[Bio-Linux] Problem with package catalogue. Nothing can be installed anymore

[Tim Booth]

Hi John,

Sorry to hear you are having these problems.  The package manager is
normally very good at keeping your system in a consistent state, but
sometimes it can get stuck and needs a bit of help.  The first thing to
do is to use the command-line tool "apt-get", as this will give you
better diagnostic information and also provides options you can't get
through the GUI.

Please open a shell terminal and give the command:

sudo apt-get -f install

This should be the same as the "repair the catalogue" option but will
give more diagnostic output.  I'm guessing that the
oracle-java8-installer package is stuck in a half-installed state so you
can tell the system to remove it:

sudo apt-get remove oracle-java8-installer

or if that fails, you can speak more firmly to it:

sudo dpkg -P --force-all oracle-java8-installer

Where does that get you?

My personal advice would be to download the regular Java 8 release from
Oracle and install it into /opt or /usr/local, as I've had similar
issues in the past with these installer-wrapper packages and you don't
really gain much by using them.

Cheers,

TIM

On Sun, 2014-07-06 at 17:06 +0100, john vollmers wrote:
> Hello,
> Ever since I ran into java-dependency problems while trying to install 
> an external python module (Twilio), I cannot install or remove anything 
> in biolinux anymore.
> 
> every time I try to open the ubuntu software center i get the following 
> message:
> "biolinux Items cannot be installed or removed until the package 
> catalogue is repaired. Do you want to repair it now?"
> 
> But wen I click "OK" it always aborts the repair process with the 
> message "Package operation failed" (however It won't let me look into 
> the details).
> 
> When I look into the Software-Center history it seems that each time it 
> tries to "repair the catalogue" it is actually trying to install 
> "Oracle-Java8-installer" but fails every time.
> 
> what can I do?
> 

-- 
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