Debian Bug report logs - #607071
octave-symbolic: Segfaults, doesn't work at all

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Message #5 received at submit@bugs.debian.org (full text, mbox, reply):

From: Jordi Gutiérrez Hermoso <jordigh@gmail.com>

To: Debian Bug Tracking System <submit@bugs.debian.org>

Subject: octave-symbolic: Segfaults, doesn't work at all

Date: Tue, 14 Dec 2010 07:55:58 -0600

Package: octave-symbolic
Version: 1.0.9-1+b1
Severity: grave

octave-symbolic is largely unusable. Calling any of its functions
other than "sym" results in C++ exceptions like this one:

     error: T& Array<T>::checkelem (2, -1, 2): range error

and eventually the package segfaults Octave.

This report is mostly a reminder to myself to either fix the package,
or to the release managers to remove this package from squeeze if I
don't manage to fix it before then.

-- System Information:
Debian Release: squeeze/sid
  APT prefers testing
  APT policy: (990, 'testing'), (500, 'unstable'), (101, 'experimental')
Architecture: amd64 (x86_64)

Kernel: Linux 2.6.32-5-amd64 (SMP w/2 CPU cores)
Locale: LANG=en_CA.UTF-8, LC_CTYPE=en_CA.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/bash

Versions of packages octave-symbolic depends on:
ii  libatlas3gf-base [libla 3.8.3-27         Automatically Tuned Linear Algebra
ii  libblas3gf [libblas.so. 1.2-8            Basic Linear Algebra Reference imp
ii  libc6                   2.11.2-7         Embedded GNU C Library: Shared lib
ii  libcln6                 1.3.1-2          Class Library for Numbers (C++)
ii  libfftw3-3              3.2.2-1          library for computing Fast Fourier
ii  libgcc1                 1:4.4.5-6        GCC support library
ii  libgfortran3            4.4.5-6          Runtime library for GNU Fortran ap
ii  libginac1.5             1.5.8-1          The GiNaC symbolic framework (runt
ii  libhdf5-serial-1.8.4 [l 1.8.4-patch1-2   Hierarchical Data Format 5 (HDF5) 
ii  liblapack3gf [liblapack 3.2.1-8          library of linear algebra routines
ii  libncurses5             5.7+20100313-4   shared libraries for terminal hand
ii  libreadline6            6.1-3            GNU readline and history libraries
ii  libstdc++6              4.4.5-6          The GNU Standard C++ Library v3
ii  octave3.2               3.2.4-8          GNU Octave language for numerical 
ii  zlib1g                  1:1.2.3.4.dfsg-3 compression library - runtime

octave-symbolic recommends no packages.

octave-symbolic suggests no packages.

-- no debconf information

Message #10 received at 607071@bugs.debian.org (full text, mbox, reply):

From: Thomas Weber <tweber@debian.org>

To: 607071@bugs.debian.org

Subject: Re: [Pkg-octave-devel] Bug#607071: octave-symbolic: Segfaults, doesn't work at all

Date: Wed, 15 Dec 2010 23:17:32 +0100

On Tue, Dec 14, 2010 at 07:55:58AM -0600, Jordi Gutiérrez Hermoso wrote:
> Package: octave-symbolic
> Version: 1.0.9-1+b1
> Severity: grave
> 
> octave-symbolic is largely unusable. Calling any of its functions
> other than "sym" results in C++ exceptions like this one:
> 
>      error: T& Array<T>::checkelem (2, -1, 2): range error
> 
> and eventually the package segfaults Octave.

Did anything change in Ginac? The package was built in February and all
tests passed.

