On 03/05/2011 08:50 AM, Matthew Pocock wrote: > OH, I see that there is a DO.db in bioconductor already: > > http://www.bioconductor.org/help/bioc- views/release/data/annotation/html/DO.db.html > > <http: www.bioconductor.org="" help="" bioc-="" views="" release="" data="" annotation="" html="" do.db.html="">That > is great. However, it doesn't seem to install for me. > >> biocLite("DO.db") > Using R version 2.11.1, biocinstall version 2.6.9. > Installing Bioconductor version 2.6 packages: > [1] "DO.db" > Please wait... > > Warning in install.packages(pkgs = pkgs, repos = repos, ...) : > argument 'lib' is missing: using > '/home/nmrp3/R/x86_64-pc-linux-gnu-library/2.11' > Warning message: > In getDependencies(pkgs, dependencies, available, lib) : > package ?DO.db? is not available > > It looks like I have bioconductor 2.6 but DO.db is packaged for 2.7. > >> source("http://bioconductor.org/biocLite.R") > BioC_mirror = http://www.bioconductor.org > Change using chooseBioCmirror(). >> biocLite() > Using R version 2.11.1, biocinstall version 2.6.9. > Installing Bioconductor version 2.6 packages: > [snip] > > So it looks like I'm being handed bioconductor 2.6 rather than 2.7 - perhaps > this is because I allowed Ubuntu to install R version 2.11.1? yes, Bioconductor is versioned to correspond with R. R.2.11.* -> Bioc 2.6; R.2.12.* -> Bioc 2.7. So update your R (and installed packages, e.g., http://bioconductor.org/install/#update-bioconductor-packages) and you'll have access to DO.db. Martin > > Matthew > > On 5 March 2011 16:14, Matthew Pocock <turingatemyhamster at="" gmail.com=""> wrote: > >> Hi, >> >> I've been using GO.db and find it very useful. I'd now like to have a >> similar API for the disease ontology (DO). Is there something I can read >> that may explain how to expose the DO data as a package? I guess I'm asking >> if there is a guide to how I would develop DO.db. >> >> Thanks, >> >> Matthew >> >> -- >> Matthew Pocock >> mailto: turingatemyhamster at gmail.com >> gchat: turingatemyhamster at gmail.com >> msn: matthew_pocock at yahoo.co.uk >> irc.freenode.net: drdozer >> (0191) 2566550 >> >> > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793