[Bio-Linux] aptitude vs apt-get vs Synaptic vs ...
Tim Booth
tbooth at ceh.ac.uk
Tue Mar 11 09:10:28 EDT 2014
Hi,
I think this is a bit like the TCSH vs BASH vs ZSH debate, and it's
really a matter of preference.
The important thing to remember is that all these applications use the
same DPKG under the hood, and while they may select slightly different
package combinations to install or remove in some circumstances they
will all install the packages correctly and you can use whichever works
best for you or indeed switch between them. And once you have verified
your installation is consistent (with "aptitude -f or "apt-get -f check"
or however) you can be confident that all pending installations
completed successfully and all required dependencies are present.
Cheers,
TIM
On Tue, 2014-03-11 at 13:09 +0000, Jan Kim wrote:
> 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
> > _______________________________________________
> > 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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