Tuesday, September 20, 2016

Basic version control with Git and GitHub in RStudio in both Windows and Ubuntu

I don't remember why, but a few months ago I decided I finally had to try out this "version control" thing.  I love it SO MUCH.  Github and git can be a bit confusing initially, especially as I had the added layers of making it work with RStudio and on two different operating systems, but now that I've got it going it's great.

I started and installed git with this tutorial for starting with RStudio and git/github on Windows.  To understand how push and pull work (as this confused me), I read through several pages.  I started with this graphic of the workflow.  That one ignores RStudio and is just about git and github.  This essay has great illustrations and more details (code to use in the shell/terminal in RStudio).  Finally this one is github/git only (no RStudio) but I still found it helpful to read about push/pull/branching in yet another way.

Next problem was that when I opened up my project on Ubuntu, git said all lines in files were modified when I had not actually changed all lines.  This turned out to be an issue between line endings in Windows and linux type systems, and this would hide any actual changes if I had just made a few, so just committing every time was not a good option.  I decided to go with adding a gitattributes file in each repository (so all users will get the same line endings regardless of who I share with).  I added a gitattributes file (I combined general settings and the R settings available here) into the main project directory.  For a directory that I had already used a lot (so lots of files with the wrong line endings) I followed these steps for the per-repository settings, including opening a shell in RStudio to input their code for refreshing my repository.  (I backed up on a separate hard drive first in case I totally messed something up.)  At first this didn't work, because I have a dual-boot situation, not using the files in two separate computers, according to this top answer.  I ran the two lines of code in the top answer's update and that fixed it.
$ git config core.eol lf
$ git config core.autocrlf input

I now copy the custom attributes file into any new R repository I have, run those two lines, and haven't had any problems going between operating systems now.  Keep in mind this is where I have two different operating systems accessing the SAME FILES on the SAME drive/partition.  If I understand correctly the gitattributes file should work fine without the extra lines if you have different computers, but I have not yet tested this.

Finally, when I tried pushing in RStudio to github, I kept getting two errors:
error: unable to read askpass response from 'rpostback-askpass'
fatal: could not read Username for 'https://github.com': No such device or address

As I had already done the git config steps to add my github username and github email address, I looked up the error and found that I needed to create a private/public key pair because RStudio has issues authenticating apparently.  I followed the top answer's links, which resulted in my changing the url in the .config file and then generating and linking an SSH key.  I did this on both Ubuntu and Windows following the same instructions, resulting in two new key pairs (one for Ubuntu, one for Windows).

2016/11/04 edit: I got the askpass response error again in a new repository, but on the same computer that already had the SSH keys.  In this case I only changed the url in the .config file and then it worked swimmingly.  I've also had consistent success with line endings using the custom .gitattributes file followed by the two git config commands above.

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