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Re: Problems with compiling and running clustalx

Le Sun, Aug 12, 2007 at 12:26:18AM -0300, Nelson A. de Oliveira a écrit :
> Hi!
> On 8/11/07, Sasa Ranisavljevic <maddox.the.god@gmail.com> wrote:
> > i have installed clustalx from official Debian package ( with apt-get ),
> > but when I try to run it i get following error:
> >
> > do_wait: drmWaitVBlank returned -1, IRQs don't seem to be working correctly.
> > Try running with LIBGL_THROTTLE_REFRESH and LIBL_SYNC_REFRESH unset.
> > Segmentation fault
> >
> > Can somebody help me whit this problem? Do anyone else have same problems.
> > I'm running Debian Etch.
> It seems to be bug #429480
> It seg faults here too (running Debian unstable). Seems to be related
> with lesstif2:
> Program received signal SIGSEGV, Segmentation fault.
> [Switching to Thread -1219742016 (LWP 6966)]
> 0xb7d2f033 in _XmRenderTableFinaliseTag () from /usr/lib/libXm.so.2
> (gdb) bt
> #0  0xb7d2f033 in _XmRenderTableFinaliseTag () from /usr/lib/libXm.so.2
> #1  0xb7de65dc in _XmStringDraw () from /usr/lib/libXm.so.2
> #2  0xb7d78bb5 in ?? () from /usr/lib/libXm.so.2
> Google didn't help with this and I don't know exactly what could be
> causing this error :-(

Ouch, that is a bad one... I just reproduced an a i386 computer running
Lenny... I have sent a private mail to lesstif2's maintainer to ask for
his opintion. By the way, I thought about increasing the bug's severity,
but then it would also pretend that clustalx is unusable on Etch because
the version numbers are the same, although it works well in this relase.

In order to help to fix this bug, I have tidied the package and moved
the patches from .diff.gz to debian/patches (using quilt). It is in the
SVN, and I have uploaded a proposed updated source pacakge in


Concerning the original error which started this thread, we figured out
that it affects some other programs running with 3D acceleration, and
that exporting LIBGL_ALWAYS_INDIRECT=true suppresses the symptoms.
( http://panela.blog-city.com/googleearth_on_linux__give_me_back_my_web.htm )
Nelson, in the meantime Sasa Ranisavljevic downgraded his system to Etch, so
it is not convenient for him to report the bug anymore. Can you report
the bug ? I think that it depends on the X setup since I can not
reproduce it on my machine running Lenny.

PS: The morale of the story is that when the popcon score drops, there
is always a reason.


Have a nice day,

Charles Plessy
Wako, Saitama, Japan

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