Merge pull request #318 from csc-training/r-lists-fix

fix list numbering in r installing tutorial

part-2/installing/r.md

@@ -13,71 +13,71 @@ permalink: /hands-on/installing/installing_hands-on_r.html
 
 💬 A pre-installed R environment is available on Puhti.
 
-1.  To check available module versions, run:
+1.  To check available module versions, run:    
 
-``` bash
-module spider r-env
-```
+    ``` bash
+    module spider r-env
+    ```
 
 2.  There are several ways to use R in `r-env` on Puhti:
 
--   Interactive jobs on a compute node, using either the R console or RStudio\
-    💡 The easiest way to launch RStudio is to use the Puhti web interface at [www.puhti.csc.fi](https://www.puhti.csc.fi/)
--   Non-interactive batch jobs
--   Interactively on the login node, using the R console (**only** for moving data, checking package availability, installing packages)
+    - Interactive jobs on a compute node, using either the R console or RStudio  
+      💡 The easiest way to launch RStudio is to use the Puhti web interface at [www.puhti.csc.fi](https://www.puhti.csc.fi/)
+    - Non-interactive batch jobs
+    - Interactively on the login node, using the R console (**only** for moving data, checking package availability, installing packages)
 
-For example, to launch the R console in an interactive job, open a shell with `sinteractive` and then
+    For example, to launch the R console in an interactive job, open a shell with `sinteractive` and then
 
-``` bash
-module load r-env
-start-r
-```
+    ``` bash
+    module load r-env
+    start-r
+    ```
 
 💡 See the [r-env documentation](https://docs.csc.fi/apps/r-env/) for further instructions on different ways to launch R on Puhti.
 
 💬 It is also possible to [install R packages yourself](https://docs.csc.fi/apps/r-env/#r-package-installations).
 
--   However, check first if what you need is already available in `r-env`. The module contains more than 1300 R packages! The easiest way to check if a package is available is trying to load it with the command `library(packagename)`.
+☝🏻 However, check first if what you need is already available in `r-env`. The module contains more than 1300 R packages! The easiest way to check if a package is available is trying to load it with the command `library(packagename)`.
 
-#### How to install an R package on Puhti
+## How to install an R package on Puhti
 
--   Note that your own package installations are:
-    -   project specific
-    -   R version specific
-    -   located in the `/projappl` directory of your project
+- Note that your own package installations are:
+  - project specific
+  - R version specific
+  - located in the `/projappl` directory of your project
 
 1.  Create a folder for your R packages in `/projappl` (open a login node shell in the [Puhti web interface](https://www.puhti.csc.fi/) or log in to Puhti with SSH):
 
-``` bash
-# First navigate to /projappl/<project>, then
-mkdir project_rpackages_<rversion>
-```
+    ``` bash
+    # First navigate to /projappl/<project>, then
+    mkdir project_rpackages_<rversion>
+    ```
 
 2.  Start an R session (launch RStudio in the [Puhti web interface](https://www.puhti.csc.fi/) or launch the R console in an interactive shell session: start the job with `sinteractive` -\> `module load r-env` -\> `start-r`). In R, add the folder you created above to the list of directories where R will look for packages:
 
-``` r
-.libPaths(c("/projappl/<project>/project_rpackages_<rversion>", .libPaths())) 
-```
+    ``` r
+    .libPaths(c("/projappl/<project>/project_rpackages_<rversion>", .libPaths())) 
+    ```
 
-Assign `libpath` to point to this directory (not strictly necessary but can make life easier):
+    Assign `libpath` to point to this directory (not strictly necessary but can make life easier):
 
-``` r
-libpath <- .libPaths()[1]
-```
+    ``` r
+    libpath <- .libPaths()[1]
+    ```
 
 3.  Install the package (again, defining `lib = libpath` to specify the installation location is not strictly necessary but recommended)
 
-``` r
-install.packages("packagename", lib = libpath)
-```
+    ``` r
+    install.packages("packagename", lib = libpath)
+    ```
 
-For example, you can try installing a package called `beepr` with
+    For example, you can try installing a package called `beepr` with
 
-``` r
-install.packages("beepr", lib = libpath)
-```
+    ``` r
+    install.packages("beepr", lib = libpath)
+    ```
 
-Finished! The R package is now ready to be loaded and used. Try loading `beepr` with `library(beepr)`.
+    Finished! The R package is now ready to be loaded and used. Try loading `beepr` with `library(beepr)`.
 
 💡 The package location is defined only for the current R session! R has to be reminded of the location at the start of every R session or script where you want to use the project-specific package by running this command again:
 
@@ -87,6 +87,6 @@ Finished! The R package is now ready to be loaded and used. Try loading `beepr`
 
 💡 Instead of installing a missing package for your own project, you can ask for a module-wide installation for all users by contacting [CSC Service Desk](mailto:[email protected])
 
-#### More information
+## More information
 
 💡 Read more about using R on Puhti in [r-env documentation](https://docs.csc.fi/apps/r-env/) in Docs CSC.