Rgraphviz problem
2
0
Entering edit mode
Marcelo Laia ▴ 450
@marcelo-laia-2007
Last seen 12 weeks ago
Brazil
Hi, I install Rgraphviz, but it dosen't load/start! > install.packages(c("Rgraphviz"),dependencies=TRUE,lib="/usr/lib/R/li brary",repos="http://www.bioconductor.org") tentando a URL 'http://www.bioconductor.org/src/contrib/Rgraphviz_1.12.3.tar.gz' Content type 'application/x-gzip' length 1504829 bytes URL aberta ================================================== downloaded 1469Kb * Installing *source* package 'Rgraphviz' ... checking for pkg-config... /usr/bin/pkg-config configure: Found graphviz 2.8 configure: creating ./config.status config.status: creating src/Makevars ** libs gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -I/usr/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=8 -fpic -g -O2 -c Rgraphviz.c -o Rgraphviz.o Rgraphviz.c: In function 'getListElement': Rgraphviz.c:51: warning: implicit declaration of function 'Rf_type2char' gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -I/usr/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=8 -fpic -g -O2 -c RgraphvizInit.c -o RgraphvizInit.o gcc -std=gnu99 -shared -o Rgraphviz.so Rgraphviz.o RgraphvizInit.o -L/usr/lib/graphviz -lgvc -L/usr/lib/R/lib -lR ** R ** inst ** save image Loading required package: graph Loading required package: geneplotter Loading required package: annotate Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()' or start with 'help(Biobase)'. For details on reading vignettes, see the openVignette help page. KernSmooth 2.22 installed Copyright M. P. Wand 1997 Creating a new generic function for "lines" in "Rgraphviz" Creating a new generic function for "plot" in "Rgraphviz" ** help >>> Building/Updating help pages for package 'Rgraphviz' Formats: text html latex example AgEdge-class text html latex example AgNode-class text html latex example AgTextLabel-class text html latex example BezierCurve-class text html latex example GraphvizAttributes text html latex example GraphvizLayouts text html latex example Ragraph-class text html latex example agopen text html latex example agwrite text html latex example boundingBox-class text html latex example buildNodeList text html latex example getDefaultAttrs text html latex example graphvizVersion text html latex example imageMap text html latex example layoutGraph text html latex example makeNodeAttrs text html latex example pEdge-class text html latex example pNode-class text html latex example pieGlyph text html latex example plot-methods text html latex example removedEdges text html latex example toDot-methods text html latex example xyPoint-class text html latex example ** building package indices ... * DONE (Rgraphviz) The downloaded packages are in /tmp/RtmpDdQSQh/downloaded_packages > > library(Rgraphviz) Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library '/usr/lib/R/library/Rgraphviz/libs/Rgraphviz.so': libgvc.so.2: cannot open shared object file: File or directory not found Error: .onLoad failed in 'loadNamespace' para 'Rgraphviz' Error: package/namespace load failed for 'Rgraphviz' > /home/kurumin# ls -al /usr/lib/R/library/Rgraphviz/libs/ total 76 drwxr-xr-x 2 kurumin kurumin 80 2007-01-19 11:54 . drwxr-xr-x 12 kurumin kurumin 400 2007-01-19 11:54 .. -rwxr-xr-x 1 kurumin kurumin 76168 2007-01-19 11:54 Rgraphviz.so /home/kurumin# > sessionInfo() R version 2.4.0 Patched (2006-11-25 r39997) i486-pc-linux-gnu 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_TELE PHONE=C;LC_MEASUREMENT=pt_BR;LC_IDENTIFICATION=C attached base packages: [1] "tools" "stats" "graphics" "grDevices" "utils" "datasets" [7] "methods" "base" other attached packages: geneplotter annotate graph Biobase "1.12.0" "1.12.1" "1.12.0" "1.12.2" > I am use Debian GNU Linux testing. 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
annotate graph Rgraphviz annotate graph Rgraphviz • 1.1k views
ADD COMMENT
0
Entering edit mode
Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 7.4 years ago
Hi Marcelo, "Marcelo Laia" <marcelolaia at="" gmail.com=""> writes: > Hi, > > I install Rgraphviz, but it dosen't load/start! I think you are almost there. I suspect that the problem is that the graphviz libraries are not in the path that ld searches. You can try: 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 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). + seth
ADD COMMENT
0
Entering edit mode
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
ADD REPLY
0
Entering edit mode
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
ADD REPLY
0
Entering edit mode
@lilongisb-sibch-1725
Last seen 7.4 years ago
