[BioC] Rgraphviz problem
Stefano Calza
stecalza at tiscali.it
Fri Jan 19 16:44:15 CET 2007
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="/usr/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 CandidateSão 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/mailman/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
Università degli Studi di Brescia - Italy
Viale Europa, 11 25123 Brescia
email: calza at med.unibs.it
Phone: +390303717653
Fax: +390303717488
More information about the Bioconductor
mailing list