[Bio-Linux] Cannot install on Ubuntu "Depends: bio-linux-base-directories:i386 (>= 1.0-1) but it is not installable"

[Tim Booth]

Hi Stephane,

Thanks for trying Bio-Linux.  The explanation for this problem is that
there are old packages on the server that no longer work but I've
neglected to clean them out as they were wanted by some users of older
systems.  Ape is one such package.  Ubuntu 10.04 wouldn't see this
package at all as it is i386/32-bit but 12.04 tries to install it anyway
and then it wants an i386 compatibility library that doesn't exist.

If you have Ubuntu 12.04, you should install the package
bio-linux-shared, which will force you to remove
bio-linux-base-directories.  Anything which insists on putting
bio-linux-base-directories back is a legacy package and either
superseded or no longer supported.  I'm going to try and sort these
things out and clear out the junk now that the initial BL7 release is
out of the way.

If you just want to run ape, we're no longer specifically supporting
that package but installing is very easy.  Just start R on the command
line and type:

install.packages('ape')

In general, I'm only putting R packages on our server now if a non-R
package depends on them or if they are particularly tricky to set up.

Cheers,

TIM

On Thu, 2012-12-06 at 14:43 +0000, Stephane Bortzmeyer wrote:
> I try to install biolinux on an existing Ubuntu 12.04. For several
> packages, I get:
> 
> # apt-get install bio-linux-ape
> Reading package lists... Done
> Building dependency tree       
> Reading state information... Done
> Some packages could not be installed. This may mean that you have
> requested an impossible situation or if you are using the unstable
> distribution that some required packages have not yet been created
> or been moved out of Incoming.
> The following information may help to resolve the situation:
> 
> The following packages have unmet dependencies:
>  bio-linux-ape:i386 : Depends: bio-linux-base-directories:i386 (>= 1.0-1) but it is not installable
> E: Unable to correct problems, you have held broken packages.
> 
> 
> But I have bio-linux-base-directories, and at a more recent version:
> 
> # apt-cache show bio-linux-base-directories
> Package: bio-linux-base-directories
> Priority: optional
> Section: science
> Installed-Size: 3488
> Maintainer: Bela Tiwari <helpdesk at envgen.nox.ac.uk>
> Architecture: all
> Version: 1.0-37
> 
> I even checked the version numbers:
> 
> # if dpkg --compare-versions 1.0-37 '>=' 1.0-1; then echo OK; fi
> OK
> 
> I am now completely lost. What is apt-get expecting?
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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
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