I'm getting an error trying to use
biocLite("BiocUpgrade") to go from Bioconductor 3.1 to 3.2 with R 3.2.2. It's telling me the only update option is to devel. On another machine I had been using devel and the update was seamless, BiocInstaller updated itself to 1.20.0 upon first use of biocLite().
> source("http://www.bioconductor.org/biocLite.R") Bioconductor version 3.1 (BiocInstaller 1.18.4), ?biocLite for help > biocLite("BiocUpgrade") Bioconductor version 3.1 (BiocInstaller 1.18.4), ?biocLite for help Error: Bioconductor version 3.1 can be upgraded, but only to 'devel'; see ?useDevel. Use biocLite() without any arguments to update installed packages In addition: Warning message: 'BiocInstaller' update failed, using version 1.18.4 > sessionInfo() R version 3.2.2 (2015-08-14) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux Server release 6.5 (Santiago) locale:  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C  LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8  LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8  LC_PAPER=en_US.UTF-8 LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  BiocInstaller_1.18.4 loaded via a namespace (and not attached):  tools_3.2.2