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 version of R changes I need to install most of the libraries again as the path of installation changes.

How do I upgrade without having to install everything back again?

Edit: I think this answers my question http://stackoverflow.com/questions/1401904/painless-way-to-install-a-new-version-of-r-on-windows

The expected location after a default installation is: `/Library/Frameworks/R.framework/Versions/3.1/Resources/library`. Using brew is not recommended by the maintainer of the OSX branch of R. And ... everyone who makes a major version update also needs to reinstall packages, so you may just be asking one of the R-FAQ questions. — IRTFM, Jan 09 '15 at 18:31
I'm not familiar with R, but this occasionally also happens with Ruby, Python, etc. package environments. I might be a flaw in Homebrew. — Peter Eisentraut, Jan 11 '15 at 22:59

score 2 · Answer 1 · answered Jan 12 '15 at 00:59

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.

answered Jan 12 '15 at 00:59

Tim Smith

Do you know if there is an advantage to this over setting `R_LIBS_USER` or `R_LIBS_SITE`? – Ellis Valentiner May 11 '16 at 18:41

score 1 · Answer 2 · edited Apr 20 '16 at 15:31

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

Before install: Backup current package list.

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

score 0 · Answer 3 · answered Jun 19 '15 at 17:47

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")
Install new version
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()

3 Answers3