Hi, Marcelo, The output is all messed up for me. Could you double check to see if you have libgvc.so and the like in your system and accessible (in the right search path)? Thanks, Li > Hi, > I install Rgraphviz, but it dosen't load/start! >> install.packages(c("Rgraphviz"),dependencies=TRUE,lib="/usr/lib/R/l ibrary",repos="http://www.bioconductor.org")tentando >> a URL >> 'http://www.bioconductor.org/src/contrib/Rgraphviz_1.12.3.tar.gz'Co ntent >> type 'application/x-gzip' length 1504829 bytesURL >> aberta==================================================downloaded >> 1469Kb > * Installing *source* package 'Rgraphviz' ...checking for pkg- config... > /usr/bin/pkg-configconfigure: Found graphviz 2.8configure: creating > ./config.statusconfig.status: creating src/Makevars** libsgcc -std=gnu99 > -I/usr/share/R/include -I/usr/share/R/include-I/usr/include/graphviz > -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=8-fpic -g -O2 -c Rgraphviz.c -o > Rgraphviz.oRgraphviz.c: In function 'getListElement':Rgraphviz.c:51: > warning: implicit declaration of function 'Rf_type2char'gcc -std=gnu99 > -I/usr/share/R/include -I/usr/share/R/include-I/usr/include/graphviz > -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=8-fpic -g -O2 -c RgraphvizInit.c -o > RgraphvizInit.ogcc -std=gnu99 -shared -o Rgraphviz.so Rgraphviz.o > RgraphvizInit.o-L/usr/lib/graphviz -lgvc -L/usr/lib/R/lib -lR** R** > inst** save imageLoading required package: graphLoading required package: > geneplotterLoading required package: annotateLoading required package: > BiobaseLoading required package: tools > Welcome to Bioconductor > Vignettes contain introductory material. To view, type > 'openVignette()' or start with 'help(Biobase)'. For details on > reading vignettes, see the openVignette help page. > KernSmooth 2.22 installedCopyright M. P. Wand 1997Creating a new generic > function for "lines" in "Rgraphviz"Creating a new generic function for > "plot" in "Rgraphviz"** help >>> Building/Updating help pages for package > 'Rgraphviz' Formats: text html latex example AgEdge-class > text html latex example AgNode-class > text html latex example AgTextLabel-class text > html latex example BezierCurve-class text html > latex example GraphvizAttributes text html latex > example GraphvizLayouts text html latex > example Ragraph-class text html latex example > agopen text html latex example > agwrite text html latex example > boundingBox-class text html latex example > buildNodeList text html latex example > getDefaultAttrs text html latex example > graphvizVersion text html latex example > imageMap text html latex example > layoutGraph text html latex example > makeNodeAttrs text html latex example > pEdge-class text html latex example > pNode-class text html latex example > pieGlyph text html latex example > plot-methods text html latex example > removedEdges text html latex example > toDot-methods text html latex example > xyPoint-class text html latex example** > building package indices ...* DONE (Rgraphviz) > The downloaded packages are in /tmp/RtmpDdQSQh/downloaded_packages> >> library(Rgraphviz)Error in dyn.load(x, as.logical(local), >> as.logical(now)) : unable to load shared library >> '/usr/lib/R/library/Rgraphviz/libs/Rgraphviz.so': libgvc.so.2: cannot >> open shared object file: File or directory not foundError: .onLoad >> failed in 'loadNamespace' para 'Rgraphviz'Error: package/namespace load >> failed for 'Rgraphviz'> > /home/kurumin# ls -al /usr/lib/R/library/Rgraphviz/libs/total 76drwxr-xr-x > 2 kurumin kurumin 80 2007-01-19 11:54 .drwxr-xr-x 12 kurumin kurumin > 400 2007-01-19 11:54 ..-rwxr-xr-x 1 kurumin kurumin 76168 2007-01-19 > 11:54 Rgraphviz.so/home/kurumin# >> sessionInfo()R version 2.4.0 Patched (2006-11-25 >> r39997)i486-pc-linux-gnu > 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 > attached base packages:[1] "tools" "stats" "graphics" "grDevices" > "utils" "datasets"[7] "methods" "base" > other attached packages:geneplotter annotate graph Biobase > "1.12.0" "1.12.1" "1.12.0" "1.12.2"> > I am use Debian GNU Linux testing. > Thank you very much! > > -- Marcelo Luiz de LaiaPh.D CandidateS??o Paulo State University > (http://www.unesp.br/eng/)School of Agricultural and Veterinary > SciencesDepartment of TechnologyVia de Acesso Prof. Paulo Donato > Castellane s/n14884-900 Jaboticabal - SP - BrazilPhone: > +55-016-3209-2675Cell: +55-016-97098526 > _______________________________________________Bioconductor mailing > listBioconductor at stat.math.ethz.chhttps://stat.ethz.ch/mailman/li stinfo/bioconductorSearch > the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD COMMENT
0
Entering edit mode
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
ADD REPLY

Login before adding your answer.

Traffic: 197 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6