[BioC] how to configure "pkgconfig"

[shen bairong]

Dear Seth:

Thanks for your help, Rgraphviz could find the
graphviz now, but I got another problem as follows,
wish to have your help.

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'
** Restoring previous
'/Library/Frameworks/R.framework/Versions/2.2/Resources/library/Rgraphviz'

Best regards,
Bairong

---------------------------------------------------------

The following is the detail.


83-102-24-177:~/Desktop bairongshen$ export
PKG_CONFIG_PATH=/usr/local/lib/graphviz/pkgconfig
83-102-24-177:~/Desktop bairongshen$  pkg-config
libgvc --modversion
2.7.20051113.0540
83-102-24-177:~/Desktop bairongshen$ R CMD INSTALL
Rgraphviz_1.9.1.tar.gz 
* 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-3.3 -no-cpp-precomp
-I/Library/Frameworks/R.framework/Resources/include
-I/opt/local/include/graphviz -DGRAPHVIZGT_1_16
-I/usr/local/include   -fno-common  -g -O2 -c
Rgraphviz.c -o Rgraphviz.o
In file included from
/opt/local/include/graphviz/render.h:45,
                 from common.h:32,
                 from Rgraphviz.c:1:
/opt/local/include/graphviz/macros.h:34:1: warning:
"NEW" redefined
In file included from common.h:15,
                 from Rgraphviz.c:1:
/Library/Frameworks/R.framework/Resources/include/Rdefines.h:134:1:
warning: this is the location of the previous
definition
gcc-3.3 -no-cpp-precomp
-I/Library/Frameworks/R.framework/Resources/include
-I/opt/local/include/graphviz -DGRAPHVIZGT_1_16
-I/usr/local/include   -fno-common  -g -O2 -c
RgraphvizInit.c -o RgraphvizInit.o
In file included from
/opt/local/include/graphviz/render.h:45,
                 from common.h:32,
                 from RgraphvizInit.c:1:
/opt/local/include/graphviz/macros.h:34:1: warning:
"NEW" redefined
In file included from common.h:15,
                 from RgraphvizInit.c:1:
/Library/Frameworks/R.framework/Resources/include/Rdefines.h:134:1:
warning: this is the location of the previous
definition
gcc-3.3 -bundle -flat_namespace -undefined suppress
-L/usr/local/lib -o Rgraphviz.so Rgraphviz.o
RgraphvizInit.o -L/opt/local/lib/graphviz -ldotneato
-lm -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'
** Restoring previous
'/Library/Frameworks/R.framework/Versions/2.2/Resources/library/Rgraphviz'


--- Seth Falcon <sfalcon at fhcrc.org> wrote:

> Hi Bairong,
> 

> > Dear Steven:
> >
> > Thank you very much for the help, I have
> downloaded
> > and installed pkg-cofig, can I have your help for
> the
> > usage of pkg-config, since it is my first time to
> use
> > pkg-config. 
> >
> > Shoud I use ./configure 'pkg-config
> > --with-graphviz=DIR ' or should I modify the
> > configure.in file. 
> 
> Can you post the output of R CMD INSTALL
> Rgraphviz_x.y.z.tar.gz
> Rgraphviz should be detecting pkg-config.
> 
> Depending on where/how graphviz was installed, you
> may need to add a
> path to PKG_CONFIG_PATH.  Perhaps something similar
> to:
> 
> export
> PKG_CONFIG_PATH=/usr/local/lib/graphviz/pkgconfig
> 
> If pkg-config and graphviz are setup correctly, then
> the following
> should work:
> 
>   pkg-config libgvc --modversion
>   2.6   
> 
> HTH,
> 
> + seth
> 
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