On Jun 23, 2009, at 8:17 , Gad Abraham wrote:
Hi,
I've tried to use R.app Package Installer to install the
BioConductor package GOstats, with "install dependencies" checked,
but R proceeded to download many other packages before I killed it:
(this is the temporary downloaded_packages directory)
$ ls
AffymetrixDataTestFiles_0.1.1.tgz R.oo_1.4.8.tgz
affxparser_1.16.0.tgz makePlatformDesign_1.8.0.tgz
R.methodsS3_1.0.3.tgz R.utils_1.1.7.tgz
hapmap100kxba_1.3.2.tgz pd.mapping50k.xba240_0.4.1.tgz
These aren't in the Depends of GOstats, http://www.bioconductor.org/packages/release/bioc/html/GOstats.html
, which lists:
Depends Biobase , Category , graph
If A depends on B then installing dependencies means that you also
have to satisfy all dependencies of B which could be C, D, E, F then
their dependencies and so on. The dependency tree in BioC can be quite
big... So R was doing what you told it to do.
Cheers,
Simon
Without "install dependencies" checked, it installs fine.
I'm using 2.9.0 from CRAN, BioC 2.4.0, OS X 10.5.7.
Thanks,
Gad
--
Gad Abraham
MEng Student, Dept. CSSE and NICTA
The University of Melbourne
Parkville 3010, Victoria, Australia
email: [email protected]
web: http://www.csse.unimelb.edu.au/~gabraham
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