	Thomas

Message #15 received at 607071@bugs.debian.org (full text, mbox, reply):

From: Jordi Gutiérrez Hermoso <jordigh@gmail.com>

To: Thomas Weber <tweber@debian.org>, 607071@bugs.debian.org

Subject: Re: [Pkg-octave-devel] Bug#607071: Bug#607071: octave-symbolic: Segfaults, doesn't work at all

Date: Wed, 15 Dec 2010 23:18:34 -0600

On 15 December 2010 16:17, Thomas Weber <tweber@debian.org> wrote:
> On Tue, Dec 14, 2010 at 07:55:58AM -0600, Jordi Gutiérrez Hermoso wrote:
>> Package: octave-symbolic
>> Version: 1.0.9-1+b1
>> Severity: grave
>>
>> octave-symbolic is largely unusable. Calling any of its functions
>> other than "sym" results in C++ exceptions like this one:
>>
>>      error: T& Array<T>::checkelem (2, -1, 2): range error
>>
>> and eventually the package segfaults Octave.
>
> Did anything change in Ginac? The package was built in February and all
> tests passed.

Are you sure? When I tried building the package today I got

     Checking package...
     warning: mark_as_command is obsolete and will be removed from a
future version of Octave
     [findsym]
       ***** test
      symbols
      x=sym("x"); y=sym("y"); f=x^2+3*x*y-y^2;
      vars = findsym (f);
      assert(vars, 'x,y');
      vars2 = findsym (f,1);
      assert(vars2, 'x');
     !!!!! test failed
     T& Array<T>::checkelem (4, -1, 2): range error[sym2poly]
     PASSES 2 out of 2 tests
     [symfsolve]
     PASSES 5 out of 5 tests

(The mark_as_command warning is from another package I have installed,
but I keep forgetting which one.) So something fishy is happening,
"!!!!! test failed" yet "PASSES 2 out of 2 tests". Can you reproduce
this? Perhaps this was happening in February so the tests were failing
but being reported as passing?

Message #20 received at 607071@bugs.debian.org (full text, mbox, reply):

From: Jordi Gutiérrez Hermoso <jordigh@gmail.com>

To: Thomas Weber <tweber@debian.org>, 607071@bugs.debian.org

Subject: Re: [Pkg-octave-devel] Bug#607071: Bug#607071: octave-symbolic: Segfaults, doesn't work at all

Date: Wed, 15 Dec 2010 23:37:44 -0600

2010/12/15 Jordi Gutiérrez Hermoso <jordigh@gmail.com>:
>     Checking package...
>     warning: mark_as_command is obsolete and will be removed from a
> future version of Octave
>     [findsym]
>       ***** test
>      symbols
>      x=sym("x"); y=sym("y"); f=x^2+3*x*y-y^2;
>      vars = findsym (f);
>      assert(vars, 'x,y');
>      vars2 = findsym (f,1);
>      assert(vars2, 'x');
>     !!!!! test failed
>     T& Array<T>::checkelem (4, -1, 2): range error[sym2poly]
>     PASSES 2 out of 2 tests
>     [symfsolve]
>     PASSES 5 out of 5 tests
>
> (The mark_as_command warning is from another package I have installed,
> but I keep forgetting which one.) So something fishy is happening,
> "!!!!! test failed" yet "PASSES 2 out of 2 tests".

Durr, I can't read debug output, it's failing the findsym test. It's
the same range error... hmm...

Message #25 received at 607071@bugs.debian.org (full text, mbox, reply):

From: Thomas Weber <tweber@debian.org>

To: Jordi Gutiérrez Hermoso <jordigh@gmail.com>, 607071@bugs.debian.org

Subject: Re: [Pkg-octave-devel] Bug#607071: Bug#607071: Bug#607071: octave-symbolic: Segfaults, doesn't work at all

Date: Thu, 16 Dec 2010 21:34:07 +0100

On Wed, Dec 15, 2010 at 11:18:34PM -0600, Jordi Gutiérrez Hermoso wrote:
> On 15 December 2010 16:17, Thomas Weber <tweber@debian.org> wrote:
> > On Tue, Dec 14, 2010 at 07:55:58AM -0600, Jordi Gutiérrez Hermoso wrote:
> >> Package: octave-symbolic
> >> Version: 1.0.9-1+b1
> >> Severity: grave
> >>
> >> octave-symbolic is largely unusable. Calling any of its functions
> >> other than "sym" results in C++ exceptions like this one:
> >>
> >>      error: T& Array<T>::checkelem (2, -1, 2): range error
> >>
> >> and eventually the package segfaults Octave.
> >
> > Did anything change in Ginac? The package was built in February and all
> > tests passed.
> 
> Are you sure? 

