[BioC] segmentation fault using Rgraphviz
Raffaele Calogero
raffaele.calogero at unito.it
Wed Jun 1 15:02:46 CEST 2005
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 at unito.it
www: www.bioinformatica.unito.it
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