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Update R and migrate R packages to new installation from within the console
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| #From https://stackoverflow.com/questions/1401904/painless-way-to-install-a-new-version-of-r | |
| # Run in the old version of R (or via RStudio) | |
| setwd("C:/Temp/") | |
| packages <- installed.packages()[,"Package"] | |
| save(packages, file="Rpackages") | |
| # INSTALL NEW R VERSION | |
| if(!require(installr)) { install.packages("installr"); require(installr)} #load / install+load installr | |
| # See here for more on installr: https://www.r-statistics.com/2013/03/updating-r-from-r-on-windows-using-the-installr-package/ | |
| # step by step functions: | |
| check.for.updates.R() # tells you if there is a new version of R or not. | |
| install.R() # download and run the latest R installer | |
| # Install library - run in the new version of R. This calls package names and installs them from repos, thus all packages should be correct to the most recent version | |
| setwd("C:/Temp/") | |
| load("Rpackages") | |
| for (p in setdiff(packages, installed.packages()[,"Package"])) | |
| install.packages(p) | |
| # Installr includes a package migration tool but this simply copies packages, it does not update them | |
| copy.packages.between.libraries() # copy your packages to the newest R installation from the one version before it (if ask=T, it will ask you between which two versions to perform the copying) |
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Great, thanks, it worked well for all CRAN packages. Maybe worth to add to the script the following 2 lines if Bioconductor packages also need to be reinstalled:
for (p in setdiff(packages, installed.packages()[,"Package"]))
BiocManager::install(p)
Cheers