Companion Notebook Troubleshooting

Author

Adam Gilbert

The following are troubleshooting tips

Troubleshooting

PROBLEM – The Notebooks Have Disappeared: This problem has randomly impacted a few of my students recently (Fall 2024), as Posit upgrades to R 4.4.1. You can get the tutorials back by using the drop-down in the top-right corner of the RStudio window to switch from R 4.4.1 back to R 4.3.3. Perhaps a better fix is to reinstall the notebooks by running each of the following, one at a time, in the console.

install.packages("remotes")
remotes::install_github("agmath/AppliedStatsInteractive")
remotes::install_github("rundel/learnrhash")

After running these commands, the notebooks will repopulate in the Tutorials tab.

I’ve installed the notebooks on R 4.4.1 at the original template, so any new copies made beyond September 2024 should not experience this problem.

PROBLEM – Notebooks Crashing on Re-Launch: Some notebooks will crash when users start the notebook, close out, and then return to complete the notebook at later time. This is caused by a RAM overflow because all exercise chunks attempt to run at once. Most notebooks permit stopping and restarting without issue – the current offenders are the Topic 13, Topic 16, and Topic 17 notebooks.

  • Update: I’m in the process of splitting the longer notebooks into smaller, more manageable components. So far, I’ve completed this for Topic 6 and Topic 16. To access these new versions, run remotes::install_github("agmath/AppliedStatsInteractive") in your console. If you’re prompted to update any additional packages, just type 1 and press enter to proceed with the updates. If you are using my grading script, it doesn’t accommodate these shorter notebooks yet – I will get to it as soon as possible.

  • If you are on a paid-tier account, use the settings gear icon in the top-right of the Posit Cloud page and click on the resources tab. Change the RAM settings to either 1.5GB or 2GB and then relaunch the notebook.

    • Once you are done with the notebook, use the Resources tab after clicking the settings gear icon to change your alotted RAM back to 1GB. Otherwise, your work in Posit Cloud will consume your access hours more rapidly than necessary.

  • If you are on a free-tiered account, you’ll need to delete the HTML file associated with the notebook. Unfortunately, this will also wipe out your progress on the notebook.

    1. In the Files tab of the lower-right pane of RStudio, click the two dots next to the green up arrow to move up one level in the file system.
    2. Click the “lib” folder to enter that directory.
    3. Click the “x86_…” folder to enter that directory.
    4. Click the “4.x” folder to enter the directory corresponding to the current R version (mine is labeled “4.3” at the time of writing this document).
    5. Click the “AppliedStatsInteractive” folder to enter it.
    6. Click the “tutorials” folder to enter it.
    7. Click on the name of the folder corresponding to the notebook you are trying to run.
    8. Check the box next to the HTML file. Make sure that only the HTML file is checked off.
    9. Click the delete button and confirm that you want to delete that one file.
    10. Click the translucent blue cube icon at the top-right corner of the File tab in the bottom-right pane. This will bring you back to the main project directory.
    11. Use the Session menu at the top of the RStudio window and select to Restart R.
    12. Use the Tutorials tab in the top-right pane of RStudio to launch the tutorial notebook.

Note: If this still doesn’t work, follow the steps above again, but delete both the HTML file and the directory XX_NotebookName_files, leaving only the Rmd file. Once this is done, you can rebuild the notebook from the tutorials pane.

PROBLEM – Notebooks Other than Topic 13, Topic 16, and Topic 17 are crashing or becoming unresponsive. I can see the notebook, but there is a gray sheen laid over it.

  • This has sometimes happened to me when I “pop-out” the notebooks from the Tutorials tab in the top-right pane of RStudio. As long as you work on the notebook from within the Tutorials tab, then this freezing should not happen.

    • If you are a paid-tier user, you can increase the RAM, which will allow the notebook to be “popped-out” without a RAM overflow issue.
    • Anytime you increase your RAM, remember to decrease it back down when you are done. Increasing the RAM results in an hour of use-time counting as more than one hour against your available “compute time”. For example, changing the RAM to 2GB results in each hour of use time consuming 1.5 “compute hours”.