4 Version control with Git and GitHub

Excuse me, do you have a moment to talk about version control?2

There is a lot to say about GitHub and why one may use it. An extensive discussion on this topic and basically everything you will learn in this chapter can be found in Happy Git and GitHub for the useR.

This chapter will introduce the basics on how to collaborate with other people using GitHub, which is probably the reason why you are reading this in the first place.

4.1 Headstart into Git and GitHub with RStudio

The following post provides a quick introduction on how to set up Git and GitHub and connect your GitHub account with RStudio: https://www.bioinformatics.babraham.ac.uk/training/RStudio_GitHub/Initial_setup.html.

Once this is done, you should be able to connect and download online GitHub repositories and are able to start collaborating on projects immediately.

4.2 Basic GitHub routine

Add files:

git add .

…

4.3 Common problems

The following should provide a summary of common problems encountered when using Git. It also serves as a reminder for myself.

4.3.1 Too large files

Original post of the answer: https://stackoverflow.com/a/17890278.

  1. Download the BFG Repo-Cleaner jar file “bfg-x.xx.x.jar” (e.g. “bfg-1.14.0.jar”) from https://rtyley.github.io/bfg-repo-cleaner/.

  2. Place the file in the directory of your R project, the same of the .git folder.

  3. Open the terminal in this folder (e.g. via RStudio > Git > Shell…)

  4. Type in the terminal:

java -jar bfg.jar --strip-blobs-bigger-than 100M

The file name “bfg.jar” must match the name of your jar file and the file size limit can be changed (e.g. 50M for 50 )

  1. If you do not encouter an error, type:
git gc --prune=now --aggressive

to clean the dead data.

If you encounter the following error Warning : no large blobs matching criteria found in packfiles - does the repo need to be packed?, refer to this post https://stackoverflow.com/q/61769785 and type git gc prior to step 4.

4.3.2 .gitignore does not instantly work

Just do:

git rm -r --cached .
git add .
git commit -m "Drop files from .gitignore"

  1. https://peerj.com/preprints/3159v2/↩︎