[BioC] Rgraphviz problem
Marcelo Laia
marcelolaia at gmail.com
Fri Jan 19 15:43:17 CET 2007
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
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