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How can I remove all installed packages except base and recommended?

ECII
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    Just out of curiosity, why would one want to do this instead of fresh R installation? – CHP May 05 '13 at 11:00
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    Updated to R 3.0.0 and have to rebuild all packages. Some give errors so I thought revert to vanilla and reinstall. – ECII May 05 '13 at 11:57
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    @geektrader that is the question I *should* have asked before attempting to answer! :-) – Simon O'Hanlon May 05 '13 at 12:56

6 Answers6

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Be CAREFUL! And read the docs before you try this:

# Pasted as a commented to prevent blindly copying and pasting
# remove.packages( installed.packages( priority = "NA" )[,1] )

By default this will remove packages from the first library in your .libPaths(). Otherwise you can specify the following argument to remove.packages():

, lib = .libPaths()[1]
Johan
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Simon O'Hanlon
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    will this return my R installation to a vanilla state? – ECII May 05 '13 at 08:53
  • Assuming default install settings and default use of install. packages and nothing fancy in. REnviron file or .RProfile file then I think so! :-) – Simon O'Hanlon May 05 '13 at 10:06
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    I just ran this code for R 3.0.0 and here are the only packages still available: base, boot, class, cluster, codetools, compiler, datasets, foreign, graphics, grDevices, grid KernSmooth, lattice, MASS, Matrix, methods, mgcv, nlme, nnet, parallel, rpart, spatial, splines, stats, stats4, survival, tcltk, tools, utils – chandler Nov 23 '14 at 20:05
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    I just ran the code and got `Error in find.package(pkgs, lib) : there are no packages called ‘assertthat’, ‘backports’, ‘brew’, ‘callr’, ‘cli’, ‘clipr’, ‘clisymbols’, ‘commonmark’, ‘crayon’, ‘curl’, ‘desc’, ‘devtools’, ‘digest’, ‘evaluate’, ‘fansi’, ‘fs’, ‘gh’, ‘git2r’, ‘glue’, ‘highr’, ‘httr’, ‘ini’, ‘jsonlite’, ‘knitr...`, How could I solve this? – Cris Apr 06 '19 at 12:35
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Instead of

Updated to R 3.0.0 and have to rebuild all packages.

just do

update.packages(..., checkBuilt=TRUE)

which is what I did on my R 3.0.0 (using lib.loc=... to point to my different local directories). This will update everything you have and which it can still get from repos such as CRAN. For install_git() etc, you are out of luck and need to reinstall.

But either way you do not need to remove the packages first.

Dirk Eddelbuettel
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  • I did `update.packages()` without the `checkBuilt=T` and run into errors. Was that the cause of my probs? – ECII May 05 '13 at 12:13
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    Well if a package no longer exists, or builds, or ... it will not work under this, but neither will it when you manually install it. This just makes your life easier. YMMV. – Dirk Eddelbuettel May 05 '13 at 12:15
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    @ECII Yes. `checkBuilt` checks if packages were built under the previous major release of R and marks them as old and in need of updating if TRUE, and will *try* to update them. – Simon O'Hanlon May 05 '13 at 12:56
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Accepted answer no longer works (R 3.6.X), but this one does:

update.packages(checkBuilt = T, ask = F)

We use checkBuilt=T because this checks whether packages were built under an older version and need to be rebuilt (sometimes).

We use ask=F because otherwise we get a prompt for each package which is annoying.

CoderGuy123
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4

Here is a solution available in the R-Blogger: 

# create a list of all installed packages
 ip <- as.data.frame(installed.packages())
 head(ip)
# if you use MRO, make sure that no packages in this library will be removed
 ip <- subset(ip, !grepl("MRO", ip$LibPath))
# we don't want to remove base or recommended packages either\
 ip <- ip[!(ip[,"Priority"] %in% c("base", "recommended")),]
# determine the library where the packages are installed
 path.lib <- unique(ip$LibPath)
# create a vector with all the names of the packages you want to remove
 pkgs.to.remove <- ip[,1]
 head(pkgs.to.remove)
# remove the packages
 sapply(pkgs.to.remove, remove.packages, lib = path.lib)

Here is the link for the original post: https://www.r-bloggers.com/how-to-remove-all-user-installed-packages-in-r/

add-semi-colons
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2

If on Linux, the easiest thing is probably to remove the library folder, which by default is located in /home/yourusername/R.

On Fedora, for example, it is called x86_64-redhat-linux-gnu-library. If the folder /home/yourusername/R/x86_64-redhat-linux-gnu-library is deleted, it is automatically recreated at the following start of R. All default libraries are regularly available.

user2100721
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giocomai
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  • *it is automatically recreated at the following start of R* → **no** – it is only recreated once you ask for installing a package, and the system library is not writable for your user. – slhck Jan 04 '19 at 16:55
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WARNING, YOU WILL DELETE A LOT OF STUFF

Sometimes uninstalling packages does not work, in which case you may want to delete the folder of the packages. This can be done from R assuming you have permissions.

sapply(paste(installed.packages( priority = "NA" )[, 2], installed.packages( priority = "NA" )[, 1], sep = "/"), unlink, recursive = T)

You can preview the paths to be delete by:

sapply(paste(installed.packages( priority = "NA" )[, 2], installed.packages( priority = "NA" )[, 1], sep = "/"), identity)

This call:

  • Gets the list of installed non-base packages
  • Makes a vector of their installed paths
  • Loops over the paths
  • Deletes each folder recursively
CoderGuy123
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