le23petit

## The first R script reads in parameters from a project-specific file that is specified in the script. This should be the only time that variables ## are specified and hard-coded. Everything downstream of this first file takes on the variables assigned here.

source("R_pipeline_R521G_readParamFile.R")
#source("R_pipeline_WTTG_readParamFile.R")

## This script loads the Biocinstaller and downloads/updates all necessary libraries for the project and analysis
source("R_pipeline_libraries.R")

## During this first script, you may be asked to press "a/s/n" (a or s or n) to indicate
## whether you wish to update all, some, or none of the packages. I suggest "a" 

le23petit

First-time gist user -- sorry if I make mistakes in reporting. 

Basic issue: I can get Homebrew to install software from any website except Sourceforge (specifically this website: http://sourceforge.net/projects/machomebrew/files/Bottles/). Installing other software may require dependencies that are found on this website (i.e. cmake, pkg-config) and the typical installation of such software fails. 

I've been through the usual procedures. My 'brew update' says I'm already up-to-date. The output of brew doctor and the install are the following:

```
Joachims-Mac-Pro:Homebrew joachimherz$ HOMEBREW_MAKE_JOBS=1 VERBOSE=1 brew install cmake
==> Downloading https://downloads.sf.net/project/machomebrew/Bottles/cmake-2.8.9.mountainlion.bottle.tar.gz
/usr/bin/curl -qf#LA Homebrew 0.9.3 (Ruby 1.8.7-358; Mac OS X 10.8.2) https://downloads.sf.net/project/machomebrew/Bottles/cmake-2.8.9.mountainlion.bottle.tar.gz -o /Library/Caches/Homebrew/cmake-2.8.9.mountainlion.bottle.tar.gz