OS X, Rgraphviz, bioconductor
1
0
Entering edit mode
@andrew-beckerman-935
Last seen 7.1 years ago
Hi all - in regards to the recent posts on both the r-mac and the bioconductor mail lists, I'll share a successful effort at getting the graph set of packages (graph, Rgraphviz, RBGL) in Bioconductor running on OS X. I'd been trying for weeks with the source of graphviz, R 1.9 and BioC 1.4, but all seems well now with R2.0, graphviz >=1.12 and Bioconductor 1.5. I am running R2.0 with OSX 10.3.5 with dev tools installed and the latest g77 from HPC http://hpc.sourceforge.net/ (very important, i think) My process was as follows 1) download graphviz 1.16 from ATT http://www.graphviz.org/pub/graphviz/ARCHIVE/graphviz-1.16.tar.gz 2) move it to your home if necessary, and gunzip it, then tar -xvf it, both from a terminal/shell window 3) cd to that folder: graphviz-1.16 4) proceed with the "standard" 3 step build process in this terminal session, ignoring errors ./configure make sudo make install 5) quit this terminal and open X11 6) now, type export LD_LIBRARY_PATH=/usr/lib/graphviz (this makes a temporary "link" in this shell to the location of the graphviz libraries, so that Rgraphviz building knows what to look for, i think) 7) now, start R (in X11) 8) type source("http://www.bioconductor.org/getBioC.R") 9) type getBioC("graph") 10) wait for everthing to build.... it builds biocondctor basics and the three graphing packages; this puts the bioconductor libraries in the globally accessible library set, rather than in your home library 11) voila. 8-10 are as the bioconductor website suggests. This worked for me, for the subset of bioconductor for graphing. Quitting X11 and restarting the aqua interface or X11now both run graph and Rgraphviz Hope this helps.... my guess is that installing the biconductor packages through X11, using getBioC() will make the effort smoother, but still allow their use in the aqua interface. andrew ---------------------------------------------------------------------- -- --------- Dr. Andrew Beckerman Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK ph +44 (0)114 222 0026; fx +44 (0)114 222 0002 http://www.shef.ac.uk/beckslab ---------------------------------------------------------------------- -- ----------
graph Rgraphviz PROcess graph Rgraphviz PROcess • 664 views
ADD COMMENT
0
Entering edit mode
stefano iacus ▴ 430
@stefano-iacus-995
Last seen 7.1 years ago
Hi Andrew, thanks for your report. I guess that steps from 5 to 11 will work under the aqua gui as well (using Sys.putenv for example and running the x11 server) stefano On Nov 3, 2004, at 10:09 AM, Andrew Beckerman wrote: > Hi all - in regards to the recent posts on both the r-mac and the > bioconductor mail lists, I'll share a successful effort at getting the > graph set of packages (graph, Rgraphviz, RBGL) in Bioconductor running > on OS X. I'd been trying for weeks with the source of graphviz, R 1.9 > and BioC 1.4, but all seems well now with R2.0, graphviz >=1.12 and > Bioconductor 1.5. > > I am running R2.0 with OSX 10.3.5 with dev tools installed and the > latest g77 from HPC http://hpc.sourceforge.net/ (very important, i > think) > > My process was as follows > > 1) download graphviz 1.16 from ATT > http://www.graphviz.org/pub/graphviz/ARCHIVE/graphviz-1.16.tar.gz > 2) move it to your home if necessary, and gunzip it, then tar -xvf it, > both from a terminal/shell window > 3) cd to that folder: graphviz-1.16 > 4) proceed with the "standard" 3 step build process in this terminal > session, ignoring errors > ./configure > make > sudo make install > 5) quit this terminal and open X11 > 6) now, type export LD_LIBRARY_PATH=/usr/lib/graphviz > (this makes a temporary "link" in this shell to the location of the > graphviz libraries, so that Rgraphviz building knows what to look for, > i think) > 7) now, start R (in X11) > 8) type source("http://www.bioconductor.org/getBioC.R") > 9) type getBioC("graph") > 10) wait for everthing to build.... it builds biocondctor basics and > the three graphing packages; this puts the bioconductor libraries in > the globally accessible library set, rather than in your home library > 11) voila. 8-10 are as the bioconductor website suggests. This worked > for me, for the subset of bioconductor for graphing. Quitting X11 and > restarting the aqua interface or X11now both run graph and Rgraphviz > > Hope this helps.... my guess is that installing the biconductor > packages through X11, using getBioC() will make the effort smoother, > but still allow their use in the aqua interface. > > andrew > > -------------------------------------------------------------------- --- > ---------- > Dr. Andrew Beckerman > Department of Animal and Plant Sciences, University of Sheffield, > Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK > ph +44 (0)114 222 0026; fx +44 (0)114 222 0002 > http://www.shef.ac.uk/beckslab > -------------------------------------------------------------------- --- > ----------- > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/r-sig-mac >
ADD COMMENT

Login before adding your answer.

Traffic: 358 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6