Yes: 
https://buildd.debian.org/pkg.cgi?pkg=octave-symbolic


> (The mark_as_command warning is from another package I have installed,
> but I keep forgetting which one.) So something fishy is happening,
> "!!!!! test failed" yet "PASSES 2 out of 2 tests". Can you reproduce
> this? Perhaps this was happening in February so the tests were failing
> but being reported as passing?

No, see the build logs available from above.

	Thomas

Message #30 received at 607071@bugs.debian.org (full text, mbox, reply):

From: Julien Cristau <jcristau@debian.org>

To: Jordi Gutiérrez Hermoso <jordigh@gmail.com>, 607071@bugs.debian.org

Subject: Re: Bug#607071: octave-symbolic: Segfaults, doesn't work at all

Date: Mon, 27 Dec 2010 00:08:58 +0100

[Message part 1 (text/plain, inline)]

user release.debian.org@packages.debian.org
usertag 607071 squeeze-will-remove
kthxbye

On Tue, Dec 14, 2010 at 07:55:58 -0600, Jordi Gutiérrez Hermoso wrote:

> This report is mostly a reminder to myself to either fix the package,
> or to the release managers to remove this package from squeeze if I
> don't manage to fix it before then.
> 
Tagging as candidate for removal, will do that in a few days if no fix
is in sight.

Cheers,
Julien

[signature.asc (application/pgp-signature, inline)]

Message #35 received at 607071@bugs.debian.org (full text, mbox, reply):

From: Jordi Gutiérrez Hermoso <jordigh@gmail.com>

To: Julien Cristau <jcristau@debian.org>

Cc: 607071@bugs.debian.org

Subject: Re: Bug#607071: octave-symbolic: Segfaults, doesn't work at all

Date: Mon, 27 Dec 2010 08:32:27 -0600

On 26 December 2010 17:08, Julien Cristau <jcristau@debian.org> wrote:
> On Tue, Dec 14, 2010 at 07:55:58 -0600, Jordi Gutiérrez Hermoso wrote:
>
>> This report is mostly a reminder to myself to either fix the package,
>> or to the release managers to remove this package from squeeze if I
>> don't manage to fix it before then.
>>
> Tagging as candidate for removal, will do that in a few days if no fix
> is in sight.

Thanks for the reminder. I'll be spending all of my free time this
week on this bug. I say that if by Friday I don't have a fix or
something very close to one, you should remove the package from
squeeze.

- Jordi G. H.

Message #40 received at 607071@bugs.debian.org (full text, mbox, reply):

From: Thomas Weber <tweber@debian.org>

To: Jordi Gutiérrez Hermoso <jordigh@gmail.com>, 607071@bugs.debian.org

Cc: Julien Cristau <jcristau@debian.org>

Subject: Re: [Pkg-octave-devel] Bug#607071: octave-symbolic: Segfaults, doesn't work at all

Date: Mon, 27 Dec 2010 21:21:51 +0100

package octave-symbolic
tags 607071 unreproducible
severity 607071 important
thanks

On Mon, Dec 27, 2010 at 08:32:27AM -0600, Jordi Gutiérrez Hermoso wrote:
> On 26 December 2010 17:08, Julien Cristau <jcristau@debian.org> wrote:
> > On Tue, Dec 14, 2010 at 07:55:58 -0600, Jordi Gutiérrez Hermoso wrote:
> >
> >> This report is mostly a reminder to myself to either fix the package,
> >> or to the release managers to remove this package from squeeze if I
> >> don't manage to fix it before then.
> >>
> > Tagging as candidate for removal, will do that in a few days if no fix
> > is in sight.

