Re: comments on suggest line of med-bio-dev

[Andreas Tille <tillea@rki.de>]

On Mon, 13 Apr 2009, Steffen Moeller wrote:

> Suggests: aceperl
> 		should this possibly be "libace-perl" ?


Yes and that's fixed in SVN as you can see at

  http://debian-med.alioth.debian.org/tasks/bio-dev.html#libace-perl

The problem will be fixed soon (really soon - we just needed blends-dev
version 0.6.3 which is available since two days).

> bioconductor
> 		bioconductor should go

Yes - I'm *really* wondering how to handle this.  Bioconductor
is just a pool of R packages which are releavant for us.  Any
suggestion to cherry pick from this pool?

> libbio-das-perl
> 		is this in the distribution? I cannot find it.

That's why it is reduced to "Suggests".  The blends tools parse the
tasks files for Dependencies and if a package is not found in the
package pool the dependency level is decreased to "Suggests".  Have
you ever read the Blends documentation at

  http://blends.alioth.debian.org/blends/ch-sentinel.en.html

We just keep track of prospective packages and the page

  http://debian-med.alioth.debian.org/tasks/bio-dev.html#libbio-das-perl

has all information we gathered about this project ...

> libbio-mage-utils-perl
> 		there is however libbio-mage-perl

Same as libace-perl.

> libbiojava-java
> 		this should be under "Recommends", i.e. under the
> 		same level as its ruby, python and perl fellas

Libbiojava-java is in contrib.  We can not Depend/Recommend packages
outside main so the Dependency was automatically reduced to Suggests.

> r-base-core
> 		this is not a particular med-bio-dev package
> 		and I would leave it aside but for general
> 		statistics. I suggest to leave it aside.

I removed it from the task file.

> seqan
> 		is this in the distribution?

No, but there is an ITP and this information is kept at

   http://debian-med.debian.net/tasks/bio-dev.html#seqan

Please read again about prospective packages.

> Steffen (who should prepare the update for the just announced biojava 1.7 this week with
> many nice changes to the structural bioinformatics world (which BioPerl is very sparse with))

Well, the most interesting change would be if it could go to main,
right? ;-)

Kind regards and many thanks for your review which was very welcome

      Andreas.

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