[BioC] how to configure "pkgconfig"

Seth Falcon sfalcon at fhcrc.org
Mon Nov 14 19:03:33 CET 2005

On 14 Nov 2005, brshen_fudan at yahoo.com wrote:

> 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'

What do you get for gcc --version?
If you don't see 3.3 then try:
sudo gcc_select 3.3
And rerun the install.

> 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

This is not a supported graphviz version.  It _may_ work and the
cc_dynamic issue is unlikely to be related to this, but if things
don't work after install, well, send us reports but be patient.

> 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

And this is quite odd because it looks like it *is* finding a
dotneato-config which suggests you are picking up an older version of
graphviz located in /opt/local/...

+ seth

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