[Bio-Linux] Bio-Linux VirtualBox broken after updates - how to fix

[Tim Booth]

Dear All,

There is a driver update problem affecting Bio-Linux 8 for VirtualBox.
If you apply the latest batch of updates via the update manager the VM
will no longer boot to a working desktop.  As far as I can tell this
issue is limited to VirtualBox/VMWare, but I may be wrong.

** Symptoms:

After rebooting the VM, you see the desktop wallpaper and nothing else.
Or you may even just see a black screen. The system appears unresponsive
but you can switch to a text terminal by holding down the Right Ctrl key
and pressing F1 to get a text console login prompt.

** If you have already applied the problem updates and need to fix:

     1. Switch to text console by holding down the Right Ctrl key and
        pressing F1 (or try Ctrl+Alt+F1 on Windows)
     2. Log in - account is manager, password manager unless you changed
        it
     3. $ sudo stop lightdm
     4. $ startx -e mate-session
     5. Now you should have some sort of usable desktop
     6. Open a new terminal (ignore the XTerm window and don't close it)
     7. $ sudo apt-get purge nvidia-331-updates
        nvidia-opencl-icd-331-updates nvidia-prime nvidia-settings
        libhwloc-plugins
     8. $ sudo reboot

That should do it!

If, at this point, you just see your Desktop icons but no panel, get
back in the text login and try this to reset your account settings:

$ mkdir my_old_dot_files
$ mv ~/.local ~/.g* my_old_dot_files/
$ sudo restart lightdm

And that should really do it.

** If you have not yet applied the updates and want to avoid the
problems, just remove two troublesome packages before updating:

$ sudo apt-get purge nvidia-libopencl1-331-updates libhwloc-plugins

You should see these two packages cleanly removed.

I'm releasing an updated VirtualBox OVF image on the website today to
address this problem.  Apologies for this glitch - it's Ubuntu's fault,
not mine, honest!!  If you are still having problems or need
clarification on the above please reply to the
bio-linux at nebclists.nerc.ac.uk mailing list.

Cheers,

TIM


-- 
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