Hi Li and Seth, *in the target!!!* yeaaahhh :) > a) exporting the LD_LIBRARY_PATH environment variable before starting > R. I think the following should work for you: > > export LD_LIBRARY_PATH=/usr/local/lib/graphviz > # then start R and try Rgraphviz I did! But not solve. My graphviz libs are under /usr/lib/graphviz: (I did export with correct path) > > b) There should be a system-wide place to add paths to the ld search > path. On SuSE it is /etc/ld.so.conf. After editing this file > (requires root), you will also need to run ldconfig -a or some such > command (also as root). I did, too! I include /usr/lib/graphviz in the /etc/ld.so.conf and run ldconfig -v After this, it works fine!!!! I am very thanks to you! Thank you very much! -- Marcelo Luiz de Laia Ph.D Candidate S?o Paulo State University (http://www.unesp.br/eng/) School of Agricultural and Veterinary Sciences Department of Technology Via de Acesso Prof. Paulo Donato Castellane s/n 14884-900 Jaboticabal - SP - Brazil Phone: +55-016-3209-2675 Cell: +55-016-97098526

Seth, that's absolutely right, thanks. For Marcelo, the ld.so.conf file is in the same place as SuSE, but the command to update is simple ldconfig (as Seth said, as root) Thanks Stefano On Fri, Jan 19, 2007 at 07:24:17AM -0800, Seth Falcon wrote: <seth>Hi Marcelo, <seth> <seth>"Marcelo Laia" <marcelolaia at="" gmail.com=""> writes: <seth> <seth>> Hi, <seth>> <seth>> I install Rgraphviz, but it dosen't load/start! <seth> <seth>I think you are almost there. I suspect that the problem is that the <seth>graphviz libraries are not in the path that ld searches. You can try: <seth> <seth>a) exporting the LD_LIBRARY_PATH environment variable before starting <seth> R. I think the following should work for you: <seth> <seth> export LD_LIBRARY_PATH=/usr/local/lib/graphviz <seth> # then start R and try Rgraphviz <seth> <seth>b) There should be a system-wide place to add paths to the ld search <seth> path. On SuSE it is /etc/ld.so.conf. After editing this file <seth> (requires root), you will also need to run ldconfig -a or some such <seth> command (also as root). <seth> <seth>+ seth <seth> <seth>_______________________________________________ <seth>Bioconductor mailing list <seth>Bioconductor at stat.math.ethz.ch <seth>https://stat.ethz.ch/mailman/listinfo/bioconductor <seth>Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Stefano Calza, PhD Researcher - Biostatistician *Sezione di Statistica Medica e Biometria Dipartimento di Scienze Biomediche e Biotecnologie Universit? degli Studi di Brescia - Italy Viale Europa, 11 25123 Brescia email: calza at med.unibs.it Phone: +390303717653 Fax: +390303717488

Hi, I'm experiencing the same problem, but I checked and I do have the shared library. Rgraphviz.so can't find libgvc.so2, which I do have. The problem is how to configure the install process to make it find it?! I do use Debian as well...might be that an issue? TIA Stefano On Fri, Jan 19, 2007 at 04:17:36PM +0100, Li.Long at isb-sib.ch wrote: <li.long> <li.long>Hi, Marcelo, <li.long> <li.long>The output is all messed up for me. Could you double check to see if you <li.long>have libgvc.so and the like in your system and accessible (in the right <li.long>search path)? <li.long> <li.long>Thanks, <li.long> <li.long>Li <li.long> <li.long>> Hi, <li.long>> I install Rgraphviz, but it dosen't load/start! <li.long>>> install.packages(c("Rgraphviz"),dependencies=TRUE,lib="/us r/lib/R/library",repos="http://www.bioconductor.org")tentando <li.long>>> a URL <li.long>>> 'http://www.bioconductor.org/src/contrib/Rgraphviz_1.12.3. tar.gz'Content <li.long>>> type 'application/x-gzip' length 1504829 bytesURL <li.long>>> aberta==================================================downloaded <li.long>>> 1469Kb <li.long>> * Installing *source* package 'Rgraphviz' ...checking for pkg-config... <li.long>> /usr/bin/pkg-configconfigure: Found graphviz 2.8configure: creating <li.long>> ./config.statusconfig.status: creating src/Makevars** libsgcc -std=gnu99 <li.long>> -I/usr/share/R/include -I/usr/share/R/include-I/usr/include/graphviz <li.long>> -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=8-fpic -g -O2 -c Rgraphviz.c -o <li.long>> Rgraphviz.oRgraphviz.c: In function 'getListElement':Rgraphviz.c:51: <li.long>> warning: implicit declaration of function 'Rf_type2char'gcc -std=gnu99 <li.long>> -I/usr/share/R/include -I/usr/share/R/include-I/usr/include/graphviz <li.long>> -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=8-fpic -g -O2 -c RgraphvizInit.c -o <li.long>> RgraphvizInit.ogcc -std=gnu99 -shared -o Rgraphviz.so Rgraphviz.o <li.long>> RgraphvizInit.o-L/usr/lib/graphviz -lgvc -L/usr/lib/R/lib -lR** R** <li.long>> inst** save imageLoading required package: graphLoading required package: <li.long>> geneplotterLoading required package: annotateLoading required package: <li.long>> BiobaseLoading required package: tools <li.long>> Welcome to Bioconductor <li.long>> Vignettes contain introductory material. To view, type <li.long>> 'openVignette()' or start with 'help(Biobase)'. For details on <li.long>> reading vignettes, see the openVignette help page. <li.long>> KernSmooth 2.22 installedCopyright M. P. Wand 1997Creating a new generic <li.long>> function for "lines" in "Rgraphviz"Creating a new generic function for <li.long>> "plot" in "Rgraphviz"** help >>> Building/Updating help pages for package <li.long>> 'Rgraphviz' Formats: text html latex example AgEdge- class <li.long>> text html latex example AgNode-class <li.long>> text html latex example AgTextLabel-class text <li.long>> html latex example BezierCurve-class text html <li.long>> latex example GraphvizAttributes text html latex <li.long>> example GraphvizLayouts text html latex <li.long>> example Ragraph-class text html latex example <li.long>> agopen text html latex example <li.long>> agwrite text html latex example <li.long>> boundingBox-class text html latex example <li.long>> buildNodeList text html latex example <li.long>> getDefaultAttrs text html latex example <li.long>> graphvizVersion text html latex example <li.long>> imageMap text html latex example <li.long>> layoutGraph text html latex example <li.long>> makeNodeAttrs text html latex example <li.long>> pEdge-class text html latex example <li.long>> pNode-class text html latex example <li.long>> pieGlyph text html latex example <li.long>> plot-methods text html latex example <li.long>> removedEdges text html latex example <li.long>> toDot-methods text html latex example <li.long>> xyPoint-class text html latex example** <li.long>> building package indices ...* DONE (Rgraphviz) <li.long>> The downloaded packages are in /tmp/RtmpDdQSQh/downloaded_packages> <li.long>>> library(Rgraphviz)Error in dyn.load(x, as.logical(local), <li.long>>> as.logical(now)) : unable to load shared library <li.long>>> '/usr/lib/R/library/Rgraphviz/libs/Rgraphviz.so': libgvc.so.2: cannot <li.long>>> open shared object file: File or directory not foundError: .onLoad <li.long>>> failed in 'loadNamespace' para 'Rgraphviz'Error: package/namespace load <li.long>>> failed for 'Rgraphviz'> <li.long>> /home/kurumin# ls -al /usr/lib/R/library/Rgraphviz/libs/total 76drwxr-xr-x <li.long>> 2 kurumin kurumin 80 2007-01-19 11:54 .drwxr-xr-x 12 kurumin kurumin <li.long>> 400 2007-01-19 11:54 ..-rwxr-xr-x 1 kurumin kurumin 76168 2007-01-19 <li.long>> 11:54 Rgraphviz.so/home/kurumin# <li.long>>> sessionInfo()R version 2.4.0 Patched (2006-11-25 <li.long>>> r39997)i486-pc-linux-gnu <li.long>> locale:LC_CTYPE=pt_BR;LC_NUMERIC=C;LC_TIME=pt_BR;LC_COLLATE =pt_BR;LC_MONETARY=pt_BR;LC_MESSAGES=pt_BR;LC_PAPER=pt_BR;LC_NAME=C;LC _ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=pt_BR;LC_IDENTIFICATION=C <li.long>> attached base packages:[1] "tools" "stats" "graphics" "grDevices" <li.long>> "utils" "datasets"[7] "methods" "base" <li.long>> other attached packages:geneplotter annotate graph Biobase <li.long>> "1.12.0" "1.12.1" "1.12.0" "1.12.2"> <li.long>> I am use Debian GNU Linux testing. <li.long>> Thank you very much! <li.long>> <li.long>> -- Marcelo Luiz de LaiaPh.D CandidateS??o Paulo State University <li.long>> (http://www.unesp.br/eng/)School of Agricultural and Veterinary <li.long>> SciencesDepartment of TechnologyVia de Acesso Prof. Paulo Donato <li.long>> Castellane s/n14884-900 Jaboticabal - SP - BrazilPhone: <li.long>> +55-016-3209-2675Cell: +55-016-97098526 <li.long>> _______________________________________________Bioconductor mailing <li.long>> listBioconductor at stat.math.ethz.chhttps://stat.ethz.ch/m ailman/listinfo/bioconductorSearch <li.long>> the archives: <li.long>> http://news.gmane.org/gmane.science.biology.informatics.conductor <li.long>> <li.long> <li.long>_______________________________________________ <li.long>Bioconductor mailing list <li.long>Bioconductor at stat.math.ethz.ch <li.long>https://stat.ethz.ch/mailman/listinfo/bioconductor <li.long>Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Stefano Calza, PhD Researcher - Biostatistician *Sezione di Statistica Medica e Biometria Dipartimento di Scienze Biomediche e Biotecnologie Universit? degli Studi di Brescia - Italy Viale Europa, 11 25123 Brescia email: calza at med.unibs.it Phone: +390303717653 Fax: +390303717488