Re: [carlos.borroto@gmail.com: [SCM] tophat branch, oneiric-ppa, updated. oneiric-ppa/1.4.0-1_oneiric3-3-g3edf06d]

[Andreas Tille <andreas@an3as.eu>]

On Tue, Feb 07, 2012 at 06:27:09PM -0500, Carlos Borroto wrote:
> 
> Oh, I didn't realize adding something to Recommends implies it will
> get installed by default just as a dependency.

Aptitude and apt-get (as well as the GUI tools depending on them) are
installing Depends and Recommends.  You can force ignoring Recommends
via

   apt-get --no-install-recommends

or use APT::Install-Recommends in apt.conf.  However, we can safely
assume that recommends will be installed by our target user.  Those
users who are ignoring Recommends usually know what they are doing.

As a consequence of this logic all packages your are listing as
Depends and Recommends need to be in Debian main - otherwise it needs
to go to contrib.

> How can I get a
> "Suggested packages: cufflinks" when apt-getting tophat? Is Enhances
> mean for this?

If you want to suggest a package simply list it as

  Suggests: cufflinks

You can suggest packages from contrib or non-free or even from
"somewhere else" - policy does not enforce suggested packages inside
Debian main.  However, a user who tries to install using

  apt-get --install-suggests

and does not include non-free in its sources.list will fail installing
this suggested package.
 
> I don't think tophat needs to be a Depends in cufflinks, as you could
> be interested in the analysis of BAM files you didn't create or BAM
> files not created with tophat. In order to run cufflinks you don't
> need tophat at all. It could be a "suggestion"(Enhances?) thou, as
> cufflinks authors do recommend mapping with tophat.

The field "Enhances" is kind of a "Reverse-Suggests".  I usually do
something like:

  Package: xy
  Suggests: xy-doc

  Package: xy-doc
  Enhances: xy

So in your case it might be useful to do:

  Package: cufflinks
  Enhances: tophat

which means exactly what you wrote:  tophat is not needed for running
cufflinks but on a system running tophat it makes sense to install
cufflinks.

The Enhances field is not (yet) widely used but it makes perfectly sense
to specify it because it can give better hints for aptitude/apt-get
dependency solvers and other tools like axi-cache (xapian index).

Kind regards

     Andreas.

-- 
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