installation path not writable R, unable to update packages

by

In general, I would advise against changing the permission in system folders, because R should work without additional administrative rights.

Thus I would likewise advise against installing packages using administrative rights, as you would be required to do so in the future every time you have to update these packages!

To backtrace this issue and prevent to minimize it in future updates, you should perform the following steps:

  1. Note which packages that fail to update (already shown in the error message).
  2. Locate the folders where all R packages are installed using .libPaths(). This should provide two results, a destination in your home folder and a system folder.

“/home/USER/R/x86_64-pc-linux-gnu-library/X.X” “/usr/lib/R/library”

  1. Install the packages with install.packages(c("PKG1", "PKG2", "PKG3")) or BiocManager::install(c("PKG1", "PKG2", "PKG3"))*
  2. Only If you have administrator rights: Manually remove the older package folders from the system folder (“/usr/lib/R/library”), using administrator rights (sudo) OR enter R with administrator rights One last time and run remove.packages(c("PKG1", "PKG2", "PKG3"), lib = "/usr/lib/R/library").

*If there are issues with the installation path, add the argument , lib = "/home/USER/R/x86_64-pc-linux-gnu-library/X.X" to either of the install functions in step 3. This argument explicitly states to install in your home folder.

There is a single issue with this approach, at least with the official R repository on Arch Linux: Whenever R is updated, the updated version still includes packages in the system folder, that can’t be updated without administrative rights. Therefore for each R update, this procedure must be repeated. I’m especially looking at you survival!!!

*Edit: It is important to note that biocLite is no longer the recommended tool for installing BioConductor packages. You should instead use BiocManager, which is in the official CRAN repository (install.packages("BiocManager")).

**Second edit: As this answer still receives votes, I have updated and cleaned up the answer.

More Related Contents:

  1. R on MacOS Error: vector memory exhausted (limit reached?)
  2. Error in model.frame.default: variable lengths differ
  3. Removing duplicate combinations (irrespective of order)
  4. Painless way to install a new version of R?
  5. How to use an image as a point in ggplot?
  6. How to efficiently calculate distance between pair of coordinates using data.table :=
  7. Convert type of multiple columns of a dataframe at once
  8. How to Reverse a string in R
  9. How do I change the formatting of numbers on an axis with ggplot? [duplicate]
  10. Place a border around points
  11. How to get name of variable in R (substitute)?
  12. Moving average of previous three values in R
  13. How do keep only unique words within each string in a vector
  14. How to concatenate factors, without them being converted to integer level?
  15. Add (subtract) months without exceeding the last day of the new month
  16. how to return number of decimal places in R
  17. How to scrape tables inside a comment tag in html with R?
  18. merge data.frames based on year and fill in missing values
  19. Unexpected ‘else’ in “else” error
  20. spearman correlation by group in R
  21. Calculate cumulative average (mean)
  22. Using ifelse in R
  23. How to extract certain columns from a list of data frames
  24. How to find out which package version is loaded in R?
  25. Put a break in the Y-Axis of a histogram
  26. ggplot geom_point() with colors based on specific, discrete values
  27. Can rbind be parallelized in R?
  28. Moving color key in R heatmap.2 (function of gplots package)
  29. Split a string every 5 characters
  30. Using a static (prebuilt) PDF vignette in R package

Leave a Comment