Commit information:
Commit id: d498610a263582b36dd63503829ba5c7befca2c6
updated README
Committed by: Kasper Daniel Hansen
Author Name: Kasper Daniel Hansen
Commit date: 2014-10-02 22:23:06 -0400
Author date: 2014-10-02 22:23:06 -0400
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rgraphviz@94891 bc3139a8-67e5-0310-9ffc-ced21a209358
khansen authored on 03/10/2014 02:23:20 | ... | ... |
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-# Rgraphviz |
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+# R package: Rgraphviz |
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+ |
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+This is the developer version of Bioconductor package [Rgraphviz](http://bioconductor.org/packages/devel/bioc/html/Rgraphviz.html). Install in R as: |
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+ |
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+```r |
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+source('http://bioconductor.org/biocLite.R')
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+biocLite(Rgraphviz') |
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+``` |
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+ |
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+# Additional installation tips |
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Rgraphviz now comes bundles with Graphviz. This should greatly simplify |
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installation on all platforms, compared with earlier versions. |
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@@ -6,32 +15,32 @@ installation on all platforms, compared with earlier versions. |
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While it should not be necessary, we still allow for the use of an external |
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Graphviz (external to Rgraphviz) at install time, except on Windows (this used |
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to be supported on Windows but this is no longer true). This is indicated by |
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-the configure option --with-graphviz. |
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+the configure option `--with-graphviz`. |
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A direct specification of an external Graphviz at install time would be |
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- R CMD INSTALL --configure-args='--with-graphviz=/usr/local' Rgraphviz_*.tar.gz |
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+ |
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+```{bash}
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+R CMD INSTALL --configure-args='--with-graphviz=/usr/local' Rgraphviz_*.tar.gz |
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+``` |
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In this case (with $DIR=/usr/local), the configure script assumes the presence |
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-of |
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- $DIR/include/graphviz |
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- $DIR/lib/graphviz |
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+of |
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+```{bash}
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+$DIR/include/graphviz |
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+$DIR/lib/graphviz |
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+``` |
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as is the default when Graphviz is installed. It is not possible to directly |
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-specifify these two directories, only $DIR |
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+specifify these two directories, only `$DIR` |
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It is also possible to get Rgraphviz to search for Graphviz, by leaving the |
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+`--with-graphviz` option empty, as |
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- R CMD INSTALL --configure-args='--with-graphviz' Rgraphviz_*.tar.gz |
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+```{bash}
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+R CMD INSTALL --configure-args='--with-graphviz' Rgraphviz_*.tar.gz |
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+``` |
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In this case, Rgraphviz will search for Graphviz using the following methods |
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- (1) First try pkg-config |
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- (2) See if Graphviz is in its default location of /usr/local |
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- |
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- |
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-## Devel repository |
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- |
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-The devel repository for Rgraphviz is at |
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- |
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-https://github.com/kasperdanielhansen/Rgraphviz |
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+1. First try pkg-config |
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+2. See if Graphviz is in its default location of `/usr/local` |
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## Notes |
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@@ -39,4 +48,7 @@ The release version of Graphviz 2.28 contains bugs that makes it not work with |
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Rgraphviz for certain layout options. The patches to the bundled Graphviz |
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2.28.0 are included in package. |
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+## R CMD check results |
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+Bioconductor: [Multiple platform build/check report](http://master.bioconductor.org/checkResults/devel/bioc-LATEST/Rgraphviz/) |
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+ |
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