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.


Instruction for cross-compiling protobuf 2.6.0 for windows (external protobuf library is not required for linux-like OS becuase it is now bundled in the package)

1. install cross-compiling tool chain on linux
2. download the source
2. first install protobuf on local linux (so that 'protoc' command is available for cross compiling later on
3. the run configure script for win64:
configure --host=x86_64-w64-mingw32 --prefix=/your_path/protobuf/x64 --enable-shared=no --with-protoc=protoc LDFLAGS='-static-libgcc'
4. then run make and make install
5. for win32:
configure --host=i686-w64-mingw32 --prefix=/your_path/protobuf/i386 --enable-shared=no --with-protoc=protoc LDFLAGS='-static-libgcc' 

Alternatively, pre-built pb binary can be downloaded from http://rglab.github.io/binaries/
Once built, set up the environment variable LIB_PROTOBUF similarly.

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.