[BioC] Rgraphviz install issues

[Andrew Beckerman]

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.
>
>
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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
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