[Bio-linux-dev] Bio-Linux 8 ready for Beta-testing

Tony Travis tony.travis at abdn.ac.uk
Mon Jun 30 05:53:15 EDT 2014

On 30/06/14 10:15, Tim Booth wrote:
> Hi Tony,
> You have to run the script at least twice, until it says "Your system
> has been fully upgraded".  Could you please tell me what errors the
> script produced?  Seeing a report like this from Aptitude is not much
> use to me.

Hi, Tim.

I already ran your script twice on my laptop "beluga" and it did not
report any errors either time: That's why I was so impressed with it!

> And, no, I refuse to believe that s/apt-get/aptitude/g is a magic bullet
> fix.  Aptitude has a nasty habit of aggressively removing stuff in order
> to satisfy dependencies.

I use "aptitude -f install" to check that the APT system is in a
consistent state before doing any upgrades and again afterwards to check
that the system is still in a stable state. The only time that aptitude
removes stuff to satisfy dependencies is when it needs to in order to
get the APT system back into a consistent state again.

I don't think it's a 'magic' bullet, but it has saved me lots of time
having to re-install systems that had become unmaintainable because of
broken dependencies and partially installed packages after installing
packages with "apt-get". I began to use "aptitude" instead when I read
that "aptitude" is now the recommended package manager for Debian:


  "aptitude is the recommended package manager for Debian GNU/Linux
  systems. It is a text-based interface to APT using the curses library,
  and can be used to perform management tasks in a fast and easy way"

I've experienced severe problems from time to time when installing and
upgrading Bio-Linux in what you might regard as 'unorthodox' ways. This
is not unexpected in a complex distribution like Bio-Linux and I'm not
criticising Bio-Linux because I've had problems. Instead, I advocate a
'defensive' strategy, using the best tools available for the task.

I ran "aptitude -f install" before running your upgrade script, which I
ran twice without any errors being reported. I subsequently checked for
and fixed any inconsistencies in the APT system by running "aptitude -f
install". My laptop then ran your upgrade script a third time without
creating further inconsistencies detectable by "aptitude -f install".

I'm upgrading my workstation today + I'll let you know how I get on.



Dr. A.J.Travis, University of Aberdeen, Institute of Biological and
Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen
AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396
http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis

The University of Aberdeen is a charity registered in Scotland, No SC013683.
Tha Oilthigh Obar Dheathain na charthannas clàraichte ann an Alba, Àir. SC013683.

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