I am trying to update my bioconductor to the latest version (3.0+). I currently have R 3.2.1 and Bioconductor 2.28. When I run BiocUpdate, it just reinstalls 2.28. I tried uninstalling and reinstalling Bioconductor, but still only got 2.28. The reasoning is that a package I am running (phyloseq) is having an error that the developer doesn't recognize. He suggested updating to the latest version of Bioconductor & R to fix it. I have updated my R version, but am unable to update my Bioconductor. Any suggestions to install Bioconductor 3.0 or 3.1?
Edit: There was a misunderstanding in how to tell what version of Bioconductor I have.
The best way to check the version of Bioconductor is to compare your version of BiocInstaller (a package within R once Bioconductor is installed) with the Bioconductor website.