repository. If problems still persist, please make note of it in this bug report. If you want to test the update, you can install it with su -c 'yum --enablerepo=updates-testing update octave-forge'. You can provide feedback for this update here: http://admin.fedoraproject.org/updates/octave-forge-20090607-16.fc12
octave-forge-20090607-16.fc13 has been pushed to the Fedora 13 testing repository. If problems still persist, please make note of it in this bug report. If you want to test the update, you can install it with su -c 'yum --enablerepo=updates-testing update octave-forge'. You can provide feedback for this update here: http://admin.fedoraproject.org/updates/octave-forge-20090607-16.fc13
(In reply to comment #23) > octave-forge-20090607-16.fc13 has been pushed to the Fedora 13 testing > repository. If problems still persist, please make note of it in this bug > report. > If you want to test the update, you can install it with > su -c 'yum --enablerepo=updates-testing update octave-forge'. You can provide > feedback for this update here: > http://admin.fedoraproject.org/updates/octave-forge-20090607-16.fc13 After installing the update, the save/load sequence does NOT give a segfault. However, when trying to exit from octave (both command-line and qt-octave) a new crash occurs. The final line after the crash is: panic: attempted clean up apparently failed -- aborting... Aborted (core dumped) This happens to me after updating octave without uninstalling the old version, and also after a clean install.
I can reproduce this problem. It appears to be related to java-1.2.6 package.
(In reply to comment #25) > I can reproduce this problem. > It appears to be related to java-1.2.6 package. Yep, me too. Yet another package we may need to disable from autoloading... :( I wish upstream would fix their octave subpackages properly.
(In reply to comment #25) > I can reproduce this problem. > It appears to be related to java-1.2.6 package. It's odd that this bug wasn't exposed through crashes on exit in the previous version of octave-forge, any ideas why that might have been the case Dmitri?
I have no idea what has changed. The latest upstream package is java-1.2.7. If I un-install octave-forge completele and install only java-1.2.7 from octave with "pkg install java-1.2.7.tar.gz" I get what appears to be the same crash.
*** Bug 609015 has been marked as a duplicate of this bug. ***
Package: octave-6:3.2.4-2.fc13 Architecture: i686 OS Release: Fedora release 13 (Goddard) How to reproduce ----- Start octave and quit it immediately. All fine with octave-forge 20090607-15.fc13 but with octave-forge 20090607-16.fc13 from updates-testing, quiting causes a crash. Comment ----- See above
java package is broken. I think it was not compiled in -15 so it did not do anything. In -16 it is compiled and as a result causes this problem. Dmitri.
*** Bug 603535 has been marked as a duplicate of this bug. ***
*** Bug 568236 has been marked as a duplicate of this bug. ***
OK, as a workaround, I'm disabling autoloading of the 'java' octave package, similar to the 'ann' package. Builds are underway.
octave-forge-20090607-17.fc13 has been submitted as an update for Fedora 13. http://admin.fedoraproject.org/updates/octave-forge-20090607-17.fc13
octave-forge-20090607-17.fc12 has been submitted as an update for Fedora 12. http://admin.fedoraproject.org/updates/octave-forge-20090607-17.fc12
octave-forge-20090607-17.fc13 has been pushed to the Fedora 13 testing repository. If problems still persist, please make note of it in this bug report. If you want to test the update, you can install it with su -c 'yum --enablerepo=updates-testing update octave-forge'. You can provide feedback for this update here: http://admin.fedoraproject.org/updates/octave-forge-20090607-17.fc13
octave-forge-20090607-17.fc12 has been pushed to the Fedora 12 testing repository. If problems still persist, please make note of it in this bug report. If you want to test the update, you can install it with su -c 'yum --enablerepo=updates-testing update octave-forge'. You can provide feedback for this update here: http://admin.fedoraproject.org/updates/octave-forge-20090607-17.fc12
Package: octave-6:3.2.4-2.fc13 Architecture: i686 OS Release: Fedora release 13 (Goddard) Comment ----- invoked QtOctave
Package: octave-6:3.2.4-2.fc13 Architecture: i686 OS Release: Fedora release 13 (Goddard) How to reproduce ----- 1.Start Qt Octave form gnome menu 2. 3.
(In reply to comment #40) > Package: octave-6:3.2.4-2.fc13 > Architecture: i686 > OS Release: Fedora release 13 (Goddard) > > > How to reproduce > ----- > 1.Start Qt Octave form gnome menu > 2. > 3. Durai, please follow the instructions in comment #37 and test the update in updates-testing. If it works for you, you can provide a +1 karma point on: http://admin.fedoraproject.org/updates/octave-forge-20090607-17.fc13 Thanks.
*** Bug 613368 has been marked as a duplicate of this bug. ***
(In reply to comment #41) > (In reply to comment #40) > > Package: octave-6:3.2.4-2.fc13 > > Architecture: i686 > > OS Release: Fedora release 13 (Goddard) > > > > > > How to reproduce > > ----- > > 1.Start Qt Octave form gnome menu > > 2. > > 3. > > Durai, please follow the instructions in comment #37 and test the update in > updates-testing. If it works for you, you can provide a +1 karma point on: > > http://admin.fedoraproject.org/updates/octave-forge-20090607-17.fc13 > > Thanks. It works. Thanks.
(In reply to comment #43) > (In reply to comment #41) > > (In reply to comment #40) > > > Package: octave-6:3.2.4-2.fc13 > > > Architecture: i686 > > > OS Release: Fedora release 13 (Goddard) > > > > > > > > > How to reproduce > > > ----- > > > 1.Start Qt Octave form gnome menu > > > 2. > > > 3. > > > > Durai, please follow the instructions in comment #37 and test the update in > > updates-testing. If it works for you, you can provide a +1 karma point on: > > > > http://admin.fedoraproject.org/updates/octave-forge-20090607-17.fc13 > > > > Thanks. > > It works. Thanks. Sorry. I don't know how to add karma. please guide me.
(In reply to comment #44) > (In reply to comment #43) > > It works. Thanks. > > Sorry. I don't know how to add karma. please guide me. Just visit: http://admin.fedoraproject.org/updates/octave-forge-20090607-17.fc13 and click "add comment" and check "Works for me", you need to provide an e-mail address and there is a captcha to avoid spam. karma is a nickname for points accrued to an update.
Note that the karma is only actually counted in the total karma value if it comes from a user registered in the Fedora Account System (FAS) and logged in with his/her FAS account. Anonymous karma is shown in the comments, but not counted towards the total.
(In reply to comment #45) > (In reply to comment #44) > > (In reply to comment #43) > > > > It works. Thanks. > > > > Sorry. I don't know how to add karma. please guide me. > > Just visit: > > http://admin.fedoraproject.org/updates/octave-forge-20090607-17.fc13 > > and click "add comment" and check "Works for me", you need to provide an e-mail > address and there is a captcha to avoid spam. karma is a nickname for points > accrued to an update. Done.
octave-forge-20090607-17.fc12 has been pushed to the Fedora 12 stable repository. If problems still persist, please make note of it in this bug report.
octave-forge-20090607-17.fc13 has been pushed to the Fedora 13 stable repository. If problems still persist, please make note of it in this bug report.
*** Bug 615604 has been marked as a duplicate of this bug. ***