I'm downgrading this bug. I can't reproduce it neither in an amd64
chroot nor an i386 physical installation.

Jordi, can you check your local installation? Maybe there's some other
package interfering here. 

	Thomas

Message #45 received at 607071@bugs.debian.org (full text, mbox, reply):

From: Geoff Gole <geoffgole@gmail.com>

To: Julien Cristau <jcristau@debian.org>, Jordi Gutiérrez Hermoso <jordigh@gmail.com>, 607071@bugs.debian.org

Subject: Re: [Pkg-octave-devel] Bug#607071: octave-symbolic: Segfaults, doesn't work at all

Date: Tue, 28 Dec 2010 05:04:03 +0800

fwiw, I can reproduce this.

$ apt-get install octave-symbolic
...
$ octave
GNU Octave, version 3.0.1
Copyright (C) 2008 John W. Eaton and others.
This is free software; see the source code for copying conditions.
There is ABSOLUTELY NO WARRANTY; not even for MERCHANTIBILITY or
FITNESS FOR A PARTICULAR PURPOSE.  For details, type `warranty'.

Octave was configured for "i486-pc-linux-gnu".

Additional information about Octave is available at http://www.octave.org.

Please contribute if you find this software useful.
For more information, visit http://www.octave.org/help-wanted.html

Report bugs to <bug@octave.org> (but first, please read
http://www.octave.org/bugs.html to learn how to write a helpful report).

For information about changes from previous versions, type `news'.

octave:1> x = sym("x")
x =

x
octave:2>  x+2
error: T& Array<T>::checkelem (0, -1, 2): range error
error: binary operator `+' not implemented for `ex' by `scalar' operations
error: evaluating binary operator `+' near line 2, column 3
octave:2> Sin(x)
error: Internal error: statement in file ./real/elem/cl_R_mul.cc, line
93 has been reached!!
Please send the authors of the program a description how you produced
this error!

Message #50 received at 607071@bugs.debian.org (full text, mbox, reply):

From: Vivek Dasmohapatra <vivek@etla.org>

To: 607071@bugs.debian.org

Subject: Bug #607071 reproducible on testing

Date: Mon, 27 Dec 2010 20:55:21 +0000 (GMT)

Reproduced here:

Package: octave-symbolic
Priority: optional
Section: math
Installed-Size: 988
Maintainer: Debian Octave Group <pkg-octave-devel@lists.alioth.debian.org>
Architecture: amd64
Source: octave-symbolic (1.0.9-1)
Version: 1.0.9-1+b1

vivek@noise:~$ octave
GNU Octave, version 3.2.4
Copyright (C) 2009 John W. Eaton and others.
This is free software; see the source code for copying conditions.
There is ABSOLUTELY NO WARRANTY; not even for MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.  For details, type `warranty'.

Octave was configured for "x86_64-pc-linux-gnu".

Additional information about Octave is available at http://www.octave.org.

Please contribute if you find this software useful.
For more information, visit http://www.octave.org/help-wanted.html

Report bugs to <bug@octave.org> (but first, please read
http://www.octave.org/bugs.html to learn how to write a helpful report).

For information about changes from previous versions, type `news'.

octave:1> x = sym("x");
octave:2> x+2
error: T& Array<T>::checkelem (0, -1, 2): range error
octave:2> Sin(x)
panic: Segmentation fault -- stopping myself...
attempting to save variables to `octave-core'...
error: octave_base_value::save_binary(): wrong type argument `ex'
save to `octave-core' complete
Segmentation fault

Message #55 received at 607071@bugs.debian.org (full text, mbox, reply):

From: Thomas Weber <tweber@debian.org>

To: Geoff Gole <geoffgole@gmail.com>, 607071@bugs.debian.org

Subject: Re: [Pkg-octave-devel] Bug#607071: Bug#607071: octave-symbolic: Segfaults, doesn't work at all

Date: Tue, 28 Dec 2010 13:24:00 +0100

On Tue, Dec 28, 2010 at 05:04:03AM +0800, Geoff Gole wrote:
> fwiw, I can reproduce this.
> 
> $ apt-get install octave-symbolic
> ...

