> Jeff - thanks for the advice, but unfortunately, no dice.... I download > the development Rgraphviz pacakge, and using the same routine with > exporting my library location for graphviz, get the same error.... any > more ideas? the offending line seems to be this: ld: can't locate file > for: -ldotneato That doesn't appear to be the same error at all, unless I'm missing something. That error means that you haven't pointed your LD_LIBRARY_PATH to where the graphviz libraries are sitting.

Hi, I have fixed my Rgraphviz issuse...sicne I was dealing with it recently..this might help because I have done it on my linux fedora core 2 OS don't do RPM thing..plz..since you have linux.... 1. download Graphviz 2. tar -xvzf 3. go to Graphviz directory ./configure --prefix=/usr --exec-prefix=/usr 4. make 5. make install 6. download Rgraphviz (from same shell) 7. just do: R CMD INSTALL Rgraphviz*.gz 8. type $ whereis graphviz graphviz: /usr/lib/graphviz /usr/local/lib/graphviz /usr/include/graphviz /usr/share/graphviz you can see above couple of path to graphviz and you will take first one(whatever is on your system): /usr/lib/graphviz 9. now, whenever you want to load Rgraphviz in to your R first from linux prompt: $ export LD_LIBRARY_PATH=/usr/lib/graphviz and $ R you can set this path in to your login script. please let me know, if you have any trouble with installing R graphviz. thanks Saurin --- Andrew Beckerman <a.beckerman@sheffield.ac.uk> wrote: > Jeff - thanks for the advice, but unfortunately, no > dice.... I download > the development Rgraphviz pacakge, and using the > same routine with > exporting my library location for graphviz, get the > same error.... any > more ideas? the offending line seems to be this: > ld: can't locate file > for: -ldotneato > > cheers > andrew > > dyn092203:~ apb$ export > LD_LIBRARY_PATH=/opt/local/lib/graphviz > dyn092203:~ apb$ sudo R CMD INSTALL > /Users/apb/Rgraphviz_1-1.4.23.tar.gz > Password: > * Installing *source* package 'Rgraphviz' ... > checking for graphviz... checking for > dotneato-config... > /opt/local/bin//dotneato-config > /opt/local/bin//dotneato-config > configure: creating ./config.status > config.status: creating src/Makevars > ** libs > gcc -no-cpp-precomp > -I/Library/Frameworks/R.framework/Resources/include > > -I/opt/local/include/graphviz -I/usr/local/include > -Wall -fno-common > -g -O2 -c Rgraphviz.c -o Rgraphviz.o > In file included from > /opt/local/include/graphviz/render.h:45, > from common.h:22, > from Rgraphviz.c:1: > /opt/local/include/graphviz/macros.h:34:1: warning: > "NEW" redefined > In file included from common.h:13, > from Rgraphviz.c:1: > /Library/Frameworks/R.framework/Resources/include/Rdefines.h:129:1: > > warning: this is the location of the previous > definition > gcc -no-cpp-precomp > -I/Library/Frameworks/R.framework/Resources/include > > -I/opt/local/include/graphviz -I/usr/local/include > -Wall -fno-common > -g -O2 -c RgraphvizInit.c -o RgraphvizInit.o > In file included from > /opt/local/include/graphviz/render.h:45, > from common.h:22, > from RgraphvizInit.c:1: > /opt/local/include/graphviz/macros.h:34:1: warning: > "NEW" redefined > In file included from common.h:13, > from RgraphvizInit.c:1: > /Library/Frameworks/R.framework/Resources/include/Rdefines.h:129:1: > > warning: this is the location of the previous > definition > gcc -bundle -flat_namespace -undefined suppress > -L/usr/local/lib -o > Rgraphviz.so Rgraphviz.o RgraphvizInit.o -Wl > -ldotneato -lm > -lcc_dynamic -framework R > ld: can't locate file for: -ldotneato > make: *** [Rgraphviz.so] Error 1 > ERROR: compilation failed for package 'Rgraphviz' > ** Removing > '/Library/Frameworks/R.framework/Versions/1.9.1/Resources/library/ > > Rgraphviz' > On 30 Sep 2004, at 18:54, Jeff Gentry wrote: > > >> I have installed, via darwinports, graphviz > (v1.16) running in x11 (I > >> dyn092203:~ apb$ sudo R CMD INSTALL > /Users/apb/Rgraphviz_1.4.0.tar.gz > >> Rgraphviz.c:244: warning: implicit declaration of > function `GD_gvc' > >> Rgraphviz.c:244: error: invalid lvalue in > assignment > > > >> Clearly, something else is missing in my > effort..... Any advice would > >> be appreciated. > > > > If you're using that new of a version of Graphviz, > you need to use the > > devel version of Rgraphviz. > > > > > ---------------------------------------------------------------------- -- > > --------- > 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 > ---------------------------------------------------------------------- -- > > ---------- > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > _______________________________ Declare Yourself - Register online to vote today!