With the release of R version 2.9.0 on 2009-04-17, Inference users have inquired about the best way to upgrade from an earlier R version without losing one's R environment configuration (e.g., installed packages).

Although there are varied ways to upgrade successfully, Inference users have found that the following steps do the trick:

1. Uninstall the old R version. From the Windows Start menu, select All Programs > R > Uninstall R <version>. IMPORTANT Note from R FAQ: "Uninstalling R only removes files from the initial installation, not (for example) packages you have installed or updated."
2. Install the new version of R. Download R 2.9.0 Windows binary from CRAN and execute the installation in the usual fashion.
3. Copy the packages to the new installation. Using Windows Explorer, navigate to the folder corresponding to the libraries of your old R version. (Depending on your OS and R settings, this is likely C:\Program Files\R\<version>\library\ or C:\Users\<UserName>\Documents\R\win-library\<version>\.) Open the library folder, then copy all the packages left behind. Paste them in the library folder of the new installation. If Windows asks whether or not you want to replace an existing folder, select No. After completing the copy, you can delete anything remaining from the old install.
4. Update the packages in the upgrade install. In the R Console window, run "update.packages(checkBuilt=TRUE, ask=FALSE)" to update all the packages in the upgrade library folder.