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

[Tim Booth]

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:

tbooth at balisaur[tbooth]dpkg -S /home
base-files: /home

(I think there may be a script or two that looks for legacy BLAST
databases in there, but if the directory is absent these should just
silently continue)

But if you have already set up automount on /home then you have a
problem because APT will try to remove the empty /home/db directory and
get eggy when it fails.  My suggestion would be to ensure the directory
isn't left empty until after the upgrade:

# touch /home/db/fakefile
# bl_do_upgrade_to7.sh
...
# dpkg -S /home
base-files: /home
# rm /home/db/fakefile
# delete_host db  ...or whatever to remove your original work-around

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.

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)

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.

Cheers,

TIM

On Mon, 2013-06-03 at 15:28 +0100, Tony Travis wrote:
> Hi, Tim.
> 
> I've had problems upgrading Bio-Linux servers that use autofs to mount
> their home directories. In this situation, /home is an automount point,
> not a folder on which a filesystem is mounted.
> 
>   host1:/export/home -> /home/host1
>   host2:/export/home -> /home/host2
>   ...
> 
> In particular, you can't create or remove a folder in an automounted
> /home because any entries in the directory representing an automount
> point are actually keys from the automount map which are themselves
> mount-points for the automounted filesystems.
> 
> This is a problem because Bio-Linux updates sometimes try to create or
> destroy /home/db - As a work-around, I faked an entry for 'host' db:
> 
>   :/export/db -> /home/db
> 
> This worked fine, until your scripts tried to delete /home/db...
> 
> I've also encountered a lot of problems recently using proprietary
> drivers for Ubuntu 12.04 LTS on my laptop and other desktops/servers
> until I discovered that Canonical have decided to upgrade the kernel
> from 3.2 to 3.5 in 12.04.2 LTS:
> 
>   https://wiki.ubuntu.com/Kernel/LTSEnablementStack
> 
> Are you planning to do a point-release based on Ubuntu 12.04.2 LTS?
> 
> I've been manually upgrading my systems to use the LTSEnablementStack
> and I would be happy to help with testing a version based on 12.04.2.
> 
> Bye,
> 
>   Tony.
> 
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-- 
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