Octave segfaults on 'clear all'

Bug #325118 reported by Matthew Wardrop
4
Affects Status Importance Assigned to Milestone
Octave
Invalid
Undecided
Unassigned
octave2.9 (Fedora)
Fix Released
Medium
octave2.9 (Ubuntu)
Invalid
Undecided
Unassigned

Bug Description

Binary package hint: octave

Typing 'clear all' in the interactive interpreter in octave, causes it to segfault.

I obviously think that crashing on clearing all is a little extreme. I also have octplot loaded by default, and I do not paginate output. Otherwise, just stock standard.

In the latest Ubuntu Jaunty version (as of Feb 4 09), I have these octave packages installed:
ii octave-ad 1.0.2-1 automatic forward differentiation in Octave
ii octave-audio 1.1.1-2 functions to work with audio files in Octave
ii octave-bioinfo 0.1.0-1 bioinformatic functions for Octave
ii octave-combinatorics 1.0.6-1 combinatorics function for Octave
ii octave-communications 1.0.6-1 communications package from octave-forge
ii octave-control 1.0.6-1 control functions for Octave from Octave-For
ii octave-data-smoothing 1.0.0-1 functions to do data smoothing on noisy data
ii octave-econometrics 1:1.0.6-3 econometrics functions for Octave
ii octave-epstk 2.2-11ubuntu1 GNU Octave encapsulated postscript toolkit
ii octave-financial 0.2.2-1 financial manipulation and plotting function
ii octave-fixed 0.7.6-2 fixed point computation for Octave
ii octave-ftp 1.0-1 Octave binding for ftplib, and MATLAB compat
ii octave-general 1.0.6-1 provide extra general functions for Octave
ii octave-graceplot 1.0.5-2 Plotting function of GNU Octave with Grace
ii octave-gsl 1.0.6-2 GSL binding for Octave
ii octave-ident 1.0.5-1 system identification functions for Octave
ii octave-image 1.0.6-3 image manipulation for Octave
ii octave-informationtheory 0.1.5-1 information theory functions for Octave
ii octave-io 1.0.6-1 input/output data functions for Octave
ii octave-irsa 1.0.5-1 irregular sampling analysis functions for Oc
ii octave-linear-algebra 1.0.5-1 additional linear-algebra functions for Octa
ii octave-miscellaneous 1.0.6-3 miscellaneous tools for Octave
ii octave-missing-functions 1.0.0-1 finds functions that are in Matlab but not i
ii octave-nan 1.0.6-1 handles data with and without missing values
ii octave-nnet 0.1.7-2 feed forward multi-layer neural network func
ii octave-octcdf 1.0.9-2 NetCDF data files interface for Octave
ii octave-octgpr 1.1.3-1 functions to smooth and interpolate scattere
ii octave-odebvp 1.0.4-1 linear ordinary differential equations packa
ii octave-odepkg 0.6.0-1 solve differential equations and initial val
ii octave-optim 1.0.3-3 unconstrained non-linear optimization toolki
ii octave-optiminterp 0.3.1-1 optimal interpolation package for Octave
ii octave-outliers 0.13.7-2 outliers detection function for Octave
ii octave-parallel 1.0.6-1 parallel execution of Octave in clusters of
ii octave-pfstools 1.6.4-2build2 octave bindings for pfstools
ii octave-physicalconstants 0.1.5-1 provide physical constants values in Octave
ii octave-plot 1.0.5-2 additional plotting tools for Octave
ii octave-plplot 5.9.0-8ubuntu1 Octave support for PLplot, a plotting librar
ii octave-signal 1.0.7-1 signal processing functions for Octave
ii octave-sockets 1.0.4-3 communication through Internet sokects in Oc
ii octave-sp 1:2003-9 Semidefinite Programming functions for GNU O
ii octave-specfun 1.0.6-1 special mathematical functions for Octave
ii octave-splines 1.0.5-1 cubic spline functions for Octave
ii octave-statistics 1.0.6-1 additional statistical functions for Octave
ii octave-strings 1.0.5-1 additional string manipulation functions for
ii octave-struct 1.0.5-1 additional structure manipulation functions
ii octave-symbolic 1.0.6-1 symbolic package for Octave
ii octave-time 1.0.7-1 date format manipulation function for Octave
ii octave-tsa 3.10.6-2 time series analysis in Octave
ii octave-vrml 1.0.6-3 VRML functions for Octave
ii octave-zenity 0.5.5-1 simple graphical user interfaces using zenit
ii octave3.0 1:3.0.1-6ubuntu1 GNU Octave language for numerical computatio
ii octave3.0-info 1:3.0.1-6ubuntu1 GNU Info documentation on the GNU Octave lan

Revision history for this message
In , Thomas (thomas-redhat-bugs) wrote :

Description of problem:
octave segfaults while executing "clear all".
It does not matter if any variables were defined.

