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README.md

R package: Rgraphviz

This is the developer version of Bioconductor package Rgraphviz. Install in R as:

source('http://bioconductor.org/biocLite.R')
biocLite('Rgraphviz')

Additional installation tips

Rgraphviz now comes bundles with Graphviz. This should greatly simplify installation on all platforms, compared with earlier versions.

While it should not be necessary, we still allow for the use of an external Graphviz (external to Rgraphviz) at install time, except on Windows (this used to be supported on Windows but this is no longer true). This is indicated by the configure option --with-graphviz.

A direct specification of an external Graphviz at install time would be

R CMD INSTALL --configure-args='--with-graphviz=/usr/local' Rgraphviz_*.tar.gz

In this case (with $DIR=/usr/local), the configure script assumes the presence of

$DIR/include/graphviz
$DIR/lib/graphviz

as is the default when Graphviz is installed. It is not possible to directly specifify these two directories, only $DIR

It is also possible to get Rgraphviz to search for Graphviz, by leaving the --with-graphviz option empty, as

R CMD INSTALL --configure-args='--with-graphviz' Rgraphviz_*.tar.gz 

In this case, Rgraphviz will search for Graphviz using the following methods

  1. First try pkg-config
  2. See if Graphviz is in its default location of /usr/local

Notes

The release version of Graphviz 2.28 contains bugs that makes it not work with Rgraphviz for certain layout options. The patches to the bundled Graphviz 2.28.0 are included in package.

R CMD check results

Bioconductor: Multiple platform build/check report