[Bio-Linux] System on Parallels broken after updates

[Tauqeer Alam]

If you restart the Parallels VM, I assume you still see the login
manager where it asks for your password?  If you click the icon next to
your name and choose "Gnome desktop (no effects)" can you log in and see
an old-style menu bar and apps menu at the top?

Yes, at the top left I see "Applications" and "Places". I t has everything
there.

sumiti at ubuntu:~$ sudo apt-get dist-upgrade

[sudo] password for sumiti:
Reading package lists... Done
Building dependency tree
Reading state information... Done
Calculating upgrade... Done
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

sumiti at ubuntu:~$ unity --replace

unity-panel-service: no process found
Checking if settings need to be migrated ...no
Checking if internal files need to be migrated ...no
Backend     : gconf
Integration : true
Profile     : unity
Adding plugins
Initializing core options...done
Initializing composite options...done
compiz (core) - Error: Couldn't load plugin '/usr/lib/compiz/libopengl.so'
: libGL.so.1: cannot open shared object file: No such file or directory
compiz (core) - Error: Couldn't load plugin 'opengl'
compiz (core) - Error: Couldn't load plugin
'/usr/lib/compiz/libcompiztoolbox.so' : libGL.so.1: cannot open shared
object file: No such file or directory
compiz (core) - Error: Couldn't load plugin 'compiztoolbox'
compiz (core) - Error: Couldn't load plugin '/usr/lib/compiz/libdecor.so' :
libGL.so.1: cannot open shared object file: No such file or directory
compiz (core) - Error: Couldn't load plugin 'decor'
Initializing vpswitch options...done
Initializing snap options...done
Initializing mousepoll options...done
compiz (core) - Error: Couldn't load plugin '/usr/lib/compiz/libresize.so'
: libGL.so.1: cannot open shared object file: No such file or directory
compiz (core) - Error: Couldn't load plugin 'resize'
Initializing place options...done
compiz (core) - Error: Couldn't load plugin '/usr/lib/compiz/libmove.so' :
libGL.so.1: cannot open shared object file: No such file or directory
compiz (core) - Error: Couldn't load plugin 'move'
compiz (core) - Error: Couldn't load plugin '/usr/lib/compiz/libwall.so' :
libGL.so.1: cannot open shared object file: No such file or directory
compiz (core) - Error: Couldn't load plugin 'wall'
compiz (core) - Error: Couldn't load plugin '/usr/lib/compiz/libgrid.so' :
libGL.so.1: cannot open shared object file: No such file or directory
compiz (core) - Error: Couldn't load plugin 'grid'
Initializing session options...done
Initializing gnomecompat options...done
compiz (core) - Error: Couldn't load plugin
'/usr/lib/compiz/libanimation.so' : libGL.so.1: cannot open shared object
file: No such file or directory
compiz (core) - Error: Couldn't load plugin 'animation'
compiz (core) - Error: Couldn't load plugin '/usr/lib/compiz/libfade.so' :
libGL.so.1: cannot open shared object file: No such file or directory
compiz (core) - Error: Couldn't load plugin 'fade'
compiz (core) - Error: Couldn't load plugin
'/usr/lib/compiz/libunitymtgrabhandles.so' : libGL.so.1: cannot open shared
object file: No such file or directory
compiz (core) - Error: Couldn't load plugin 'unitymtgrabhandles'
compiz (core) - Error: Couldn't load plugin
'/usr/lib/compiz/libworkarounds.so' : libGL.so.1: cannot open shared object
file: No such file or directory
compiz (core) - Error: Couldn't load plugin 'workarounds'
compiz (core) - Error: Couldn't load plugin '/usr/lib/compiz/libscale.so' :
libGL.so.1: cannot open shared object file: No such file or directory
compiz (core) - Error: Couldn't load plugin 'scale'
compiz (core) - Error: Couldn't load plugin '/usr/lib/compiz/libexpo.so' :
libGL.so.1: cannot open shared object file: No such file or directory
compiz (core) - Error: Couldn't load plugin 'expo'
compiz (core) - Error: Couldn't load plugin '/usr/lib/compiz/libezoom.so' :
libGL.so.1: cannot open shared object file: No such file or directory
compiz (core) - Error: Couldn't load plugin 'ezoom'
compiz (core) - Error: Couldn't load plugin
'/usr/lib/compiz/libunityshell.so' : libGL.so.1: cannot open shared object
file: No such file or directory
compiz (core) - Error: Couldn't load plugin 'unityshell'
Setting Update "main_menu_key"
Setting Update "run_key"

window is stuck here

Thanks

Tauqeer

On Tue, May 21, 2013 at 12:10 PM, Tim Booth <tbooth at ceh.ac.uk> wrote:

> Hi Tauqeer,
>
> That's not good!  First thing is to see if you can get a fallback
> desktop.  It's not really a fix but you will at least be able to use
> your Bio-Linux system.
>
> If you restart the Parallels VM, I assume you still see the login
> manager where it asks for your password?  If you click the icon next to
> your name and choose "Gnome desktop (no effects)" can you log in and see
> an old-style menu bar and apps menu at the top?
>
> I'd like to see if the update process failed somehow and left the system
> in an inconsistent state.  If you can get to the command line, can you
> run:
>
> sudo apt-get dist-upgrade
>
> What does it say?
>
> And finally, what happens if you then run:
>
> unity --replace
>
> Cheers,
>
> TIM
>
> On Tue, 2013-05-21 at 16:48 +0100, Tauqeer Alam wrote:
> > Hi Tim
> > I have BioLinux installed on my iMac through Parallels Virtual
> > Machine. Everything was working absolutely fine until today. This
> > morning, I ran update manager (from the left side panel) and now I do
> > not see my side and tope panel. I just see my desktop, nothing else.
> >
> >
> > Please help
> >
> >
> > Tauqeer
>
> --
> Tim Booth <tbooth at ceh.ac.uk>
> NERC Environmental Bioinformatics Centre
>
> Centre for Ecology and Hydrology
> Maclean Bldg, Benson Lane
> Crowmarsh Gifford
> Wallingford, England
> OX10 8BB
>
> http://nebc.nerc.ac.uk
> +44 1491 69 2705
>
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>



-- 
*********************************************
Md Tauqeer Alam, Ph.D
Division of Infectious Diseases
Emory University School of Medicine
615 Michael Street, Atlanta, GA 30322, USA
tauqeer9 at gmail.com
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