The Ubuntu Incident

Problem

You want to use R Markdown. How to install it?

(Inside R Markdown, you can embed Python too. Actually, that’s what I want to use.)

Solution

First, you must have R:

$ sudo apt install r-base-core

Make sure that it’s installed correctly. Start the R shell with the command “R“. Exit with Ctrl+d.

Install RStudio (optional, but recommended):

• visit https://www.rstudio.com/products/rstudio/
• download RStudio Desktop and install it

Launch RStudio. Select File -> New File -> R Markdown… RStudio will offer to install a lot of packages that are necessary for working with .Rmd files. Select Yes and let it work. It’ll take a few minutes.

To have Python support, install the package “reticulate”. Enter the following in the R shell:

> install.packages("reticulate")

Visual Studio Code support

For working with .Rmd files, you don’t have to use R Studio. Personally, I prefer VS Code. To have R support, install the extension “R” by Yuki Ueda. It provides syntax highlighting for .Rmd files and lots of other goodies.

This VS Code extension requires the R package “‘languageserver”. Install it in the R shell:

> install.packages("languageserver")

For the first time it failed for me. It turned out that the Ubuntu package libcurl-dev was missing. This is a metapackage and I had to install the package libcurl4-openssl-dev. After this, install.packages("languageserver") in the R shell succeeded.

Restart VS Code, open an .Rmd file and now everything should be OK. Right click on the file name, select Open Preview, and you should see the rendered output.

Examples

See here: https://github.com/jabbalaci/blog-assets/tree/master/20210929-Rmd

Update (20211018)

VS Code is great, but it doesn’t update the PDF. When you open a preview, it generates a temporary HTML output. If you want to update the PDF output automatically, read this post of mine.

Update (20211216)

After a system update, I got an error that some .so file was missing. In this case, launch R and issue the command “update.packages()“. This command updates all installed packages.

If you get a warning that some packages won’t be updated, try this: “update.packages(oldPkgs = old.packages())“.

I also got a warning that the permission of /usr/lib/R/library is not OK. I launched R as a normal user and I had no write permission on this folder. I changed the owner of this folder to my normal user and the issue got solved.

Update (20230128) — Installing under Manjaro Linux

I installed the whole thing on a fresh Manjaro box and here are the steps I had to perform. This is a short(er) summary of everything mentioned above.

In the following, $ signifies the Bash shell and > signifies the R shell.

Install RStudio:

$ yay -S rstudio-desktop-bin

Don’t launch it yet. Verify if R is available:

$ R

Tap Ctrl-D twice to quit the R shell.

Install these packages:

$ yay -S openssl-1.1
$ yay -S texlive-core texlive-latexextra
$ yay -S gcc-fortran
$ yay -S pandoc
$ yay -S tk
$ yay -S okular

Modify the owner of /usr/lib/R/library to make it writable by you:

$ cd /usr/lib/R
$ sudo chown -R {user}:{group} library/

Where {user} is your username and {group} is your group. The value of the two may be the same.

Start RStudio:

$ /usr/lib/rstudio/rstudio &

It’s a good idea to make a launcher script for it.

In RStudio: File -> New File -> R markdown…, then choose “Yes” to install the dependencies.

RStudio will (probably) install the following R packages:

• base64enc
• digest
• evaluate
• glue
• highr
• htmltools
• jsonlite
• knitr
• magrittr
• markdown
• mime
• rmarkdown
• stringi
• stringr
• xfun
• yaml

Install the following R packages too. Remember, now > means the R shell:

> install.packages("reticulate")
> install.packages("Matrix")
> install.packages("languageserver")

Finally, update all R packages:

> update.packages()

If you get an error, you may have to redo this step:

$ cd /usr/lib/R
$ sudo chown -R {user}:{group} library/

Issue this command again:

> update.packages()

If everything went well, it won’t update anything (since everything is already up to date).

At the end, try to convert an .Rmd file to PDF:

$ Rscript -e "rmarkdown::render('test.Rmd')"

It should work.

Now that everything is installed, you can remove RStudio if you want. We’ll be able to compile .Rmd files to PDF in the command line, we won’t need RStudio for that. This step is optional:

$ yay -R rstudio-desktop-bin

Update (20230131) — Installing under Ubuntu 22.04

I installed the whole thing on a fresh Ubuntu 22.04 box too. This is a short(er) summary of everything mentioned above. Note that I had problem with installing RStudio (openssl conflict), so I skipped that part. However, RStudio is not necessary, it was just optional.

In the following, $ signifies the Bash shell and R> signifies the R shell.

Here are the steps:

$ sudo apt install r-base r-base-dev
$ sudo apt install libxml2-dev
$ sudo apt install texlive
$ sudo apt install texlive-latex-extra
$ sudo apt install pandoc

Verify if R is available:

$ R

Tap Ctrl-D twice to quit the R shell.

Make the folder site-library/ writable:

$ cd /usr/local/lib/R
$ sudo chown -R {user}:{group} site-library/

Where {user} is your username and {group} is your group. The value of the two may be the same.

Install these R packages:

R> install.packages("base64enc")
R> install.packages("digest")
R> install.packages("evaluate")
R> install.packages("glue")
R> install.packages("highr")
R> install.packages("htmltools")
R> install.packages("jsonlite")
R> install.packages("knitr")
R> install.packages("magrittr")
R> install.packages("markdown")
R> install.packages("mime")
R> install.packages("rmarkdown")
R> install.packages("stringi")
R> install.packages("stringr")
R> install.packages("xfun")
R> install.packages("yaml")
R>
R> install.packages("reticulate")
R> install.packages("Matrix")
R> install.packages("languageserver")

Make these folders writable:

$ cd /usr/local/lib/R
$ sudo chown -R {user}:{group} site-library/

$ cd /usr/lib/R
$ sudo chown -R {user}:{group} library/

Update all the R packages:

R> update.packages()

Finally, try to convert an .Rmd file to PDF:

$ Rscript -e "rmarkdown::render('test.Rmd')"

It should work.

Acknowledgement

I would like to say thanks to my students, Erik Pál and Antal Svec for their help for testing the installation process under Manjaro and Ubuntu.

Links

• R Markdown installation for Windows
• example: https://github.com/jabbalaci/blog-assets/tree/master/20210929-Rmd