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README
==================== Installing Rgraphviz ==================== Current as of 24 April, 2009 What version of Graphviz do I need? =================================== Graphviz uses a numbering scheme where odd version numbers are development versions and even version numbers are stable releases (meaning 2.23 is a development version). Graphviz greater than 2.2.1 is required. In the context of Rgraphviz, little has changed in the Graphviz internals since version 2.8 or so. There is generally no reason to go for a newer version, it will not provide extra functionality. Indeed using a "new" version of Graphviz often cause Rgraphviz to break. See below for platform specific notes on this. For Windows and OS X, it is common to use a binary version of Rgraphviz. Installation problems typically occur when Rgraphviz is being _used_ not while _installing_ it. In order to check that Rgraphviz is working properly, it is advised to try R> example(layoutGraph) If this runs without an error, most like Rgraphviz is working properly. Windows ======= Most users would want to use a binary (by which we mean pre-compiled) version of Graphviz. When preparing the binary version, it is assumed that a _specific_ version of Graphviz exists on the user's computer - using a different version of Graphviz will most likely cause Rgraphviz to fail. Rgraphviz will inform you of any version inconsistency when loaded. The right version of Graphviz for Bioconductor 2.4 is version 2.20.3. This version will not work with Vista 64 bit, so the Vista 64 bit user will need to compile from source, and in addition make sure that a version strictly greater than 2.22. Here are the steps to INSTALL Graphiz/Rgraphviz if you want to use the _binary_ version. Using the Windows binary ------------------------ o. install Graphviz ***2.20.3.1*** Windows ***binary*** distribution from http://www.graphviz.org/pub/graphviz/stable/windows/graphviz-2.20.3.1.msi in a directory that we'll call $DIR. We use the following as an example: C:\Graphviz-2.20.3 If you install it in other dir, just use your dir correspondingly. o. Add Graphviz' bin diretory to the user PATH variable, e.g., c:\Graphviz-2.20.3\bin o. Check the configuration by starting a new DOS window and displaying the PATH environment variable, e.g., c:\> echo %PATH% o. Use biocLite('Rgraphviz') to install Rgraphviz Compiling from source on Windows -------------------------------- If you want to compile Rgraphviz from source you can use any version of Graphviz you want (but in general, stay away from development versions). Older versions of Graphviz (2.2.1 to say 2.16) might not work). o. Install Graphviz as outlined in the previous section o. Set the following Windows environment variables accordingly (control panel -> systems -> Advanced -> Environment Variables ): (a) create new user variables: GRAPHVIZ_INSTALL_DIR (e.g., C:\/Graphviz-2.22) GRAPHVIZ_INSTALL_MAJOR (e.g., 2) GRAPHVIZ_INSTALL_MINOR (e.g., 22) GRAPHVIZ_INSTALL_SUBMINOR (e.g., 2) Notice the way "\/" are used for the paths above. (b) add to user variable 'PATH': %GRAPHVIZ_INSTALL_DIR%/bin e.g., C:/Graphviz-2.22/bin o. run "R CMD INSTALL Rgraphviz" or "biocLite("Rgraphviz")' as usual OSX installation ================ Most users would want to use a binary version of Rgraphviz. This means obtaining the exact same version of Graphviz as is being used on the build machine. Rgraphviz will inform you of any version inconsistencies when loaded. At the moment the Graphviz website only distribute binaries for Leopard. For Bioconductor 2.4 you will need version 2.22.2 from their website. For OS X Tiger you will need to compile from source (Bioconductor 2.4 uses a binary version of Graphviz from Simon Urbanek, but he has removed his link to this version). According to Eric Wexler (ewexler@ucla.edu): Rgraphviz will not load (at least under leopard) unless the user has the developer Xcode tools installed. It was very frustrating untill I figured this out. Please pass it on in the Rgraphviz install under OSX instructions Source based installation ========================= The Rgraphviz package depends on the Graphviz library which can be obtained from http://www.graphviz.org/. At present, Rgraphviz is known to work with Graphviz versions greater than or equal to 2.2 (note however that a bug in the neato layout routine makes it preferable not to use versions 2.4, 2.6 and 2.8) To install Graphviz: 1. Download the source tarball from http://www.graphviz.org/ 2. Unpack the distribution (tar -xzvf) 3. Read the Graphviz installation instructions. Basically, you should be able to do: ./configure make make install A word of warning, especially on the Mac OS X platform: Rgraphviz may not work if Graphviz is compiled with optimization. In order for Rgraphviz to find your version of Graphviz you can either make sure that pkg-config is installed on your system (http://pkgconfig.freedesktop.org/wiki/), you can use the default location (/usr/local) or you can use --with-graphviz as a installation argument (use it like # R CMD INSTALL --command-args='--with-graphviz=/usr/local' Rgraphviz_**** ) If you install Graphviz to a non-standard location and you are using pkg-config, you may need to set the PKG_CONFIG_PATH environment variable to tell pkg-config where the Graphviz metadata lives. Here is an example: export PKG_CONFIG_PATH=/home/me/graphviz/lib/pkgconfig Note that older versions of Graphviz use a configure script called dotneato-config which must be in your PATH for Rgraphviz to find it. This is instead of the pkg-config setup.