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R clustering not working - R env variable config?

#12

I tried to run an analysis with the hierarchical clustering option turned on and it threw an exception:

Here's the developement log entry:

[Thu Jan 15 16:45:22 2009] [error] [client 127.0.0.1] Premature end of script headers: visualize, referer: http://local.snplotyper.mcw.edu/... cannot find system Renviron Fatal error: unable to open the base package

Looks like it cant find the R Environment variable or something similar. I have this set in my shell environment which may be why it used to work before. Need to figure out where to set this variable for passenger

Reported by simont · January 16th, 2009 @ 09:03 AM

State: resolved
Milestone: none
Assigned to: jgeiger jgeiger

Activity

  1. jgeiger
    jgeiger
    • Tag set to environmental, passenger, r, r_home
    • State changed from new to resolved

    The R_HOME variable is set in config/initializers/startup.rb

    for me it's set to ENV['R_HOME']='/opt/local/lib/R/' and below that, it properly sets the variable for dione and atlas.

    Depending on where your R is located, you may need to change that variable.

    Another solution would be to setup something like described here, but it would still require modifications to the startup file to remove the settings in there. http://blog.phusion.nl/2008/12/1...

    January 16th, 2009 @ 09:16 AM

  2. simont
    simont
    • Tag cleared.

    Yes - that is the problem. R is located at '/Library/Frameworks/R.framework/Resources' on my machine (I didnt use macports for the install). I had just found the blog post you referenced.

    It would seem like we should put this type of environment configuration code into the appropriate config/environments/*.rb files (or maybe in the global config/environment.rb) so that they can be set for local development and production, rather than having the various dev and production machine setups in the startup.rb

    I think that either way will work but maybe using the config/environment* approach is more appropriate? What do you think?

    January 16th, 2009 @ 09:36 AM

  3. jgeiger
    jgeiger

    This was one of the things that I was going to need to deal with when we release the source code, since it's going to be different for everyone.

    I think I had the idea to set it up in the different environments, but left it in startup.rb since it was common to everything, and if I decide to run my local installation as a production setup, I don't need to mess with changing that every time. It's a variable that needs to be set per machine, and not really per rails environment.

    January 16th, 2009 @ 09:59 AM

  4. sara ceejay
    sara ceejay
    • Milestone order changed from 0 to 0

    I’ll definitely be subscribing to your site. Keep up the good posts cars for sale

    August 14th, 2011 @ 02:50 PM

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