[Pkg-octave-devel] Bug#783034: octave-ltfat breaks Octave rcond. Yields segmentation fault

Charlie Hagedorn charlie.hagedorn at gmail.com
Mon Apr 20 23:14:06 UTC 2015


I agree that there's no obvious way for a subcomponent package to affect a
core-compiled function, but I see this effect on all three machines I have
access to today, all running testing ( vanilla testing install, upgraded
crouton install, upgraded Compute Engine instance) . For the machines where
I initially discovered this crashing problem, uninstalling the ltfat
package appears to have resolved the problem with rcond completely.

Here's the octave-related package list from a machine that displays the
problem (minus octave-ltfat) :

$ dpkg -l 'octave*' | grep ^ii
ii  octave                       3.8.2-4      amd64        GNU Octave
language for numerical computations
ii  octave-audio                 1.1.4-5      amd64        functions to
work with audio files in Octave
ii  octave-bim                   1.1.5-1      all          PDE solver using
a finite element/volume approach in Octave
ii  octave-common                3.8.2-4      all
 architecture-independent files for octave
ii  octave-communications        1.2.0-2+b1   amd64        communications
package for Octave
ii  octave-communications-common 1.2.0-2      all          communications
package for Octave (arch-indep files)
ii  octave-control               2.6.6-1      amd64        control
functions for Octave from Octave-Forge
ii  octave-data-smoothing        1.3.0-3      all          functions to do
data smoothing on noisy data
ii  octave-dataframe             1.0.1-1      all          manipulate data
in Octave similar to R data.frame
ii  octave-econometrics          1:1.1.1-2+b1 amd64        econometrics
functions for Octave
ii  octave-financial             0.4.0-2      all          financial
manipulation and plotting functions
ii  octave-fpl                   1.3.4-2      all          plot data on
unstructured triangular and tetrahedral meshes in Octave
ii  octave-ga                    0.10.0-2     all          genetic
optimization code for Octave
ii  octave-general               1.3.4-2      amd64        provide extra
general functions for Octave
ii  octave-geometry              1.7.0-2      amd64        geometric
computing functions for Octave
ii  octave-gsl                   1.0.8-6      amd64        GSL binding for
Octave
ii  octave-image                 2.2.2-1      amd64        image
manipulation for Octave
ii  octave-io                    2.2.4-1      amd64        input/output
data functions for Octave
ii  octave-linear-algebra        2.2.0-3      amd64        additional
linear-algebra functions for Octave
ii  octave-ltfat-common          2.0.1-1      all          Large
Time/Frequency Analysis Toolbox (arch-indep files)
ii  octave-msh                   1.0.10-1     amd64        create and
manage meshes for FE or FV solvers in Octave
ii  octave-optim                 1.4.0-1      amd64        unconstrained
non-linear optimization toolkit for Octave
ii  octave-signal                1.3.0-1      amd64        signal
processing functions for Octave
ii  octave-splines               1.2.7-2      all          cubic spline
functions for Octave
ii  octave-struct                1.0.10-2     amd64        additional
structure manipulation functions for Octave
$

Thanks for looking into this so quickly!  By uninstalling the package, it's
no longer a blocker for my work, but after spending more than a day
narrowing down the problem, I'd like to save someone else the effort! :).

Charlie


On Mon, Apr 20, 2015 at 2:29 PM, Charlie Hagedorn <
charlie.hagedorn at gmail.com> wrote:

> Package: octave-ltfat
> Version: 2.0.1-1
> Severity: important
>
> Dear Maintainer,
>
> I've had inconsistent Octave seg-faults on several jessie machines that
> I've traced to at least the octave-ltfat package. The seg-faults are
> triggered calls to the Octave function rcond. Installing octave-ltfat makes
> it break, uninstalling restores expected behavior (i.e. not crashing
> Octave).
>
> I discovered this problem when chasing down a segmentation fault in
> octave-optim's leasqr function. rcond breaks only on matrices of size
> greater than 9 (31 is used below), so it will only turn up when fitting
> functions of ten or more parameters.
>
> Example breakage:
>
> cah49 at charlie:~$ octave --quiet
> octave:1> rcond(magic(31))
> ans =  0.030391
> octave:2> cah49 at charlie:~$
> cah49 at charlie:~$ sudo apt-get install octave-ltfat
> Reading package lists... Done
> Building dependency tree
> Reading state information... Done
> The following NEW packages will be installed:
>   octave-ltfat
> 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
> Need to get 0 B/561 kB of archives.
> After this operation, 7,074 kB of additional disk space will be used.
> Selecting previously unselected package octave-ltfat.
> (Reading database ... 100497 files and directories currently installed.)
> Preparing to unpack .../octave-ltfat_2.0.1-1_amd64.deb ...
> Unpacking octave-ltfat (2.0.1-1) ...
> Setting up octave-ltfat (2.0.1-1) ...
> cah49 at charlie:~$ octave --quiet
> octave:1> rcond(magic(31))
> Segmentation fault
> cah49 at charlie:~$ sudo apt-get remove octave-ltfat
> Reading package lists... Done
> Building dependency tree
> Reading state information... Done
> The following package was automatically installed and is no longer
> required:
>   octave-ltfat-common
> Use 'apt-get autoremove' to remove it.
> The following packages will be REMOVED:
>   octave-ltfat
> 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded.
> After this operation, 7,074 kB disk space will be freed.
> Do you want to continue? [Y/n] y
> (Reading database ... 100544 files and directories currently installed.)
> Removing octave-ltfat (2.0.1-1) ...
> cah49 at charlie:~$ octave --quiet
> octave:1> rcond(magic(31))
> ans =  0.030391
> octave:2>
>
> I will update this bug report if I find any other packages that break
> *** Reporter, please consider answering these questions, where appropriate
> ***
>
>    * What was the outcome of this action?
>    * What outcome did you expect instead?
>
> *** End of the template - remove these template lines ***
>
>
> -- System Information:
> Debian Release: 8.0
>   APT prefers testing-updates
>   APT policy: (500, 'testing-updates'), (500, 'testing')
> Architecture: amd64 (x86_64)
>
> Kernel: Linux 3.16.0-4-amd64 (SMP w/8 CPU cores)
> Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
> Shell: /bin/sh linked to /bin/dash
> Init: systemd (via /run/systemd/system)
>
> Versions of packages octave-ltfat depends on:
> ii  libblas3 [libblas.so.3]            1.2.20110419-10
> ii  libc6                              2.19-18
> ii  libfftw3-double3                   3.3.4-2
> ii  libfftw3-single3                   3.3.4-2
> ii  libgcc1                            1:4.9.2-10
> ii  libgfortran3                       4.9.2-10
> ii  liblapack3 [liblapack.so.3]        3.5.0-4
> ii  liboctave2                         3.8.2-4
> ii  libopenblas-base [liblapack.so.3]  0.2.12-1
> ii  libquadmath0                       4.9.2-10
> ii  libstdc++6                         4.9.2-10
> ii  octave                             3.8.2-4
> ii  octave-ltfat-common                2.0.1-1
>
> octave-ltfat recommends no packages.
>
> octave-ltfat suggests no packages.
>
> -- no debconf information
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.alioth.debian.org/pipermail/pkg-octave-devel/attachments/20150420/19a7faae/attachment-0001.html>


More information about the Pkg-octave-devel mailing list