Quantum Forest

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Rstudio and asreml working together in a mac

December and January were crazy months, with a lot of travel and suddenly I found myself in February working in four parallel projects involving quantitative genetics data analyses. (I’ll write about some of them very soon)

Anyhow, as I have pointed out in repeated occasions, I prefer asreml-R for mixed model analyses because I run out of functionality with nlme and lme4 very quickly. Ten-trait multivariate mixed model with a pedigree, anyone? I thought so. Well, there are asreml-R versions for Windows, Linux and OS X; unsurprisingly, I use the latter. Installation in OS X is not particularly complicated (just follow the instructions in this PDF file) and remember to add and export the following environment variables in your .bash_profile:

These instructions work fine if one uses asreml-R in a Terminal window or if one uses a text editor (emacs + ESS, VIM + VIM-R, Textmate + R + R console bundles, etc). However, I couldn’t get the default R GUI in OS X (R.app) or Rstudio (my favorite way to work with R these days) working.

I would use library(asreml) or require(asreml), which would create no problems, but as soon as I used the function asreml(...) I would get an error message stating that I did not have a valid license. Frustrating to say the list (I even considered using emacs for the rest of my life, can you believe it?), because it meant that Rstudio was not being able to ‘see’ the environment variables (as posted in this question). The discussion on that question points to a very useful part of the R help system, which explains the startup process for R, suggesting a simple solution: create an .Renviron file in your home directory.

Thus, I simply copied the previously highlighted code in a text file called .Renviron, saved it in my home directory and I can now call asreml-R from Rstudio without any problems. This solution should also work for any other time when one would like to access environment variables from Rstudio for OS X. Incidentally, Rstudio is becoming really useful, adding ‘projects’ and integrating version control, which means that now I have a(n almost) self-contained working environment.

P.S. Note to self: While I was testing environment variables in my .bash_profile I wanted to refresh the variables without rebooting the computer. The easiest way to do so is typing . .bash_profile (yes, that starts with dot space). To check the exported value of a specific variable one can use the echo command as so echo $ASREML_LICENSE_FILE, which should return the assigned value (/Applications/asreml3/bin/asreml.lic in my case).

6 Comments

  1. Hi Luis, very helpful post. Though, have you had any trouble running update() on a previously run asreml model?

    • Luis

      2012/02/21 at 10:23 pm

      Haven’t tried really. I’m not much of an update type of person. I’ll give it a go tomorrow to see what happens Update: no problems with update().

  2. Hi Luis, have you ever considered running mixed-model analyses in parallel with foreach package and AsREML ?

    I’ve got some variables issues, perhaps due to the manage of environment by foreach.

    Thanks.

    • Luis

      2012/05/06 at 9:29 am

      Hi Kevin,

      I haven’t tried it before, but it sounds useful enough to give it a go. A while ago I needed to run a bit over 2,000 bivariate analyses and I just left running the program for over a week. I’ll try to run a small subset with foreach this coming week (although I have only a couple of cores in the computer). It would be neat to run ASReml in our supercomputer, but I’d need the source to compile it.

  3. Marcio Resende

    2013/04/18 at 2:00 pm

    Thanks Luis,
    I was already frustrated with that. Very helpful topic
    Regards,

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