learnr.proto

Learnr tutorials for the Functional Genomics course.

Run

To run these tutorials as a student (a user on the server where the tutorials are deployed), run:

.libPaths("/path/to/learnr.proto/renv/library/R-3.6/x86_64-pc-linux-gnu");
learnr.dashboard::start_tutorial("fg1");  # available tutorials: fg1, fg2, fg3

The tutorials can also be started as a background process (not occupying Rstudio). To start background tutorials, run:

learnr.dashboard::start_background_tutorial("fg1")

If the tutorials are missing exercises, images or behave oddly, try restarting R with .rs.restartR()

Run on rstudio.science.ru.nl

1. If you are working remotely, log into the science.ru.nl network with a VPN (eduVPN or vpnsec)

2. Go to rstudio.science.ru.nl

3. Log in with your science account

4. run:

.libPaths("/scratch/learnr/learnr.proto/renv/library/R-3.6/x86_64-pc-linux-gnu");
learnr.dashboard::start_background_tutorial("fg1");  # available tutorials: fg1, fg2, fg3

Development install

1. Install R 3.6.3.

   Conda example

   conda create -c conda-forge -n R_3.6 conda-forge::r-base=3.6.3 r-renv r-curl \
   r-boot r-class r-cluster r-codetools r-foreign r-KernSmooth r-lattice r-MASS \
   r-Matrix r-mgcv r-nlme r-nnet r-rpart r-spatial r-survival --yes;
   
   conda activate R_3.6;
   

2. Install Rstudio (Server).

3. In Rstudio, create a "New Project..." > select "Version Control" > "Git" > Repository URL: https://github.com/vanheeringen-lab/learnr.proto

4. Install all packages with renv::restore(). On Windows you will need to install Rtool35.

Deployment

Deployment makes the tutorials, including the required libraries, available to all users on a machine.

1. Perform the development install to create the renv library.

2. Install the tutorials in this library, and make the library accessible to all users with learnr.dashboard:::deploy_learnr_pkg()

3. Update the .libPaths() command in the Run section with the location of the renv library.

Development notes & troubleshooting

• The learnr.dashboard package has manual pages for each function. In the R console, type ?learnr.dashboard::: and use autocomplete to browse all functions (including the reserved ones).

• Tutorials may not work on rstudio.science.ru.nl in markdown mode (because the host adress is not localhost).

• To run a tutorial as Markdown (quick, but may differ from tutorials), open the .Rmd file and press "Run document"

• The settings menu (gear wheel symbol) can be used to change the display method of the tutorial.

• To add a new tutorial to the repo, copy the template folder in inst/tutorial and rename both the folder and .Rmd file (example: inst/tutorials/fg4/fg4.Rmd). Keep the name simple and short, as they must be typed to start the tutorial.

• If there are no boxes to input code, try restarting R with .rs.restartR().

• If the tutorial did not update after a change, remove the .html file and try again.

• If you pressed "Run document" and got an error mentioning "file exists", remove the .html file and try again.