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1. Log in to IDAS from https://notebooks.hpc.uiowa.edu/.
2. In the RStudio “Files” pane, click to navigate to the “R/x86_64-pc-linux-gnu-library” folder as shown in the screenshot below. Then click the check box in front of the folder “3.6” and click “Rename”.
3. In the dialogue box, rename the folder to “3.6-231025”. (You can choose to rename the 3.6 folder using a different name.) Then click "OK".
4. After renaming, your “Files” pane will look like the following:
5. Follow the steps here to restart your IDAS server.
6. When you log into IDAS again, select R 3.6.1 in the Server Options form. More info about filling out the Server Options form can be found in this support article.
7. When you start RStudio again, a new “3.6” folder will be created:
8. That “3.6” folder will be empty, giving you a blank slate to reinstall packages:
9. By renaming the "3.6" folder, we created a backup of the packages that were installed for R 3.6 in case you want to look back at them. Since these folders can be large and take up space, when you are sure that you no longer need the old versions, you can simply delete them.
10. To reinstall packages to R 3.6, first use .libPaths() in R to check that you have the correct R version. In this example, we're reinstalling packages to R 3.6 and we see that .libPaths() is displaying the correct version:
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> .libPaths() [1] "/home/HawkID/R/x86_64-pc-linux-gnu-library/3.6" "/opt/R/lib/R/library" |
If .libPaths() is not showing the correct R version that you are using, you may need to set the user library path, using the following R command:
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> .libPaths("~/R/x86_64-pc-linux-gnu-library/3.6") |
11. Then you can reinstall packages using install.packages() as usual.
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> install.packages("abind")
Installing package into ‘/home/HawkID/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/abind_1.4-5.tar.gz'
Content type 'application/x-gzip' length 21810 bytes (21 KB)
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downloaded 21 KB
* installing *source* package ‘abind’ ...
** package ‘abind’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (abind)
The downloaded source packages are in
‘/tmp/RtmplD36Sc/downloaded_packages’ |
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