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/Rgraph viz' ** Restoring previous '/Library/Frameworks/R.framework/Versions/2.2/Resources/library/Rgraph viz' 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/Rgraph viz' ** Restoring previous '/Library/Frameworks/R.framework/Versions/2.2/Resources/library/Rgraph viz' --- 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >

Dear Seth: Thanks for your kind help, I have successfully installed Rgraphviz, by "sudo gcc_select 3.3 " and rerun the insatll. (I also removed the /opt directory, which is a fink darwin port version) Best regards, Bairong --- Seth Falcon <sfalcon at="" fhcrc.org=""> wrote: > 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/Rgraph viz' > > ** Restoring previous > > > '/Library/Frameworks/R.framework/Versions/2.2/Resources/library/Rgraph viz' > > 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >