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Duncan Murdoch provides Rtools which ease the installation of tools that are needed to do R package development/testing on MS Windows. The Rtools is a collection of various tools. However, if you also use Cygwin on MS Windows, you can expect problems since Rtools also includes some tools from Cygwin. The problem is the version collision of fundamental Cygwin libraries. Basically, this means that you will not be able to use Cygwin and if you have C:/Cygwin/bin in the PATH envorinmental variable, you can expect problems also in the Command Prompt. You can try to fuse both “worlds” as described in the documentation, but is seems tricky. I just used the following to make my life easier:
• Install Rtools and do not modify the PATH envorinmental variable –> this means that you will still be able to use Cygwin without problems
• Create a BAT script (say on the Desktop) with the following content
rem --- Add RTools to the PATH ---
set PATH=c:ProgramsRRtoolsbin;c:ProgramsRRtoolsperlbin;c:ProgramsRRtoolsMinGWbin;%PATH%

rem --- Start the Command Prompt ---
cmd
• Start the script with the double click and you will get a working environment for R package development/testing
Btw. under Linux or Mac you can test the functionality of R package under MS Windows using the win builder at http://win-builder.r-project.org provided by Uwe Ligges