Version-Release number of selected component (if applicable):
octave-3.0.1-1.fc9.x86_64
octave-forge-20080429-1.fc9.x86_64
atlas-3.6.0-15.fc9.x86_64

How reproducible:
always

Steps to Reproduce:
just execute octave --eval "clear all"

Actual results:
segmentation fault

Expected results:
no segmentation fault ;)

Additional info:
(gdb) run -q --eval "clear all"
Starting program: /usr/bin/octave -q --eval "clear all"
warning: "/usr/lib/debug/usr/lib64/atlas/liblapack.so.3.0.debug": The separate
debug info file has no debug info
warning: "/usr/lib/debug/usr/lib64/atlas/libblas.so.3.0.debug": The separate
debug info file has no debug info
[Thread debugging using libthread_db enabled]
[New Thread 0x7f8ddaa76700 (LWP 5636)]

Program received signal SIGSEGV, Segmentation fault.
0x00000032d95b8496 in symbol_record::clear (this=<value optimized out>) at ov.h:392
392 { return rep->is_defined (); }
Current language: auto; currently c++

Revision history for this message
In , Thomas (thomas-redhat-bugs) wrote :

The Windows version also segfaults:

C:\Programme\Octave>bin\octave -q --eval "clear -all"
 - Use `pkg list' to see a list of installed packages.
 - SciTE editor installed. Use `edit' to start the editor.
 - MSYS shell available (C:\Programme\Octave\msys).
 - Graphics backend: jhandles.

panic: Segmentation violation -- stopping myself...
attempting to save variables to `octave-core'...
save to `octave-core' complete

Revision history for this message
In , Thomas (thomas-redhat-bugs) wrote :

It seems that some SWIG-based packages (ann, ftp) are the cause of this problem,
so this only happens with octave-forge installed.

This is also discussed on octave's mailing list:
http://www.cae.wisc.edu/pipermail/bug-octave/2008-May/006094.html

Revision history for this message
In , Oscar (oscar-redhat-bugs) wrote :

Hi,

I followed the suggested link in #2 and ran:

> pkg rebuild -noauto ftp database ann

at the octave command prompt (octave was run as superuser) and the problem went away.... as far as you don't use ann or the other packages.

Hope this helps (and thanks to Thomas)

Oscar

Revision history for this message
In , Rakesh (rakesh-redhat-bugs) wrote :

Thanks folks for input - will look into it this weekend.

Revision history for this message
In , Rakesh (rakesh-redhat-bugs) wrote :

Can you folks reproduce for 3.0.2 and give me the input ?

Revision history for this message
In , Thomas (thomas-redhat-bugs) wrote :

I just tested the packages in rawhide and it still crashes when the octave-forge packages "ftp" or "ann" are loaded.

$ rpm -q octave octave-forge
octave-3.0.2-1.fc10.x86_64
octave-forge-20080831-2.fc10.x86_64

$ octave -q
octave:1> clear all
octave:2> pkg load ftp
octave:3> clear all
panic: Segmentation fault -- stopping myself...
attempting to save variables to `octave-core'...
save to `octave-core' complete
Segmentation fault

Revision history for this message
In , Rakesh (rakesh-redhat-bugs) wrote :

Thanks for input ... I will get back to it soon.

Revision history for this message
In , Alex (alex-redhat-bugs) wrote :

I can verify that this is still present in 3.0.3 release. Seems to be an upstream issue in combination with some octave-forge packages perhaps?

Revision history for this message
In , Mark (mark-redhat-bugs) wrote :

I confirm that
this bugs still occurs with the combination octave-3.0.3-1.fc10.i386
and octave-forge-20080831-2.fc10.i386.

Luckily the workaround from #3 still works.

Revision history for this message
Octavio (torn-acl) wrote :

Thank you for taking the time to report this bug and helping to make Ubuntu better. This particular bug has already been reported and confirmed in the Octave Bug mailing list:
http://www-old.cae.wisc.edu/pipermail/bug-octave/2009-January.txt

From the mailing list:
"This is a known problem. One workaround is to "clear global" first.
Another workaround is to reinstall octave and during package selection,
do not select ftp, database and ann packages."

