4.4 years ago by
The short answer is to upgrade your version of R to it's current release and try again.
A medium answer is to upgrade your Bioconductor installation to the most recent version of Bioconductor that works with your version of R --
A faster answer would (likely) have come by posting on the Bioconductor support site.
Here's the longer explanation:
In the original post, the error is
ERROR: dependencies ‘S4Vectors’, ‘GenomeInfoDb’ are not available for package ‘methylKit’
methylKit is a CRAN package with dependencies on Biocodonductor packages. All CRAN packages that work with the 3.0 series of R currently depend on the most recent released version of the underlying Bioconductor package compatible with the 3.0 series of R.
Bioconductor actually has two versions that work(ed) with the 3.0 versions of R. During the first six months of R 3.0's life, Bioconductor 2.12 was available. During the next six months of 3.0's life, Bioconductor 2.13 was available. There are often substantial changes in (some) Bioconductor packages between releases (this is the motivation for the Bioconductor model of a devel branch and periodic releases -- the release provides a coherent set of stable packages for reproducible results by the end user, while the devel branch provides an opportunity for rapid innovation).
The original poster likely started using R 3.0 / BioC 2.12 (check out
BiocInstaller::biocVersion()). Since then of course Bioc 2.13 has come out (on October 15, 2013). Now when the original poster tries to install the CRAN package methylKit, they get the version of methylKit that works with Bioc 2.13 instead of Bioc 2.12. biocLite("BiocUpgrade") will update the user installation to Bioc 2.13 (still more than a year out of date), and the version mismatch will be resolved. Using the most recent R will get the version of methylKit that builds against the current release of Bioconductor (released on October 14, 2014).