I recently upgraded to R 3.2.0 and yet R seems to revert back to an older version of Bioconductor 2.13. I am trying to get Bioc 3.1 installed which is to my understanding what pairs with the new R version that I have.
> source("http://bioconductor.org/biocLite.R") Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help
> version$version.string  "R version 3.2.0 (2015-04-16)"
However if I try the below, I am successful in installing Bioc 3.0 (which is a good fix for nw, but ideally I would like 3.1)
> remove.packages("BiocInstaller") > biocLite("BiocUpgrade") Would you like to use a personal library instead? (y/n) y
I thought maybe it has to do with my library paths, so I have that here and my sessionInfo() for after Bioc 3.0 is installed.
> .libPaths()  "/home/mistrm82/R/x86_64-pc-linux-gnu-library/3.2" "/usr/local/lib/R/site-library"  "/usr/lib/R/site-library" "/usr/lib/R/library"
> sessionInfo() R version 3.2.0 (2015-04-16) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu precise (12.04.5 LTS) 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_1.16.4 loaded via a namespace (and not attached):  tools_3.2.0
If anyone has any thoughts on this, your help would be much appreciated. Thank you,