[Bio-Linux] Updated QIIME package 1.8.0

Tue Mar 11 09:09:45 EDT 2014

Dear Tim,

On Tue, Mar 11, 2014 at 11:53:23AM +0000, Tim Booth wrote:
> Hi Tony and Jason,
> 
> Upgrade-system may be worth trying but Bio-Linux has always used
> "cron-apt" for automated updates so Jason will also need to disable that
> before switching to "upgrade-system".  I've switched off unattended
> upgrades on my own machine and I just use the graphical update manager
> that pops up in Unity so that approach should also be fine, as should
> running apt-get or aptitude or synaptic or any of the other package
> managers.
> 
> I personally don't like the "aptitude" software and in my opinion they
> removed it from Ubuntu for good reason - it breaks as many things as it
> fixes.  I jsut use apt-get.

out of interest, what's wrong with aptitude? I use that pretty much in
the way you use the graphical package manager, and my understanding is
that it's based on the same Debian package management libraries as
apt-get, dpkg and the GUI based stuff.

Best regards, Jan

> My advice would be to run "apt-get dist-upgrade" and if that gives an
> error when working out which packages to upgrade please post the
> details.  Normally you'll find that there are one or two packages
> gumming up the works and once these are manually updated the rest all
> follows.  Aptitude is supposed to work these things out more
> intelligently than apt-get but I'm always wary of intelligent software.
> 
> Cheers,
> 
> TIM
> 
> On Tue, 2014-03-11 at 11:29 +0000, Tony Travis wrote:
> > On 11/03/14 11:05, Bramwell, Jason wrote:
> > > Tim,
> > > What do I have to do to get these (and other) updates? The documentation
> > > is saying that updates should occur every night but this does not seem
> > > to be the case for me (689 packaged required yesterday and 689 packages
> > > still required today). So far I've been running apt-get update/upgrade
> > > but is this the correct way or is there a 'bio-linux' way of doing this?
> > 
> > Hi, Jason.
> > 
> > You can do 'unattended' upgrades if you want, using the "upgrade-system"
> > package. This updates the APT database, then downloads and installs
> > upgrades. However, you *MUST* edit its configuration file or
> > "upgrade-system" will remove 'redundant' packages too aggressively.
> > Change the "deborphan" priority to 6:
> > 
> >   sudo -i
> >   apt-get install upgrade-system
> >   vim /etc/upgrade-system.conf
> >   ...
> >   ORPHANOPTS="--guess-all --libdevel --priority=6"
> >   ...
> > 
> > The "upgrade-system" command is run daily from:
> > 
> >   /etc/cron.daily/upgrade-system
> > 
> > This only updates the databases, but you can edit it to run
> > "upgrade-system" once a day by adding the command at the end of the cron
> > job:
> > 
> >   vim /etc/cron.daily/upgrade-system
> >   ...
> >   upgrade-system
> >   #EOF
> >   ...
> > 
> > > So far when I update a fresh install there are 689 update packages which
> > > I can install but then FastTree, Glimmer, Galaxy, Mira and QIIME are
> > > held back. Am I doing this correctly or should i be following an
> > > alternate method?
> > 
> > Before you upgrade anything, I recommend installing "aptitude" and using
> > it to check the consistency of your APT database:
> > 
> >   apt-get install aptitude
> >   aptitude update
> >   aptitude -f install
> > 
> > Ubuntu no longer installs "aptitude" by default, but it is recommended
> > by Debian for managing packages from the command-line:
> > 
> >   https://www.debian.org/doc/manuals/debian-faq/ch-pkgtools.en.html
> > 
> > > 8.1.3 aptitude
> > >
> > > aptitude is a package manager for Debian GNU/Linux systems that provides a frontend to the apt package management infrastructure. aptitude is a text-based interface using the curses library, it can be used to perform management tasks in a fast and easy way.
> > >
> > > aptitude provides the functionality of dselect and apt-get, as well as many additional features not found in either program:
> > >
> > >     aptitude offers easy access to all versions of a package.
> > >
> > >     aptitude makes it easy to keep track of obsolete software by listing it under "Obsolete and Locally Created Packages".
> > >
> > >     aptitude includes a fairly powerful system for searching particular packages and limiting the package display. Users familiar with mutt will pick up quickly, as mutt was the inspiration for the expression syntax.
> > >
> > >     aptitude can be used to install the predefined tasks available. For more information see tasksel, Section 8.1.5.
> > >
> > >     aptitude in full screen mode has su functionality embedded and can be run by a normal user. It will call su (and ask for the root password, if any) when you really need administrative privileges
> > >
> > > You can use aptitude through a visual interface (simply run aptitude) or directly from the command line. The command line syntax used is very similar to the one used in apt-get. For example, to install the foo package, you can run aptitude install foo.
> > >
> > > Note that aptitude is the preferred program for daily package management from console.
> > 
> > You do NOT have to run "aptitude" from a TUI (Full-Screen Text User
> > Interface). If you want to you can, but I don't recommend it. The main
> > reason I prefer aptitude is that it is good at fixing broken packages.
> > 
> > HTH,
> > 
> >   Tony.
> > 
> > --
> > 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.
> > _______________________________________________
> > Bio-Linux mailing list
> > Bio-Linux at nebclists.nerc.ac.uk
> > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> 
> -- 
> 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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> Bio-Linux at nebclists.nerc.ac.uk
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-- 
 +- Jan T. Kim -------------------------------------------------------+
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