[R-SIG-Mac] rgraphviz again

[Julin Maloof]

Hi Seth (and everybody),

Thanks for the help.  Problem solved, details below.

First, here are the vitals:

iMAC 1.8GHz G5 running 10.4.5
Xcode 2.2
g77 from the R .dmg package installer
R installed from the binary .dmg
> version
         _                        
platform powerpc-apple-darwin7.9.0
arch     powerpc                  
os       darwin7.9.0              
system   powerpc, darwin7.9.0     
status                            
major    2                        
minor    2.1                      
year     2005                     
month    12                       
day      20                       
svn rev  36812                    
language R  

graphviz 2.8 installed by
./configure
make
make install

That installed it in /usr/local (the libs are in /usr/local/lib/graphviz)

Unfortunately, using the '--with-graphviz...' doesn't work... it is still looking for dot-neato

===================================================
Castle:~ jadmin$ R CMD INSTALL --configure-args='--with-graphviz=/usr/local/lib/graphviz' Rgraphviz_1.8.0.tar.gz 
* Installing *source* package 'Rgraphviz' ...
checking for graphviz... /usr/local/lib/graphviz/bin/dotneato-config
./configure: line 1: /usr/local/lib/graphviz/bin/dotneato-config: No such file or directory
./configure: line 1: /usr/local/lib/graphviz/bin/dotneato-config: No such file or directory
./configure: line 1: /usr/local/lib/graphviz/bin/dotneato-config: No such file or directory
./configure: line 1263: test: -eq: unary operator expected
./configure: line 1281: test: -eq: unary operator expected
failed
configure: error: please specify a valid path to
              'dotneato-config' version >= 1.12 using
              --with-graphviz=DIR
ERROR: configuration failed for package 'Rgraphviz'
** Removing '/Library/Frameworks/R.framework/Versions/2.2/Resources/library/Rgraphviz'
======================================================

However, I realized that I do have pkg-config installed, so I also tried what Seth suggested to Michael Kubovy.  This gets me closer, but there are some linking problems.

=======================================================
Castle:~ jadmin$ export PKG_CONFIG_PATH=/usr/local/lib/pkgconfig
Castle:~ jadmin$ R CMD INSTALL Rgraphviz_1.8.0.tar.gz
* Installing *source* package 'Rgraphviz' ...
checking for graphviz... checking for dotneato-config... not found
checking for pkg-config... /sw/bin/pkg-config
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc-3.3 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/usr/local/include/graphviz   -DGRAPHVIZGT_2_4 -I/usr/local/include   -fno-common  -g -O2 -c Rgraphviz.c -o Rgraphviz.o
gcc-3.3 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/usr/local/include/graphviz   -DGRAPHVIZGT_2_4 -I/usr/local/include   -fno-common  -g -O2 -c RgraphvizInit.c -o RgraphvizInit.o
gcc-3.3 -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o Rgraphviz.so Rgraphviz.o RgraphvizInit.o -L/usr/local/lib/graphviz -lgvc   -lcc_dynamic -F/Library/Frameworks/R.framework/.. -framework R
ld: can't locate file for: -lcc_dynamic
make: *** [Rgraphviz.so] Error 1
ERROR: compilation failed for package 'Rgraphviz'
** Removing '/Library/Frameworks/R.framework/Versions/2.2/Resources/library/Rgraphviz'
=============================================================

After a little web-research I realized that I needed to "gcc_select" to ensure that the lcc_dynamic file existed.  After gcc_select 3.3, everything works!!

Thanks,

Julin



Seth Falcon writes:
> 
> If you installed a recent graphviz, then there is no dotneat-config
> script.  Instead, for the autoconf tools to work, you need the
> pkg-config program installed and PKG_CONFIG_PATH set appropriately
> (/blah/lib/pkgconfig).
> 
> But it should also work to pass the --with-graphviz configure option.
> Something like:
> 
> R CMD INSTALL --configure-args='--with-graphviz=/blah/graphviz' \
>     Rgraphviz_x.y.z.tar.gz
> 
> So I would try this first.  If you still are having troubles, report
> back, but please include R version and how you installed, graphviz
> version and how/where installed, Rgraphviz version, height, weight...
> 
> cheers,
> 
> + seth


-- 
Julin Maloof
Assistant Professor
Section of Plant Biology
University of California, Davis
1 Shields Ave
Davis, CA, 95616

voice: (530) 752-8077
fax:   (530) 752-5410