Hi, I have graphviz v2.21 installed along with R 2.8 and Rgraphviz. I am not able to get Rgraphviz to function, on win XP and Vista pc's.There has been a lot of discussion on this, both in the bioconductor and the R mailing list. I would like to know what the current situation and recommended procedure is. I get the error message that cdt.dll is missing when trying to load Rgraphviz in R. Also, the following output : > library(Rgraphviz) Loading required package: graph Loading required package: grid Error in inDL(x, as.logical(local), as.logical(now), ...) : unable to load shared library 'C:/Users/Ravi/R/win-library/2.8/Rgraphviz/libs/Rgraphviz.dll': LoadLibrary failure: Det g?r inte att hitta den angivna modulen. The sessionInfo command gives the following output : > sessionInfo() R version 2.8.0 (2008-10-20) i386-pc-mingw32 locale: LC_COLLATE=Swedish_Sweden.1252;LC_CTYPE=Swedish_Sweden.1252;LC_MONETAR Y=Swedish_Sweden.1252;LC_NUMERIC=C;LC_TIME=Swedish_Sweden.1252 attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] graph_1.20.0 loaded via a namespace (and not attached): [1] cluster_1.11.11 tools_2.8.0 What is the solution to this problem. Should I switch to an earlier version of graphviz? Where do I find it? Should I add something to the path in the environmental variable list? Thanking You, Ravi

ravi <rv15cap at="" gmail.com=""> writes: > Hi, > I have graphviz v2.21 installed along with R 2.8 and Rgraphviz. I am > not able to get Rgraphviz to function, on win XP and Vista pc's.There > has been a lot of discussion on this, both in the bioconductor and the Ravi -- Likely you need to o. install graphviz ***2.16*** Windows ***binary*** distribution from http://www.graphviz.org/Download_windows.php say, in dir $DIR. We use the following as an example: C:\R-tools\graphviz-2.16 If you install it in other dir, just use your dir correspondingly. o. set the following Windows environment variables accordingly (control panel -> systems -> Advanced -> Environment Variables ): (a) create new user variables: GRAPHVIZ_INSTALL_DIR (e.g., C:\/R-tools\/graphviz-2.16) GRAPHVIZ_INSTALL_MAJOR (e.g., 2) GRAPHVIZ_INSTALL_MINOR (e.g., 16) Notice the way "\/" are used for the paths above. (b) add to user variable 'path': $GRAPHVIZ_INSTALL_DIR/bin e.g., C:\R-tools\graphviz-2.16\bin This is from the instructions in the README file of Rgraphviz. Some functionality remains unavalable, especially exporting to .dot files. Martin > R mailing list. I would like to know what the current situation and > recommended procedure is. > I get the error message that cdt.dll is missing when trying to load > Rgraphviz in R. Also, the following output : >> library(Rgraphviz) > Loading required package: graph > Loading required package: grid > Error in inDL(x, as.logical(local), as.logical(now), ...) : > unable to load shared library > 'C:/Users/Ravi/R/win-library/2.8/Rgraphviz/libs/Rgraphviz.dll': > LoadLibrary failure: Det g?r inte att hitta den angivna modulen. > > The sessionInfo command gives the following output : >> sessionInfo() > R version 2.8.0 (2008-10-20) > i386-pc-mingw32 > > locale: > LC_COLLATE=Swedish_Sweden.1252;LC_CTYPE=Swedish_Sweden.1252;LC_MONET ARY=Swedish_Sweden.1252;LC_NUMERIC=C;LC_TIME=Swedish_Sweden.1252 > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] graph_1.20.0 > > loaded via a namespace (and not attached): > [1] cluster_1.11.11 tools_2.8.0 > > What is the solution to this problem. Should I switch to an earlier > version of graphviz? Where do I find it? Should I add something to the > path in the environmental variable list? > Thanking You, > Ravi > > _______________________________________________ > 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 -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793

ravi <rv15cap at="" gmail.com=""> writes: > Martin, > Thanks for your prompt reply. On the graphviz link that you have > provided, I am only able to find graphviz version 2.20.3. I find no > archives there to locate v2.16. Will the rest of the procedure work > with v2.20.3. Otherwise, how do I find v2.16? Try http://www.graphviz.org/pub/graphviz/stable/windows/ and specifically http://www.graphviz.org/pub/graphviz/stable/windows/graphviz-2.16.1.ex e > Next, I would like to confirm that I have to create the following user > variables. > variable : GRAPHVIZ_INSTALL_DIR > value : C:\/graphviz-2.16 ##### I don't have R-tools installed (do > I still have to include the V in front?) The '\/' is not a V. It must be there. > variable : GRAPHVIZ_INSTALL_MAJOR > value : 2 > variable : GRAPHVIZ_INSTALL_MINOR > value : 16 > > For example, I have the following user variable right now : > Variable : INCLUDE > Value :C:\WATCOM\H;C:\WATCOM\H\NT > > Will the above procedure work if I enter 2 and 20 for version 2.20.3 > of graphviz (instead of 2 and 16 respectively)? If you are using the Rgraphviz build by Bioconductor you MUST use graphviz 2.16. So these numbers must be 2 and 16. > Next, for the PATH (a system variable), > I will add : > C:\graphviz2.20\bin > > I am sorry to bore you with these details, but it seems to be > necessary to follow the exact procedure. > This is the reason for my spelling out all the details, and wanting > confirmation. > > I will also try to dig into the the use of Rtools and see if I can > install from the source. That can be useful for other cases as well. > Thanking you, > Ravi -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793