[BioC] Rgraphviz problem

[Li.Long at isb-sib.ch]

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/library",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 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 CandidateSão 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
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