[gentoo-science] G-CRAN works, testing needed

[gentoo-science] G-CRAN works, testing needed

[Auke Booij]

Hi there, fellow scientists!

So I guess that if you haven't lived under a rock for the past few
months (and did not recently join gentoo-science), you have probably
heard about my efforts to help y'all install R extension packages
(CRAN and bioconductor are the obvious targets, since they are the
most popular R package repositories). My project is pretty much
complete now, and I'd like to tell you how to use my code and start
using R packages.

Now, I solved the problem slightly differently from packages like
g-cpan and g-octave. Instead of generating ebuilds as they are needed,
I've written another package called g-common which gives us
transparent access to non-ebuild package repositories (although
currently only R repos and PEAR are supported). To make our life even
easier, I've written a layman patch to be able to access R package
repositories just like we would access a regular ebuild overlay.

The code is not in portage yet, of course, so this is how you install,
as a simple example, the "zoo" package from CRAN:
-add the kuroo and science overlays if you don't have them yet
-install =layman-8888 from kuroo and g-cran from science (g-common is
currently included in g-cran)
-save the attached repositories.xml to /var/lib/repositories.xml (or
whatever you think is appropriate)
-edit /etc/layman/layman.cfg and add file:///var/lib/repositories.xml
to "overlays" (on its own line)
-layman -a CRAN
-emerge -av dev-R/zoo
For your convenience, I also added the bioconductor repositories to
repositories.xml. If you'd like to try these, please note that the
"annotation" part of bioconductor depends on the "bioc" part (and all
the gene databases and stuff are in "annotation", so you'll probably
want to get both).

Please test packages, and tell me about everything that you think
could be improved. Build errors, usability problems... tell me what
you think, so that we can make Gentoo the first distribution which can
directly install non-native packages using the package manager!

Should you have any questions or remarks, you can often find me on IRC
(#gentoo-soc, #gentoo-science, or just privmsg me), but I regularly
read my email too.
Auke Booij / tulcod.

[gentoo-science] Re: G-CRAN works, testing needed

[Auke Booij]

[-- Attachment #1: Type: text/plain, Size: 255 bytes --]

On Sat, Aug 7, 2010 at 7:00 PM, Auke Booij <auke@tulcod.com> wrote:
> -save the attached repositories.xml to /var/lib/repositories.xml (or
> whatever you think is appropriate)

... and of course I made the classic mistake of not attaching the attachment.

[-- Attachment #2: repositories.xml --]
[-- Type: text/xml, Size: 1121 bytes --]

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE repositories SYSTEM "http://www.gentoo.org/dtd/repositories.dtd">
<repositories xmlns="" version="1.0">
  <repo quality="experimental" status="unofficial">
    <name><![CDATA[Bioconductor_bioc]]></name>
    <description><![CDATA[Bioconductor software packages]]></description>
    <homepage>http://www.bioconductor.org/</homepage>
    <source type="g-common">cran http://bioconductor.org/packages/devel/bioc/</source>
  </repo>
  <repo quality="experimental" status="unofficial">
    <name><![CDATA[Bioconductor_annotation]]></name>
    <description><![CDATA[Bioconductor annotation packages]]></description>
    <homepage>http://www.bioconductor.org/</homepage>
    <source type="g-common">cran http://bioconductor.org/packages/devel/data/annotation/</source>
  </repo>
  <repo quality="experimental" status="unofficial">
    <name><![CDATA[CRAN]]></name>
    <description><![CDATA[CRAN R extension packages]]></description>
    <homepage>http://www.r-project.org/</homepage>
    <source type="g-common">cran http://cran.r-project.org/</source>
  </repo>
</repositories>