[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
>
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