Too many dependencies with BioConductor packages?
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: gabraham at csse.unimelb.edu.au web: http://www.csse.unimelb.edu.au/~gabraham