I managed to have the Rgraphviz working on the release 1.5 of Bioconductor on a suse 9.2, but when I then updated R2.0.1 to 2.1.0 and I installed bioconductor 1.6. I tryed the initial example of Rgraphviz vignette library(Rgraphviz) set.seed(123) V <- letters[1:10] M <- 1:4 g1 <- randomGraph(V, M, 0.2) z <- plot(g1, "neato") and I got a "segmentation fault" I check the installation of Rgraphviz and I found the following warnings: R CMD INSTALL Rgraphviz_1.5.10.tar.gz * Installing *source* package 'Rgraphviz' ... checking for graphviz... checking for dotneato-config... /usr/bin/dotneato-config /usr/bin/dotneato-config configure: creating ./config.status config.status: creating src/Makevars ** libs gcc -I/usr/lib/R/include -I/usr/include/graphviz -DGRAPHVIZ_1_12 -I/usr /local/include -fPIC -c Rgraphviz.c -o Rgraphviz.o In file included from /usr/include/graphviz/render.h:49, from common.h:22, from Rgraphviz.c:1: /usr/include/graphviz/macros.h:28:1: warning: "NEW" redefined In file included from common.h:13, from Rgraphviz.c:1: /usr/lib/R/include/Rdefines.h:129:1: warning: this is the location of the previous definition gcc -I/usr/lib/R/include -I/usr/include/graphviz -DGRAPHVIZ_1_12 -I/usr /local/include -fPIC -c RgraphvizInit.c -o RgraphvizInit.o In file included from /usr/include/graphviz/render.h:49, from common.h:22, from RgraphvizInit.c:1: /usr/include/graphviz/macros.h:28:1: warning: "NEW" redefined In file included from common.h:13, from RgraphvizInit.c:1: /usr/lib/R/include/Rdefines.h:129:1: warning: this is the location of the previous definition Any suggestion to have the Rgraphviz working again? Raffaele -- ---------------------------------------- Prof. Raffaele A. Calogero Bioinformatics and Genomics Unit Dipartimento di Scienze Cliniche e Biologiche c/o Az. Ospedaliera S. Luigi Regione Gonzole 10, Orbassano 10043 Torino tel. ++39 0116705420 Lab. ++39 0116705408 Fax ++39 0119038639 Mobile ++39 3333827080 email: raffaele.calogero@unito.it www: www.bioinformatica.unito.it

On 1 Jun 2005, raffaele.calogero@unito.it wrote: > I managed to have the Rgraphviz working on the release 1.5 of > Bioconductor on a suse 9.2, but when I then updated R2.0.1 to 2.1.0 > and I installed bioconductor 1.6. What version of graphviz do you have installed? Here's what I get on a SuSE 9.2 system where Rgraphviz is working: dotneato-config --version 2.2.1 I'll also mention that when you install graphviz you need to set LD_LIBRARY_PATH to include the installed location of the libs or edit the right ldconfig file to include this path. Upgrading graphviz is the first thing I would try. + seth