Just add one thing to what Kasper already said: I suspect that the issue is that the .so from graphviz are not visible to the loader. You can fix up the LD_LIBRARY_PATH in someway: "make install" from graphviz has some msgs like
============================================================= PATH="$PATH:/sbin" ldconfig -n /home/vital-it/lilong/bin/graphviz-2.12/lib ---------------------------------------------------------------------- Libraries have been installed in: /home/vital-it/lilong/bin/graphviz-2.12/lib ...... ============================================================== that hints how to do it. I didn't see "ldconfig" quoted in the msg... Li > Your example works fine for me on Mac OS X ppc 10.4.8 with R-2.4.1 > and graphviz 2.12 compiled from source. > > You can check your graphviz version from R by doing > R> graphvizVersion() > > You have an error in the Graphviz version reported below, I assume > you are talking about Rgraphviz' version. When you run it in the X11 > xterm (which I assume you are talking about), it seems as if some > PATH/library settings are messed up. I don't know anything about > Darwinports configuration, so I am afraid I cannot help much. > > Getting Rgraphviz to work requires some connection between graphviz > and Rgraphviz, and it is important for us to know what you installed, > and especially how. I assume Darwinports compile from source? Since > you have installed several different flavours of Graphviz, are you > certain that you have cleaned up after you? Using the Graphviz binary > provided by Simon Urbanek should work, but I find it bit puzzling > which versions (and how you installed them) you are discussing below. > > So, try to reinstall Rgraphviz the way you describe below. Note what > version of Graphviz R is linking to, both by looking at the compile > statements when installing the package (which is why you need to > reinstall) as well as trying > R> graphvizVersion() > and then see if something is not matching. > > Btw. you are most certainly not running Graphviz 2.8 under MS > Windows, unless you have taken major pains to do so. > > Personally, Graphviz used to be a pain to install on the Mac, but the > new version (2.12) compiled easily for me. > > Kasper > > > > On Feb 1, 2007, at 1:45 PM, Gavai, Anand wrote: > >> >> Hello everyone, >> I am having problems making Rgraphviz working with graphviz. >> I installed R from Darwin ports "http://darwinports.opendarwin.org/ >> getdp/" >> >> by >>> sudo port install r >> >> I set my environment variables in my .bash_profile e.g export PATH=/ >> opt/local/bin:$PATH >> >> I also installed other packages which are required for Rgraphviz >> like "graphviz" and "pkgconfig" by >> >>> sudo port install graphviz >> >>> sudo port install pkgconig >> >> both these commands will also install dependencies which are >> required. After this >> >> I start up an R session being root and get the latest version of >> bioconductor packages by sourcing it from bioconductor website >> >>> source("http://www.bioconductor.org/biocLite.R";) >>> biocLite() >> >> waited for a while and then install >> >>> biocLite("Rgraphviz",depend=TRUE,type="source") >> >> >> it worked fine when i opened it in a Terminal window, only the >> loading part but when I run something like this >> >>> library("Rgraphviz") >>> a<-c(1,0) >>> b<-c(1,1) >>> d<-rbind(a,b) >>> graphObj = ftM2graphNEL(d) >>> plot(graphObj) >> it gives me the following error messages >> >> *** caught bus error *** >> address 0x40, cause 'non-existent physical address' >> >> Traceback: >> 1: .Call("Rgraphviz_doLayout", graph, as.integer(type), PACKAGE = >> "Rgraphviz") >> 2: layoutGraph(g) >> 3: agopen(x, name = name, layout = TRUE, layoutType = y, attrs = >> attrs, nodeAttrs = nodeAttrs, edgeAttrs = edgeAttrs, subGList = >> subGList, recipEdges = recipEdges) >> 4: .local(x, y, ...) >> 5: plot(graphObj) >> 6: plot(graphObj) >> >> Possible actions: >> 1: abort (with core dump) >> 2: normal R exit >> 3: exit R without saving workspace >> 4: exit R saving workspace >> Selection: >> >> I cannot put here the sessionInfo() as i need to abort it, the >> >> the Graphviz version i have is 1.310. I also tried to install and >> configure 2.8 previously with no luck. >> >> >> in X11 >> when i load this library("Rgraphviz") in X11 interface it gives >> following error message >> >> Error in dyn.load(x, as.logical(local), as.logical(now)) : >> unable to load shared library '/Library/Frameworks/ >> R.framework/Resources/library/Rgraphviz/libs/i386/Rgraphviz.so': >> dlopen(/Library/Frameworks/R.framework/Resources/library/ >> Rgraphviz/libs/i386/Rgraphviz.so, 6): Symbol not found: _agfstnode >> Referenced from: /Library/Frameworks/R.framework/Resources/ >> library/Rgraphviz/libs/i386/Rgraphviz.so >> Expected in: dynamic lookup >> Error: .onLoad failed in 'loadNamespace' for 'Rgraphviz' >> Error: package/namespace load failed for 'Rgraphviz' >> >> the sessionInfo() here is >> >>> sessionInfo() >> R version 2.4.1 (2006-12-18) >> i386-apple-darwin8.8.1 >> >> locale: >> C >> >> attached base packages: >> [1] "tools" "stats" "graphics" "grDevices" "utils" >> "datasets" >> [7] "methods" "base" >> >> other attached packages: >> geneplotter annotate Biobase graph >> "1.12.0" "1.12.1" "1.12.2" "1.12.0" >> >> Any help in this regard is appreciated. I had simimar problem in >> the past with Suse Linux we managed to solve it, and my Windows >> station is working fine with Graphviz 2.8 and Rgraphviz >> >> only my mac system (intel tiger) is a bit of a problem. I manually >> tried to install graphviz and Rgraphviz using the source files and >> setting LD_LIBRARY_PATH and PKG_LIBRARY_PATH but in vain the only >> way to install them together without errors is through a darwinport. >> >> >> Regards, >> Anand >> >> _______________________________________________ >> R-SIG-Mac mailing list >> [email protected] >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > _______________________________________________ > Bioconductor mailing list > [EMAIL PROTECTED] > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
