[BioC] Rgraphviz problem

[Marcelo Laia]

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 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_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 Laia
Ph.D Candidate
São 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