[BioC] Rgraphviz install issues

[Saurin Jani]

Hi,

I have fixed my Rgraphviz issuse...sicne I was dealing
with it recently..this might help because I have done
it on my linux fedora core 2 OS

don't do RPM thing..plz..since you have linux....

1. download Graphviz 
2. tar -xvzf 
3. go to Graphviz directory

./configure --prefix=/usr --exec-prefix=/usr

4. make
5. make install

6. download Rgraphviz (from same shell)
7. just do: R CMD INSTALL Rgraphviz*.gz
8. type $ whereis graphviz
graphviz: /usr/lib/graphviz /usr/local/lib/graphviz
/usr/include/graphviz /usr/share/graphviz

you can see above couple of path to graphviz and you
will take first one(whatever is on your system):
/usr/lib/graphviz

9. now, whenever you want to load Rgraphviz in to your
   R first from linux prompt:
  $ export LD_LIBRARY_PATH=/usr/lib/graphviz

and $ R


you can set this path in to your login script. 

please let me know, if you have any trouble with
installing R graphviz.


thanks
Saurin





--- Andrew Beckerman <a.beckerman at sheffield.ac.uk>
wrote:

> Jeff - thanks for the advice, but unfortunately, no
> dice.... I download  
> the development Rgraphviz pacakge, and using the
> same routine with  
> exporting my library location for graphviz, get the
> same error.... any  
> more ideas?  the offending line seems to be this:
> ld: can't locate file  
> for: -ldotneato
> 
> cheers
> andrew
> 
> dyn092203:~ apb$ export
> LD_LIBRARY_PATH=/opt/local/lib/graphviz
> dyn092203:~ apb$ sudo R CMD INSTALL
> /Users/apb/Rgraphviz_1-1.4.23.tar.gz
> Password:
> * Installing *source* package 'Rgraphviz' ...
> checking for graphviz... checking for
> dotneato-config...  
> /opt/local/bin//dotneato-config
> /opt/local/bin//dotneato-config
> configure: creating ./config.status
> config.status: creating src/Makevars
> ** libs
> gcc -no-cpp-precomp
> -I/Library/Frameworks/R.framework/Resources/include 
> 
> -I/opt/local/include/graphviz  -I/usr/local/include 
> -Wall -fno-common   
> -g -O2 -c Rgraphviz.c -o Rgraphviz.o
> In file included from
> /opt/local/include/graphviz/render.h:45,
>                   from common.h:22,
>                   from Rgraphviz.c:1:
> /opt/local/include/graphviz/macros.h:34:1: warning:
> "NEW" redefined
> In file included from common.h:13,
>                   from Rgraphviz.c:1:
>
/Library/Frameworks/R.framework/Resources/include/Rdefines.h:129:1:
>  
> warning: this is the location of the previous
> definition
> gcc -no-cpp-precomp
> -I/Library/Frameworks/R.framework/Resources/include 
> 
> -I/opt/local/include/graphviz  -I/usr/local/include 
> -Wall -fno-common   
> -g -O2 -c RgraphvizInit.c -o RgraphvizInit.o
> In file included from
> /opt/local/include/graphviz/render.h:45,
>                   from common.h:22,
>                   from RgraphvizInit.c:1:
> /opt/local/include/graphviz/macros.h:34:1: warning:
> "NEW" redefined
> In file included from common.h:13,
>                   from RgraphvizInit.c:1:
>
/Library/Frameworks/R.framework/Resources/include/Rdefines.h:129:1:
>  
> warning: this is the location of the previous
> definition
> gcc -bundle -flat_namespace -undefined suppress
> -L/usr/local/lib -o  
> Rgraphviz.so Rgraphviz.o RgraphvizInit.o -Wl
> -ldotneato -lm  
> -lcc_dynamic -framework R
> ld: can't locate file for: -ldotneato
> make: *** [Rgraphviz.so] Error 1
> ERROR: compilation failed for package 'Rgraphviz'
> ** Removing  
>
'/Library/Frameworks/R.framework/Versions/1.9.1/Resources/library/
> 
> Rgraphviz'
> On 30 Sep 2004, at 18:54, Jeff Gentry wrote:
> 
> >> I have installed, via darwinports, graphviz
> (v1.16) running in x11 (I
> >> dyn092203:~ apb$ sudo R CMD INSTALL
> /Users/apb/Rgraphviz_1.4.0.tar.gz
> >> Rgraphviz.c:244: warning: implicit declaration of
> function `GD_gvc'
> >> Rgraphviz.c:244: error: invalid lvalue in
> assignment
> >
> >> Clearly, something else is missing in my
> effort..... Any advice would
> >> be appreciated.
> >
> > If you're using that new of a version of Graphviz,
> you need to use the
> > devel version of Rgraphviz.
> >
> >
>
------------------------------------------------------------------------
> 
> ---------
> Dr. Andrew Beckerman
> Department of Animal and Plant Sciences, University
> of Sheffield,
> Alfred Denny Building, Western Bank, Sheffield S10
> 2TN, UK
> ph +44 (0)114 222 0026; fx +44 (0)114 222 0002
> http://www.shef.ac.uk/beckslab
>
------------------------------------------------------------------------
> 
> ----------
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
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> 



		
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