[Bio-linux-dev] Bio-Linux upgrade problems

[Tony Travis]

On 03/06/13 15:59, Tim Booth wrote:
> Hi Tony,
> 
> The good news is that /home/db is dead, or will be once you get the
> upgrade to work, as can be verified on a BL7 machine by running:
> [...]
> Does that make sense?  I expect this problem only impacts a couple of
> people, and is a one-off, so I'd prefer to avoid the effort of adding
> the fix to the script if that's OK.

Hi, Tim.

OK, and it's good to know that /home/db is no longer required :-)

> Regarding the 3.5 series kernel, this is already the default in the
> latest Bio-Linux ISO, but it is not the default if you upgrade from BL6
> - you get 3.2 the same as other Ubuntu upgraders.  My logic is that the
> new kernel is most useful for those with new hardware and thus not
> relevant to most upgraders.  (I'm using 3.2 until I see a good reason
> not to - it never seems to crash on my laptop and everything works)

Ah, I've just run the latest Bio-Linux ISO under VirtualBox to look.
Sorry, I didn't realise that it is already based on 12.04.2 LTS. I've
been doing 6->7 upgrades, rather than clean installs of Bio-Linux 7.

> I'm inclined to think that proprietary drivers will cause aggro whatever
> I do, but if you think there is something obvious I need to change to
> help out with these issues then let me know.

I caused these driver problems by installing the 'quantal' kernel as a
side-effect of trying to make the package inventory of my upgraded
systems the same as your iso, and I ended up with an unsupported LTS
hardware enablement stack package combination. The link I posted is the
correct way to update 12.04.1 LTS to the 3.5 kernel and X.org stack.

It might be worth mentioning as a comment/printout at the end of the
upgrade script otherwise people might not realise that the result of the
upgrade is not quite the same as doing a clean install from the
Bio-Linux 7 DVD. I didn't, and I should have known about this issue!

Bye,

  Tony.