It also appears in the Red Hat Bugzilla:
https://bugzilla.redhat.com/show_bug.cgi?id=448467

Changed in octave2.9:
status: New → Confirmed
Octavio (torn-acl)
Changed in octave:
status: New → Confirmed
Changed in octave2.9:
status: Unknown → In Progress
Revision history for this message
In , Rakesh (rakesh-redhat-bugs) wrote :

I did check mailing list and this issue hasn't been been fixed yet. I have asked for status. Waiting for response.

Revision history for this message
In , Rakesh (rakesh-redhat-bugs) wrote :

No response .. this seems to be hanging long!

Revision history for this message
In , Mark (mark-redhat-bugs) wrote :

Still in Fedora 11 with Octave 3.0.5 and
octave-forge-20080831-8.fc11.

Work around still valid.

Revision history for this message
In , Bug (bug-redhat-bugs) wrote :

This message is a reminder that Fedora 9 is nearing its end of life.
Approximately 30 (thirty) days from now Fedora will stop maintaining
and issuing updates for Fedora 9. It is Fedora's policy to close all
bug reports from releases that are no longer maintained. At that time
this bug will be closed as WONTFIX if it remains open with a Fedora
'version' of '9'.

Package Maintainer: If you wish for this bug to remain open because you
plan to fix it in a currently maintained version, simply change the 'version'
to a later Fedora version prior to Fedora 9's end of life.

Bug Reporter: Thank you for reporting this issue and we are sorry that
we may not be able to fix it before Fedora 9 is end of life. If you
would still like to see this bug fixed and are able to reproduce it
against a later version of Fedora please change the 'version' of this
bug to the applicable version. If you are unable to change the version,
please add a comment here and someone will do it for you.

Although we aim to fix as many bugs as possible during every release's
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The process we are following is described here:
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Revision history for this message
In , Mark (mark-redhat-bugs) wrote :

Please update: still present in FC11.

Revision history for this message
In , Alex (alex-redhat-bugs) wrote :

*** Bug 517482 has been marked as a duplicate of this bug. ***

Revision history for this message
In , Alex (alex-redhat-bugs) wrote :

Can dupe in F-11 when octave-forge is installed and it goes away if octave-forge is removed. The underlying reason does seem to be described in comment #6. These are swig-based packages and reports on the upstream mailing lists suggest that they cause problems. Ideally probably should remove these packages from the octave-forge bundle. Will look into this soon.

Revision history for this message
In , Alex (alex-redhat-bugs) wrote :

At least in the case of the "ann" package, I can't reproduce the error with the update in updates-testing (soon to be pushed to F-11 stable):

http://admin.fedoraproject.org/updates/F11/FEDORA-2009-10548

octave:1> clear all
octave:2> pkg load ann
octave:3> clear all
octave:4>

However, the "ftp" package has been temporarily removed as it failed to build upstream against Octave 3.2.x.

Revision history for this message
In , Fedora (fedora-redhat-bugs) wrote :

mathgl-1.9-6.fc11.1, plplot-5.9.5-1.fc11, pfstools-1.7.0-8.fc11, GMT-4.5.0-4.fc11, octave-forge-20090607-15.fc11, octave-3.2.3-1.fc11 has been pushed to the Fedora 11 stable repository. If problems still persist, please make note of it in this bug report.

Changed in octave2.9 (Fedora):
status: In Progress → Fix Released
Revision history for this message
Mike Miller (mtmiller) wrote :

Marking this bug invalid in upstream Octave. As mentioned in comment #1, the crash is a result of certain Octave Forge packages being installed, not a bug in Octave itself.

Changed in octave:
status: Confirmed → Invalid
Revision history for this message
Mike Miller (mtmiller) wrote :

Thank you for reporting this bug to Ubuntu. Ubuntu 9.04 reached EOL on October 23, 2010.
See this document for currently supported Ubuntu releases: https://wiki.ubuntu.com/Releases

I've tried recreating this bug with Ubuntu 13.04 and was unable to, given the information you've provided. Please upgrade to the latest version and re-test. If the bug is still reproducible, increase the verbosity of the steps to recreate it so we can try again.

Do feel free to report any other bugs you may find.

Changed in octave2.9 (Ubuntu):
status: Confirmed → Invalid
Changed in octave2.9 (Fedora):
importance: Unknown → Medium
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