Question: [R-SIG-Mac] Mac os x graphviz-Rgraphviz problem
0
12.7 years ago by
United States
Kasper Daniel Hansen6.4k wrote:
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 > R-SIG-Mac at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/r-sig-mac ADD COMMENTlink modified 12.7 years ago by Seth Falcon7.4k • written 12.7 years ago by Kasper Daniel Hansen6.4k Answer: [R-SIG-Mac] Mac os x graphviz-Rgraphviz problem 0 12.7 years ago by Seth Falcon7.4k Seth Falcon7.4k wrote: Li.Long at isb-sib.ch writes: > Hi, > > A note regarding lib paths for graphviz: (based on my own installations) > > .../graphviz-2.8/lib: /graphviz/{libgvc.so, etc} > /pkconfig > .../graphviz-2.12/lib: libgvc.so, etc. > /graphviz/{libgvplugin_* , etc) > /pkconfig > > For 2.8, it's sufficient to have > .../graphviz-2.8/lib/graphviz > in my LD_LIBRARY_PATH. While for 2.12, I've got to (manually) add > .../graphviz-2.12/lib > to my LD_LIBRARY_PATH to make libgvc.so visible to the loader. > > This is probably where the path was not set quite right for graphviz > 2.12. Just a note regarding the install location change between graphviz 2.8 and 2.12... In the devel version of Rgraphviz, the configure script has been patched to detect these and do the right thing (worked in my testing, but confirmation would be great). Also, for the OS X users, you don't get to set LD_LIBRARY_PATH, but instead DYLD_LIBRARY_PATH. + seth ADD COMMENTlink written 12.7 years ago by Seth Falcon7.4k Answer: [R-SIG-Mac] Mac os x graphviz-Rgraphviz problem 0 12.7 years ago by Li.Long@isb-sib.ch510 wrote: 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 >> R-SIG-Mac at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > ADD COMMENTlink written 12.7 years ago by Li.Long@isb-sib.ch510 Answer: [R-SIG-Mac] Mac os x graphviz-Rgraphviz problem 0 12.7 years ago by Li.Long@isb-sib.ch510 wrote: Hi, A note regarding lib paths for graphviz: (based on my own installations) .../graphviz-2.8/lib: /graphviz/{libgvc.so, etc} /pkconfig .../graphviz-2.12/lib: libgvc.so, etc. /graphviz/{libgvplugin_* , etc) /pkconfig For 2.8, it's sufficient to have .../graphviz-2.8/lib/graphviz in my LD_LIBRARY_PATH. While for 2.12, I've got to (manually) add .../graphviz-2.12/lib to my LD_LIBRARY_PATH to make libgvc.so visible to the loader. This is probably where the path was not set quite right for graphviz 2.12. 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 >> R-SIG-Mac at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >