Page Comparison

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• Operating System: what ever floats your boat.
• IDE: Eclipse commonly used and free
• Wiki / Issue Tracker / Code Browsing and Reviewing / Automated Builds: we have a Jira Studio subscription  (Mike Kellen as admin)
• Code versioning: SubversionGit, hosted by Atlassian as part of our Jira Studio subscriptionon GitHub.
• Build System: Maven
• Build repository manager: see Sage's hosted Artifactory service see jFrog website for info (John Hill and Mike Kellen as admins)

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You can also use Jacoco for code coverage. For more information, see Jacoco Code Coverage.

Java

Libraries

At this point we don't have any strict licensing requirements, however to maintain flexibility we have to be careful about licenses for software we choose to incorporate into our system.  The best licenses are open source licenses without copy-left provisions (e.g. Apache License) that give us maximal flexibility in what we later do with the code base.  Some strong copy-left licenses (e.g. GPL) would impose licensing requirements on us (e.g. force us to use GPL ourselves) if we chose to redistribute the code base at a later date. For now, we should just be aware of the mix of licenses incorporated into our projects, and have a bias for open source, non-copy left licenses.

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• R Installation
• Bioconductor
• Eclipse Plugin for R
  • Getting Started Guide for R Eclipse Plugin
• You'll also need to install some tools that R package builds depend upon:
  • Windows
    1. Download and unpack https://s3.amazonaws.com/nicole.deflaux/RStuff/DocumentationAndToolsForBuildingRPackageOnWindows.zip
    2. Follow the instructions on the first three slides of doc/buildingPackages110406.pdf for how to install all the toolsR Tools
    3. If you have Cygwin installed, do NOT install the Cygwin DLLs (the installer has more detailed instructions)
    4. Install MikTeX
  • Mac OSX
    1. Install XCodeso that you have a C compiler
       • Be sure to select installation option "UNIX Development Support"
       • If you install from the "App Store" and are not presented with this option, the following is a work-around:

         • After installing Xcode, go to XCode>Preferences...

         • Go to Downloads > Command Line Tools > Install

         • Follow the prompts to register as an Apple Developer and download the tools.

    2. Install MacTex

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