Eric C. Anderson's Work-life

Open research with GitHub

Working in Windows, minimally

20 October 2015

I used to have a virtual Windows machine set up on my Mac laptop and I would use that for compiling programs up for Windows, and testing things on the Windows side. That laptop was replaced, so I had to set up a new environment for cross compiling. My goal in this is to have to deal with Windows as little as possible, and, when I am in the Windows environment, try to use tools that are familiar (i.e. Rstudio for R programming and a bash shell for nearly everything else.)

In a nutshell here is what I did:

  1. VirtualBox for running a virtual machine
  2. Windows 7 package that Anthony had for the lab.
  3. MinGW/msys for having a Unix-like environment and a C compiler
  4. Git for getting files and repositories into the Windows world
  5. R and Rstudio.

Detailed notes

Setting up VirtualBox

For this, I followed Anthony’s detailed instructions:

MinGW and msys

For this I did a standard install following the directions here


I downloaded and installed Git from Simple install. If you want to use it on the msys command line, you have to put it in the PATH (see below). But, then you also have to configure it, as usual. In the msys terminal I did this:

git config --global ""
git config --global "Eric C. Anderson (From PC)"

# and while at it, did this too:
git config --global credential.helper wincred

and that takes care of it for command line use of git in the msys window. However, it appears that Rstudio takes the settings from elsewhere (or runs git in the dos prompt and it is incapable of getting to the msys-set configs from there). So, in the PC Command Window (not the msys terminal), I did this:

"C:\Program Files\Git\bin\git.exe" config --global ""
"C:\Program Files\Git\bin\git.exe" config --global "Eric C. Anderson (From PC)"

and while you are at it, you should do this, too:

"C:\Program Files\Git\bin\git.exe" config --global credential.helper wincred

which will let Rstudio cache my password so I can push to my repos without putting my password in every time.

msys configuration

In my home directory on msys I created a file .profile that looks like:

exec bash

Then I put there a .bash_profile with this:

if [ -f ~/.bashrc ]; then
    . ~/.bashrc

And then a .bashrc that I put this into:

export PATH='/c/Program Files/Git/bin':$PATH

Here I have set the PATH to look in the bin directory of the Git folder which was installed into C:\Program Files. The single quotes apparently let msys deal with the space in the file name. So, I can access git from the command line on the msys terminal.

R and Rstudio

I just downloaded these and did standard installs. Under Tools -> Global Options I had to point it to the git binary at C:\Program Files\Git\bin\git.exe. It all seems to be working beautifully. One big note, if I want to be able to push stuff up to my repositories on GitHub from the virtual machine I need to check them out from GitHub (through Rstudio, for example) with my GitHub username (eriqande). So, for example, the URL I use for my newhybrids repo when making a new Rstudio project is


A text editor

Anthony recommended notepad++ as a text editor. I downloaded and installed it. Seems to work great.

Opening files from the command line

At this point, just about everything is working well. I made a shortcut to C:\MinGW\msys\1.0\msys.bat which is what gives me an msys terminal that starts in my home directory. Inside that I have a directory called git-repos into which I can clone any repos I need to work on in Windows. And when I am done I can push any changes up.

I pretty much abhor using the Windows Explorer to navigate around, and double-clicking on things bothers the sh*t out of me, so the final thing I want to make sure I can do is open up files on the command line. Turns out that there is a start command in Windows that is already known in the msys bash shell, so all I need to do is add this to my .bashrc:

alias rs='start rstudio'
alias np='start notepad++'

Note that those have to be single quotes.

Now, things are pretty clean. When I get onto my virtual machine I just go to the start menu and choose msys.bat shortcut and I get a bash shell. Then:

cd git-repos/lobster_checkin
rs lobster_checkin.Rproj

opens my lobster_checkin project in Rstudio.


Phew! I can now compile programs up and test on Windows while having to as little ugly Windows interaction as possible. It’s all good except that all the Windows updater crap and its general slow bloatedness that I have to deal with. But, it’s only for a brief tortured time that I have to reside in that world…