On Jun 23, 2009, at 8:55 , Gad Abraham wrote:
On 23/6/09 10:42 PM, Simon Urbanek wrote:
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.
Does "install dependencies" only install Depends or also Suggests?
It's equivalent to install.packages(dependencies=TRUE)
Cheers,
S
The downstream Depends for GOstats are pretty minimal and don't
include any of the packages I listed:
GOstats: Biobase , Category , graph
Biobase: R , methods , utils
Category: AnnotationDbi , Biobase
graph: R , methods
AnnotationDbi: R , methods , utils , Biobase
--
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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