You need the following C/C++ libraries to build flowWorkspace from source (using Rtools for windows users). -- libxml2 Linux users ============= These libraries are installed in non-standard locations, please pass their 'prefix' to the configure script. e.g. R CMD INSTALL flowWorkspace/ --configure-args='--with-xml=/home/yourname/xml_dir' Also make sure these libraries can be found by R at run-time by adding them to LD_LIBRARY_PATH environment variable. e.g. export LD_LIBRARY_PATH=/home/yourname/xml_dir:$LD_LIBRARY_PATH Add this to your `~/.profile` file can avoid doing so next time. Windows users ============= To install libxml2: 1. Download the pre-built binary from http://rglab.github.io/binaries/ 2. unzip it (e.g. to c:\libxml2) and you should see the directory structure like below in both i386 and x64 folder |-include |---libxml2 |-----libxml (all *.h are here) |-lib (we should have static libary libxml2.a here) 3. set up the environment variable LIB_XML2 in order for flowWorkspace to find its library files and header files. You can do this by: * right click "Computer" and select "Properties" * click "Advanced system settings" and select "Advanced" tab * click the "Environment Variables" button and bring up the dialog box * click the "New" button and enter "LIB_XML2" in the "Variable name" field, and /path/to/your/libxml2 (e.g. c:/libxml2) in the "Variable value" field. Remember to use "/" instead of "\" as the directory delimiter. You can download Rtools at http://www.murdoch-sutherland.com/Rtools/ which provides the resources for building R and R packages. You should add to the Path variable the paths to the various components of Rtools. Please read the "Windows Toolset" appendix at http://cran.r-project.org/doc/manuals/R-admin.html#The-Windows-toolset for more details.