Using the ‘Devel’ Version of Bioconductor

Which version of R?

Package developers want to develop against the version of R that will be available to users when the Bioconductor devel branch becomes the Bioconductor release branch.

R has a ‘.y’ release in x.y.z every year, but Bioconductor has a .y release (where current devel becomes release) every 6 months.

When the next (typically mid-April) .y releases of R and Bioconductor coincide, Bioc-devel is based on R-devel.

When the next (typically mid-October) .y release of Bioconductor corresponds to no change in R’s y, Bioc-devel is based on release R.

This means that, from mid-October through mid-April, Bioconductor developers should be developing against R-devel. From mid-April to mid-October, developers should use R-release (actually, the R snapshot from the R-x-y-branch) for Bioconductor development.

Using Bioc-devel

In order to use the devel version of Bioconductor during the current release cycle, you must install R-devel:

Then, make sure that your version of BiocInstaller is current and your packages up-to-date. Do this by removing all versions of BiocInstaller

remove.packages("BiocInstaller")  # repeat until R says there is no
                                  # package 'BiocInstaller' to remove
source("https://bioconductor.org/biocLite.R")  # install correct version
BiocInstaller::biocValid()
Fred Hutchinson Cancer Research Center