Ehm, the part above would have been interesting, because
> $ octave
> GNU Octave, version 3.0.1

3.0.1 is only available in Lenny.

	Thomas

Message #60 received at 607071@bugs.debian.org (full text, mbox, reply):

From: Mehdi Dogguy <mehdi@dogguy.org>

To: Thomas Weber <tweber@debian.org>, 607071@bugs.debian.org

Subject: Re: Bug#607071: [Pkg-octave-devel] Bug#607071: Bug#607071: octave-symbolic: Segfaults, doesn't work at all

Date: Tue, 28 Dec 2010 13:37:45 +0100

On 28/12/2010 13:24, Thomas Weber wrote:
> On Tue, Dec 28, 2010 at 05:04:03AM +0800, Geoff Gole wrote:
>> fwiw, I can reproduce this.
>>
>> $ apt-get install octave-symbolic ...
>
> Ehm, the part above would have been interesting, because
>> $ octave GNU Octave, version 3.0.1
>
> 3.0.1 is only available in Lenny.
>

Yes, but as Vivek showed, it's also reproducible in a clean Squeeze
chroot. (and I just made the test and it leads to same failure). So, in
any case, this issue remains RC.

Regards,

-- 
Mehdi Dogguy مهدي الدڤي
http://dogguy.org/

Message #65 received at 607071@bugs.debian.org (full text, mbox, reply):

From: Jordi Gutiérrez Hermoso <jordigh@gmail.com>

To: 607071@bugs.debian.org

Subject: Works in svn

Date: Tue, 28 Dec 2010 18:19:04 -0600

Just an update, there's a small update of this package in upstream's
svn that seems to no longer display this problem. Upstream is
reluctant to release it, because this svn version has a similar
problem on Mac OS X.

I'm going to attack the Mac OS X problem. If I solve it, I can work
with upstream to make a bugfix release based on the svn version. If
not, I'll backport the svn fix into Debian. Point is, a fix is in
sight.

- Jordi G. H.

Message #72 received at 607071@bugs.debian.org (full text, mbox, reply):

From: Thomas Weber <tweber@debian.org>

To: Julien Cristau <jcristau@debian.org>, 607071@bugs.debian.org

Cc: Jordi Gutiérrez Hermoso <jordigh@gmail.com>

Subject: Re: [Pkg-octave-devel] Bug#607071: octave-symbolic: Segfaults, doesn't work at all

Date: Tue, 4 Jan 2011 23:17:46 +0100

Hi Julien, 

On Mon, Dec 27, 2010 at 12:08:58AM +0100, Julien Cristau wrote:
> user release.debian.org@packages.debian.org
> usertag 607071 squeeze-will-remove
> kthxbye
> 
> On Tue, Dec 14, 2010 at 07:55:58 -0600, Jordi Gutiérrez Hermoso wrote:
> 
> > This report is mostly a reminder to myself to either fix the package,
> > or to the release managers to remove this package from squeeze if I
> > don't manage to fix it before then.
> > 
> Tagging as candidate for removal, will do that in a few days if no fix
> is in sight.

we probably have a one-liner patch from upstream for this. The package
was already hinted out of testing. Any chance of getting a fixed package
into testing?

