[Bio-linux-dev] Some broken programs

[Sasa Paporovic]

To omegamap:No, I expect nothing to see. A remove of the menu icon would be the right thing.
To TaxInspector and pedro: No, I don´t want to use it in the moment in anyway.

What if done was to have a glance of the abilities of biolinux. And I´ve by the way just seen some trivial bugs and send the informations about it to you.

There is one think that is more important for me:

I run biolinux as guest in virtualbox. I´ve some problems to get the actual guest additions run.
I´ve tried to install the 4.04 guest additions with it´s autorun.sh skript. The installations finished with succes, but causes some visual defects when biolinux starts the next time.

I have got a indermediate guest addition(4.05) from the developers, but the visual defects happends in the same way.

When you want to get a look, I´ve filed it in the virtualbox bugtracker(with screenshot):

http://www.virtualbox.org/ticket/8708

The problem is, that I think it is not so much a problem with virtualbox, because with the guest additions from the ubuntu repro(3.2) the visual system of the guest works properly.
I´ve also tried to get biolinux upgraded to the ubuntu 10.10 version to get a newer guest addition, but exept from a problem with blcr(I just deleted the package, than it works), it transform biolinux in a not bootable state.

Why all of this:
I need some newer guest additions, because I have a bulk of genome data on my host system and want to get acces to this from biolinux with the virutalbox share folder. A run with the 3.2 additions seems not to be a great idea, but I will try it in the next hours I think(last nearby option). 

When you have an idea to get this running or bring a adapted version of the additions up to your repro, it would be great.






----- Ursprüngliche Nachricht -----
Von: Tim Booth <tbooth at ceh.ac.uk>
Datum: Donnerstag, 7. April 2011, 13:30
Betreff: Re: [Bio-linux-dev] Some broken programs
An: Bio-Linux technical discussion <bio-linux-dev at nebclists.nerc.ac.uk>

> Hi,
> 
> Many thanks for the bug reports.  I'm aware that several 
> bits of
> software are now out of date but most of these problems are new 
> to me.
> 
> > The programs that are affected are:
> > pfaat: there is a missing java file needed for starting,
> 
> This was an issue with in /usr/share/applications/pfaat.desktop giving
> the wrong path to javaws - I've updated the package.
> 
> >  omegamap:there is no starting
> 
> I think the icon needs to be removed altogether, as OmegaMap now needs
> to be run from the command line.  Would you expect to see 
> anything when
> running OmegaMap from the menu?
> 
> > sequin:it is older than a year
> 
> OK, I may remove this entirely as Webin is our favoured way to 
> do INSDC
> submissions now.
> 
> > TaxInspector:failed to fetching date on startup and is not in the
> > documentation
> 
> I need to sort out a new download mirror for the files to make 
> this work
> again, but TaxInspector is fairly useless as it stands.  
> Unless you want
> to use it with Pedro?
> 
> >  tetra: is not in the documentation.
> 
> OK, I'll look into this.
> 
> 
> Cheers,
> 
> TIM
> 
> -- 
> 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
> 
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