[BioC] comparing GO lists

[Herve Pages]

Hi Ana, Robert,

Robert Gentleman wrote:
> 
>     thanks for pointing these out, I did manage to download GOsim, I am 
> not sure why it is only on CRAN given that it seems to depend on a lot 
> of BioC packages.
>    You should be able to install it if you use install.packages, and if 
> not I would contact the maintainer.

In this case, it will be easier if you use biocLite. I just tried it with
from R-2.5.1 and R-devel and it worked fine:

  > source("http://bioconductor.org/biocLite.R")
  > biocLite("GOsim")
  ... it can take a while ...
  > library(GOSim)
  > sessionInfo()
  R version 2.5.1 (2007-06-27)
  x86_64-unknown-linux-gnu

  locale:
LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY=en_US;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C

  attached base packages:
  [1] "splines"   "tools"     "stats"     "graphics"  "grDevices" "utils"
  [7] "datasets"  "methods"   "base"

  other attached packages:
         GOSim       mclust      cluster      GOstats     Category       Matrix
       "1.0.2"      "3.1-1"     "1.11.7"      "2.2.6"      "2.2.3" "0.999375-0"
       lattice   genefilter     survival         KEGG         RBGL     annotate
     "0.15-11"     "1.14.1"       "2.32"     "1.16.1"     "1.12.0"     "1.14.1"
       Biobase           GO        graph
      "1.14.0"     "1.16.0"     "1.14.2"

biocLite "knows" where to pickup the dependencies and it will choose the
Bioconductor pkgs that correspond to _your_ version of R.

Cheers,
H.

> 
>    best wishes
>     Robert
>