cranpkg - script for installing R libraries

Allan · 2007-10-03 16:19:53

Hi everyone,

I have created a script for installing R libraries using pacman. You can download it at http://allan.mcrae.googlepages.com/cranpkg (currently v0.3.0).

For example, the "genetics" library is installed using

> cranpkg -i genetics
CRANPKG v0.2
Copyright (C) 2007 Allan McRae

Examining R installation...

Installing package genetics...
  Downloading package information...
    Version: 1.3.0
    Dependancies: combinat gdata gtools MASS mvtnorm 

  Resolving dependancies...
    Installing combinat...
    Installing gdata...
    Installing mvtnorm...

  Downloading package source...
  Building package...
  Installing package...

Done

> pacman -Qs cran
local/cran-combinat 0.0.6-1
    R library - combinat. Built with cranpkg
local/cran-gdata 2.3.1-1
    R library - gdata. Built with cranpkg
local/cran-genetics 1.3.0-1
    R library - genetics. Built with cranpkg
local/cran-gtools 2.4.0-1
    R library - gtools. Built with cranpkg
local/cran-mvtnorm 0.8.1-1
    R library - mvtnorm. Built with cranpkg

This should be fairly robust against failures and leave log files in /tmp/cranpkg if anything fails. Please let me know if you run into trouble with this.

There a a few variables that you may need to modify at the top of the script. For example, the mirror you wish to download from.

Wget is used by default for the downloading and package installation is done with a "sudo pacman" command.

Any problems/success please let me know.

Last edited by Allan (2007-12-31 04:51:27)

Allan · 2007-10-20 02:44:38

Here is some information on cranpkg status at v0.2:

Installs and loads fine in R:
adegenet, allelic, ape, bayesSurv, classifly, coda, combinat, e1071, gdata, gee, genetics, glpk, gstat, gtools, HardyWeinberg, kinship, mcmc, mvtnorm, nortest, qtl, reshape, RGtk2, smoothSurv, sp, tree.

Installs but fails to load in R:
graph, rggobi

Thats greater than 90% success rate... The packages that fail to load have no files in them (pacman -Ql <pkg> returns nothing).

Update: graph requires R>=2.6.0 (latest) which hasn't made it to Arch yet. rggobi require external software called ggobi so fails. These errors are caught in v0.2.1.

Last edited by Allan (2007-10-20 15:13:57)

Allan · 2007-12-31 04:50:36

v0.3 is available. This includes the ability to upgrade either individual or all installed packages.

Anyone actually use this?

dyfrgi · 2009-11-12 22:03:41

You'd be a lot more likely to get users of this if it were in AUR and thus a bit more findable.

Does the script work with current pacman, R etc.?

Allan · 2009-11-12 22:46:20

No idea. I haven't looked at this in two years and do not even know if I have a copy or the script anymore... R's internal package manager is good enough really.

This is a prime example of why you should not bump old posts: http://wiki.archlinux.org/index.php/For … Bumping.27

Closing.

Arch Linux

#1 2007-10-03 16:19:53

cranpkg - script for installing R libraries

#2 2007-10-20 02:44:38

Re: cranpkg - script for installing R libraries

#3 2007-12-31 04:50:36

Re: cranpkg - script for installing R libraries

#4 2009-11-12 22:03:41

Re: cranpkg - script for installing R libraries

#5 2009-11-12 22:46:20

Re: cranpkg - script for installing R libraries

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