Everytime I upgrade R using homebrew I need to install most packages again

Question

R Packages are installed to /usr/local/Cellar/r/3.1.2_1/R.framework/Versions/3.1/Resources/library

Whenever I run brew upgrade r and the versio

Answer 1

Expanding on other answers by including packages from BioConductor as well as CRAN.

1. Before install: Backup current package list.

   tmp <- installed.packages() installedpkgs <- as.vector(tmp[is.na(tmp[,"Priority"]), 1]) save(installedpkgs, file="installed_old.rda")

2. Install new version of R

3. Reload packages from CRAN

   load("installed_old.rda") tmp <- installed.packages() installedpkgs.new <- as.vector(tmp[is.na(tmp[,"Priority"]), 1]) missing <- setdiff(installedpkgs, installedpkgs.new) install.packages(missing) update.packages()

4. Reload packages from BioConductor

   chooseBioCmirror() biocLite() load("installed_old.rda") tmp <- installed.packages() installedpkgs.new <- as.vector(tmp[is.na(tmp[,"Priority"]), 1]) missing <- setdiff(installedpkgs, installedpkgs.new) for (i in 1:length(missing)) biocLite(missing[i])

Answer 2

I put .libPaths("/Users/tim/.R/packages") in my ~/.Rprofile so that packages are installed to a path that doesn't disappear after a version bump.

Answer 3

1. Save a list of your packages as an R data file

   tmp <- installed.packages() installedpkgs <- as.vector(tmp[is.na(tmp[,"Priority"]), 1]) save(installedpkgs, file="installed_old.rda")

2. Install new version

3. Load the list, then download the old packages from CRAN

   oad("installed_old.rda") tmp <- installed.packages() installedpkgs.new <- as.vector(tmp[is.na(tmp[,"Priority"]), 1]) missing <- setdiff(installedpkgs, installedpkgs.new) install.packages(missing) update.packages()