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

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@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@charlie:~$ octave --quiet
octave:1> rcond(magic(31))
ans = 0.030391
octave:2> cah49@charlie:~$
cah49@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@charlie:~$ octave --quiet
octave:1> rcond(magic(31))
Segmentation fault
cah49@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@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 ***

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* What outcome did you expect instead?

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-- 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