Dev Instructions - nolanlab/spade GitHub Wiki


  1. R 3.x. Note that many of SPADE's dependencies are no longer available for R 2.15.x as of October 2013.
  2. igraph
  3. flowCore

Building and Installing

The SPADE package has a C++ core that must be built before use. SPADE successfully builds on Linux, OSX and Windows (with Rtools), although Windows users will not be able to take advantage of the OpenMP parallelization used within SPADE. SPADE can be installed from the command line via


On Windows, you will need to install the Rtools that matches your R distribution. After installation make sure that your PATH contains the neccessary Rtools binary directories, e.g.:

  1. Open Control Panel -> System

  2. Click on Advanced Tab and then on Environment Variables

  3. Highlight PATH and click Edit

  4. In the character string in Variable Value, make sure the following appear (before other/older compilers):

    c:\Rtools\bin;c:\Rtools\gcc-4.6.3\bin;c:\Program Files\R<your R version>\bin;

Building Packages

Source packages can be built with

$ R CMD build <SPADE PATH>

and binary packages with

$ R CMD build --no-vignettes --binary <SPADE PATH>

Tips and Resources

⚠️ ** Fallback** ⚠️