Current as of 25 Oct, 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
If this runs without an error, most like Rgraphviz is working properly.
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
The right version of Graphviz for Bioconductor 2.5 is version
188.8.131.52. This version will not work with Vista 64 bit, so the user will
need to compile from source, and in addition make sure that a version
strictly greater than 2.22 is used.
Here are the steps to INSTALL Graphiz/Rgraphviz if you want to use the
Using the Windows binary
o. install Graphviz ***184.108.40.206*** Windows ***binary*** distribution from
in a directory that we'll call $DIR. We use the following as an example:
If you install it in other dir, just use your dir correspondingly.
o. Add Graphviz' bin diretory to the user PATH variable, e.g.,
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
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:\/Graphviz2.20)
GRAPHVIZ_INSTALL_MAJOR (e.g., 2)
GRAPHVIZ_INSTALL_MINOR (e.g., 20)
GRAPHVIZ_INSTALL_SUBMINOR (e.g., 3)
Notice the way "\/" are used for the paths above.
(b) add to user variable 'PATH': %GRAPHVIZ_INSTALL_DIR%/bin
o. run "R CMD INSTALL Rgraphviz" or "biocLite("Rgraphviz", type = "source")'
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 2.5 you will need version 2.22.2 from their
For OS X Tiger you will need to compile from source (Bioconductor 2.5
uses a binary version of Graphviz from Simon Urbanek, but he has
removed his link to this version).
According to Eric Wexler (firstname.lastname@example.org): 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:
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 --configure-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:
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.