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Hi there, fellow scientists! |
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|
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So I guess that if you haven't lived under a rock for the past few |
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months (and did not recently join gentoo-science), you have probably |
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heard about my efforts to help y'all install R extension packages |
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(CRAN and bioconductor are the obvious targets, since they are the |
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most popular R package repositories). My project is pretty much |
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complete now, and I'd like to tell you how to use my code and start |
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using R packages. |
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|
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Now, I solved the problem slightly differently from packages like |
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g-cpan and g-octave. Instead of generating ebuilds as they are needed, |
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I've written another package called g-common which gives us |
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transparent access to non-ebuild package repositories (although |
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currently only R repos and PEAR are supported). To make our life even |
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easier, I've written a layman patch to be able to access R package |
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repositories just like we would access a regular ebuild overlay. |
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|
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The code is not in portage yet, of course, so this is how you install, |
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as a simple example, the "zoo" package from CRAN: |
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-add the kuroo and science overlays if you don't have them yet |
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-install =layman-8888 from kuroo and g-cran from science (g-common is |
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currently included in g-cran) |
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-save the attached repositories.xml to /var/lib/repositories.xml (or |
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whatever you think is appropriate) |
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-edit /etc/layman/layman.cfg and add file:///var/lib/repositories.xml |
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to "overlays" (on its own line) |
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-layman -a CRAN |
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-emerge -av dev-R/zoo |
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For your convenience, I also added the bioconductor repositories to |
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repositories.xml. If you'd like to try these, please note that the |
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"annotation" part of bioconductor depends on the "bioc" part (and all |
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the gene databases and stuff are in "annotation", so you'll probably |
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want to get both). |
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|
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Please test packages, and tell me about everything that you think |
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could be improved. Build errors, usability problems... tell me what |
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you think, so that we can make Gentoo the first distribution which can |
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directly install non-native packages using the package manager! |
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|
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Should you have any questions or remarks, you can often find me on IRC |
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(#gentoo-soc, #gentoo-science, or just privmsg me), but I regularly |
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read my email too. |
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Auke Booij / tulcod. |