Thursday, February 20, 2014

How to Install Shiny Server on OSX

I want to set up the shiny-server to run on an iMac at work so that we can run multiple R-apps over the intranet. According to the docs for Shiny server, OSX is not supported yet (version 1.1.0) so we are going to build it from source and hope for the best!

Instructions for building from source are here. We follow them pretty closely but there are a few gotchas.

The full HowTo is on our GitHub Wiki, here

Monday, September 16, 2013

Creating a Mountain Lion development environment

So I had to set up a new dev environment at work on Mountain Lion. It uses the following components

  • Hombrew
  • Python 2.7.5
  • Django 1.5.2
  • Apache 2.2.25
  • Postgres 9.2.4
  • R 3.0.1
  • Virtualenv
and a bunch of other python libraries and stuff. This system is set up for Bioinformatics development, so there are things that are specific to that. The build is documented on our internal wiki, but I copied the build instructions to the *new* code.ex(python) wiki in my personal github account. The direct link to the build instructions is here.

Friday, September 13, 2013

Understanding Django static files

In struggling to setup a new development/production server on Mountain Lion, I came across this good explanation of django static files and how to configure them.

http://bitsoul.com/2012/10/04/understanding-django-static-files-for-beginners/

Also, this link was also helpful in setting up the environment

http://thecodeship.com/deployment/deploy-django-apache-virtualenv-and-mod_wsgi/

Cheers.

Wednesday, August 28, 2013

Zipping a python dict of lists

Have a python dictionary containing lists. Want to zip the lists together, but don't know the keys. Solution provided from Stackoverflow

http://stackoverflow.com/questions/9828072/zipping-a-python-dict-of-lists


Tuesday, August 20, 2013

How to install mod_wsgi on Mountain Lion

There are apparently changes Apple made in XCode between Lion and Mountain Lion that cause the standard install method to fail. The conventional fix that comes up most often in a Google search at the time of this writing is to create a symlink between the new name of a Toolchain folder and the old name that the installer is supposedly looking for, like this 

sudo ln -s /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/ /Applications/Xcode.app/Contents/Developer/Toolchains/OSX10.8.xctoolchain 

I did this and tried to make mod_wsgi using Homebrew but it throws a cryptic apxs error. Long story short, I eventually compiled mod_wsgi from source myself, but it continued to through various errors, even though things seemed to be configured properly. I went back to a different Mountain Lion machine I had configured earlier using MacPorts. When I did that machine, I had no problems with mod_wsgi or the need for this toolchain symlink. Examining the Portfile for mod_wsgi gives the key. The missing element is adding the --disable-framework flag to the config file. After that, everything works fine. 

This flag should be added to the Homebrew Formula for mod_wsgi. I have never made a Formula before, but maybe one day I will do it. Below is the Gist showing what I did and how it worked.



Monday, August 12, 2013

Fix locate command on Mountain Lion

So apparently upgrading to the Macintosh system Mountain Lion (10.8) breaks the unix "locate" command because it deletes the "nobody" user that was used to own the database. I found this gist that gives instructions how to get it working again. However, in my case I also had to enable the root user and then log in as root in Terminal and run the command /usr/libexec/locate.updatedb as root. Then it finally worked. Sheesh.

Thursday, July 25, 2013

Understanding R plot margins

Came across this great VISUAL explanation of the differences between margins (mar) and outer margin (oma) regions. This is very helpful.