Upgrading Out-Of-Date Bioconductor

Question

[Daniel Standage]

When I run the bioconductor installer, it tells me my installation is out-of-date and refers me to the bioconductor install page for upgrade instructions.

> source("http://bioconductor.org/biocLite.R")
Your Bioconductor is out-of-date, upgrade to version 2.12 by following
instructions at http://bioconductor.org/install.
Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help

I've followed every set of instructions on that page, including recompiling all bioconductor packages from source, and yet when I restart R and load biocLite.R I get the same warning message about bioconductor being out of date. How can I upgrade my bioconductor installation?

If it makes any difference, I'm running R 2.15.3 on Mac OS 10.8.4.

[David Westergaard]

I believe Bioconductor 2.12 requires R3.0, so you're probably stuck with that warning 'till you upgrade.

Answer 1

[Steve Lianoglou]

As David mentioned in his comment, versions of Bioconductor are tied to the versions of R. So, to use bioconductor 2.12, you need to be using R 3.0.x. If you are running R 2.15.x, you are stuck with the bioconductor 2.11 release train.

This fact is also mentioned at the very top of the the bioconductor.org/install page that the biocLite function points you to:

The current release of Bioconductor is version 2.12; it works with R version 3.0.1. Users of older R and Bioconductor versions must update their installation to take advantage of new features.

Answer 2

[yalbibalderas]

I had the same problem, but I realized that I had to use: biocLite("BiocUpgrade"), this is not mentioned in the page: http://www.bioconductor.org/install/ neither in ?biocLite

Regards,