	Thomas

Message #77 received at 607071@bugs.debian.org (full text, mbox, reply):

From: Julien Cristau <jcristau@debian.org>

To: Thomas Weber <tweber@debian.org>

Cc: 607071@bugs.debian.org, Jordi Gutiérrez Hermoso <jordigh@gmail.com>

Subject: Re: [Pkg-octave-devel] Bug#607071: octave-symbolic: Segfaults, doesn't work at all

Date: Tue, 4 Jan 2011 23:37:43 +0100

[Message part 1 (text/plain, inline)]

On Tue, Jan  4, 2011 at 23:17:46 +0100, Thomas Weber wrote:

> Hi Julien, 
> 
> On Mon, Dec 27, 2010 at 12:08:58AM +0100, Julien Cristau wrote:
> > user release.debian.org@packages.debian.org
> > usertag 607071 squeeze-will-remove
> > kthxbye
> > 
> > On Tue, Dec 14, 2010 at 07:55:58 -0600, Jordi Gutiérrez Hermoso wrote:
> > 
> > > This report is mostly a reminder to myself to either fix the package,
> > > or to the release managers to remove this package from squeeze if I
> > > don't manage to fix it before then.
> > > 
> > Tagging as candidate for removal, will do that in a few days if no fix
> > is in sight.
> 
> we probably have a one-liner patch from upstream for this. The package
> was already hinted out of testing. Any chance of getting a fixed package
> into testing?
> 
Yes, if a suitable fix is uploaded this week we should be able to get it
back in.

Cheers,
Julien

[signature.asc (application/pgp-signature, inline)]

Message #82 received at 607071-close@bugs.debian.org (full text, mbox, reply):

From: Thomas Weber <tweber@debian.org>

To: 607071-close@bugs.debian.org

Subject: Bug#607071: fixed in octave-symbolic 1.0.9-2

Date: Thu, 06 Jan 2011 22:21:28 +0000

Source: octave-symbolic
Source-Version: 1.0.9-2

We believe that the bug you reported is fixed in the latest version of
octave-symbolic, which is due to be installed in the Debian FTP archive:

octave-symbolic_1.0.9-2.diff.gz
  to main/o/octave-symbolic/octave-symbolic_1.0.9-2.diff.gz
octave-symbolic_1.0.9-2.dsc
  to main/o/octave-symbolic/octave-symbolic_1.0.9-2.dsc
octave-symbolic_1.0.9-2_amd64.deb
  to main/o/octave-symbolic/octave-symbolic_1.0.9-2_amd64.deb



A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 607071@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Thomas Weber <tweber@debian.org> (supplier of updated octave-symbolic package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Format: 1.8
Date: Thu, 06 Jan 2011 22:51:58 +0100
Source: octave-symbolic
Binary: octave-symbolic
Architecture: source amd64
Version: 1.0.9-2
Distribution: unstable
Urgency: low
Maintainer: Debian Octave Group <pkg-octave-devel@lists.alioth.debian.org>
Changed-By: Thomas Weber <tweber@debian.org>
Description: 
 octave-symbolic - symbolic package for Octave
Closes: 571870 607071
Changes: 
 octave-symbolic (1.0.9-2) unstable; urgency=low
 .
   * debian/control:
     - Remove Rafael Laboissiere from Uploaders (Closes: #571870)
     - Remove Ólafur Jens Sigurðsson <ojsbug@gmail.com> from Uploaders
   * New patch: register_symbols, ensure that symbols from the package are
     registered. Patch taken from upstream SVN (closes: #607071)
Checksums-Sha1: 
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 b56f03feb146fb1f9457a9b6764edeeb157feaf0 2797 octave-symbolic_1.0.9-2.diff.gz
 b0039f11494011f853c9a0937450e130029f964b 259848 octave-symbolic_1.0.9-2_amd64.deb
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Files: 
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 8e28ba5a73fc150abd7286534a6761fe 2797 math optional octave-symbolic_1.0.9-2.diff.gz
 195faab34369af04ad35d2f1d350a9b3 259848 math optional octave-symbolic_1.0.9-2_amd64.deb

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