[Bio-Linux] BioLinux 8 - Hangs after Login

[Dubay, Christopher J]

Thanks Tim, Tony, and Steve,

Yes. Using MATE works for me. Neither the Ubuntu Default, or Gnome Flashback (either Compiz or Metacity) worked.

Trying unity form the terminal gave an 'Error: plugin 'opengl' not loaded' in the startup (???).

I have tried this with my VMware display settings as: 'host setting' and 'specified number of monitors' each with 3D graphics on and off. And still only MATE works for me.

Previously to this issue, I did try doing an install of some Illumina software (bcl2fastq) which was a bit problematic (needed BOOST and other components), and ended up doing an RPM package install with alien. I am guessing that is where I screwed something up as Tim suggested by removing conflicting packages somewhere.

I was ready to blame it on the new 'green berries'!

At least I am back up again (albeit in MATE now).

I am willing to do more troubleshooting of this. Tim: I could try 'sudo apt-get --reinstall ubuntu-desktop'; however I want to do a backup of the VM first. Other ideas?

Thanks everyone!

Christopher



-----Original Message-----
From: Tim Booth [mailto:tbooth at ceh.ac.uk]
Sent: Wednesday, January 07, 2015 2:26 AM
To: Bio-Linux help and discussion
Subject: Re: [Bio-Linux] BioLinux 8 - Hangs after Login

Hi Christopher,

I've seen a similar situation twice recently due to packages being inadvertently removed from the system.  In the first case the user had wanted to install a Deb package file directly and got the message "this conflicts with existing packages - do you want to remove the conflicting packages?"  So they did, and the desktop stopped working because they had removed essential desktop packages.

In the second case, the user had an NVidia graphics card on their physical machine so they figured they would install the NVidia accelerated drivers under Linux to take advantage of it.  Not only does this not work, but unfortunately the NVidia drivers break the VirtualBox drivers and then can't be removed without directly restoring some system files.  This one was quite tricky to fix.

Do you think you might have done anything like this on your own VM?

The thing to appreciate is that the GUI on Linux is just a regular application that happens to stick itself to the side of the screen.  You can try running it from the terminal by typing "unity" and see what it says - any informative errors?  Ensure that the ubuntu-desktop package is still on your system as this meta-package depends on all the crucial desktop components like unity.

Cheers,

TIM

On Tue, 2015-01-06 at 19:36 +0000, Dubay, Christopher J wrote:
> On my first booting-up of BioLinux this year (2015), in a VMware under
> Windows 7 environment that had been working well, I was greeted with a
> new login screen image (green berries). Nice.
>
> I logged in, and never get to a working GUI (the same thing happens
> for the Guest account), I get a GUI window with no menus/icons (just
> green berries). I can Alt+Ctrl+F1 to a terminal, but cannot restart
> the GUI ('sudo service lightdm restart' just returns me to the GUI
> window with no menus/icons as before).
>
> I tried an 'sudo apt-get update', no joy. I am willing to try a
> reinstall, however I wanted to check with the community to see if this
> a Ubuntu or BioLinux problem. Seeing the login desktop image change
> just made me wonder; and I have never had a Ubuntu VM act this way.
>
> Has anyone else ever seen this behavior?
>
> Thanks, and Happy New Year...
>
> Christopher
>
>
> Christopher Dubay, PhD
> Biomedical Informatics Program Manager Laboratory of Molecular and
> Tumor Immunology Earle A. Chiles Research Institute Providence Cancer
> Center
> 4805 NE Glisan St.- 2N57
> Portland, OR 97213  USA
> T: (503) 215-7981
> F: (503) 215-6841
>
> christopher.dubay at providence.org
>
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--
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre

Centre for Ecology and Hydrology
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Wallingford, England
OX10 8BB

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