RStudio: Pushing to Github with ssh-authentication

If RStudio prompts you for a username and password every time you try to push your project to Github, open the shell (Git menu: More/Shel...) and do the following:

1) Set username and email (if you did not do that before)

git config --global user.name "your_username"
git config --global user.email "your_email@example.com"

2) Create SSH key

ssh-keygen -t rsa -C "your_email@example.com" 

In RStudio, go to menu Tools / Global options / Git SVN / View public key and copy the key to your Github account setting (Edit profile / SSH keys / Add SSH key).

To check that ssh-authentication works, try to run

ssh -T git@github.com

and you should get something like

Hi your_username! You've successfully authenticated, but GitHub does not provide shell access. 

3) Change remote.origin.url from HTTPS to HTTP 

It might be Windows specific, but after 1)+2) RStudio still asks me for user name and password. After a long Google search, I have found a solution here and that is

git config remote.origin.url git@github.com:your_username/your_project.git

Hip, Hip, Hurrah!



If it was trivial for you, I do apologize. I am still very bad in guessing what could be useful for somebody and what not so much. That is why I have this blog and Github account in the first place.

One example, last year I published a paper in JSPI journal that improves a test for interaction in some very specific 2-way ANOVA situation (just one observation per group). The paper submission was an odyssey, mostly because of me. In one moment I doubted whether to retract the paper or not and I even did not upload the package to CRAN at first, just put it on Github.

Then I discovered that some guys found it and had built their package using it. They presented the results at UseR! 2013 conference. I might have met one of those biologists but I am sure I never mentioned my package to them. Finally, - and this is a bit embarrassing - I received an email from Fernando Tusell that I misspelled his name in one of my functions.

In summary, even if you see your work as non-essential from your perceptive, the others may have different view. Just do your best and share your results. Github is a perfect place for this.

Get a path to your Dropbox folder

I am currently designing my RStudio - Dropbox - Mardown/Knitter/Wordpress - Github workflow. One problem is that working on multiple machines with different version of Windows means I somehow need to tell R where my Dropbox folder is located.

I used to set the working directory at the beginning of my R scripts but it became tedious to change the path all the time. The solution might be to add definition of 'dropbox.folder.path' variable to .Rprofile files. Or there is a hard way - to write a script detecting Dropbox location automatically.

How to display R code on a web page

Starting to write a blog I need a way how to publish my R codes. One possibility would be to just add some formatting with Pretty R. Nice, but I miss a repository with all codes ever submitted and possibility to make corrections.

The final solution was to create an account on Github and submitting codes via Gist. The only problem was you cannot see the code in the Google Reader. I believe I can live with it.

Getting Genetics Done: Syntax Highlighting R Code, Revisited