Monnie, As you mentioned, Rgraphviz requires Graphviz being installed on your machine. The BioC Mac OS X build machines both use the Graphviz distribution located at Simon Urbanek's research site: http://r.research.att.com/ http://r.research.att.com/graphviz-2.12.dmg Here is a look at the dependencies for Rgraphviz shared object on the Mac: pitt:~/sandbox/Rgraphviz/libs/i386 biocbuild$ otool -L Rgraphviz.so Rgraphviz.so: Rgraphviz.so (compatibility version 0.0.0, current version 0.0.0) /usr/local/lib/libgvc.3.dylib (compatibility version 4.0.0, current version 4.0.0) /Library/Frameworks/R.framework/Versions/2.8/Resources/lib/libR.dylib (compatibility version 2.8.0, current version 2.8.0) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFou ndation (compatibility version 150.0.0, current version 368.35.0) /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 88.3.10) If you don't use the Graphviz mentioned above, make sure you either change the link to libgvc.3.dylib or install Graphviz in /usr/local. Patrick McGee, Monnie wrote: > Dear Martin, > > Thanks for your help. It seems to me that both Rgraphviz and Graphviz must be compiled from source code, at least, that's what the README file leads me to believe. I don't suppose that anyone out there knows how to get Rgraphviz working using binaries? > > Anyway, I search my computer for libgvc.3.dylib and the file does not exist. Perhaps this goes back to the source code issue. Also, here are the results when I type Sys.getenv("LD_LIBRARY_PATH") on my computer: > > >> Sys.getenv("LD_LIBRARY_PATH") >> > LD_LIBRARY_PATH > "" > I suppose that LD_LIBRARY_PATH should say something different, but I am not sure what it should be or how to set it. > > I am going to try compiling from source and see what happens. > > Thanks again, > Monnie > ________________________________________ > From: Martin Morgan [mtmorgan at fhcrc.org] > Sent: Monday, November 17, 2008 5:28 PM > To: McGee, Monnie > Cc: Raffaele calogero; bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] (no subject) > > Hi Monnie -- I'm hoping that someone with Mac experience will provide > specific guidance. The error message says that the file libgvc.3.dylib > is not found. This is likely because it is installed somewhere that > Rgraphviz does not know about. I don't know if this is an issue with > the way graphviz was installed on your Mac (where is libgvc.3.dylib?) > or how Rgraphviz looks for this package (what does > Sys.getenv("LD_LIBRARY_PATH") say from within R?). > > The 'README' file I was referring to was the README file in the > Rgraphviz package; visit > > http://bioconductor.org/packages/2.3/bioc/html/Rgraphviz.html > > download and unpack the 'Package source' link to view. > > Martin > > "McGee, Monnie" <mmcgee at="" mail.smu.edu=""> writes: > > >> Dear Martin, >> >> Thank you. What are the steps for Macintosh? I've copied in the error and my sessionInfo below. >> >> As far as I can tell, the version of Graphviz that I downloaded for the Mac (Version 2.20 (2.20.3)) does not have a README file. Do I need to download that from the Graphviz website, also? >> >> Thanks, >> Monnie >> >> ##### Error I received ###### >> >>> library(Rgraphviz) >>> >> Error in dyn.load(file, DLLpath = DLLpath, ...) : >> unable to load shared library '/Library/Frameworks/R.framework/Re sources/library/Rgraphviz/libs/i386/Rgraphviz.so': >> dlopen(/Library/Frameworks/R.framework/Resources/library/Rgraphvi z/libs/i386/Rgraphviz.so, 6): Library not loaded: /usr/local/lib/libgvc.3.dylib >> Referenced from: /Library/Frameworks/R.framework/Resources/librar y/Rgraphviz/libs/i386/Rgraphviz.so >> Reason: image not found >> Error : .onLoad failed in 'loadNamespace' for 'Rgraphviz' >> Error: package/namespace load failed for 'Rgraphviz' >> >> ### Session Info ##### >> >>> sessionInfo() >>> >> R version 2.7.2 (2008-08-25) >> i386-apple-darwin8.11.1 >> >> locale: >> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] tools grid stats graphics grDevices utils datasets methods >> [9] base >> >> other attached packages: >> [1] Rintact_1.2.0 hypergraph_1.12.0 XML_1.96-0 yeastExpData_0.9.11 >> [5] RBGL_1.16.0 RColorBrewer_1.0-2 Biobase_2.0.1 graph_1.18.1 >> >> loaded via a namespace (and not attached): >> [1] cluster_1.11.11 >> >> ________________________________________ >> From: Martin Morgan [mtmorgan at fhcrc.org] >> Sent: Monday, November 17, 2008 5:10 PM >> To: Raffaele calogero >> Cc: McGee, Monnie; bioconductor at stat.math.ethz.ch >> Subject: Re: [BioC] (no subject) >> >> Raffaele calogero wrote: >> >>> On Mon, Nov 17, 2008 at 4:59 PM, McGee, Monnie <mmcgee at="" mail.smu.edu=""> wrote: >>> Dear Monnie, >>> thank you for your answer. >>> I Rgraphviz is always somehow problematic on windows computers. >>> I do not think I have to download Graphviz since it was never >>> necessary before on packages compiled for windows. The strange point >>> is that I can load and use without problems the Bioconductor 2.1 >>> Rgraphviz version. >>> >> Windows versions of Rgraphviz working with R 2.7.* or 2.8.* require that >> you have graphviz installed. It must be a specific version of Graphviz. >> The README file for the CURRENT version (for use with R-2.8.*) of >> Rgraphviz says >> >> >>> Windows >>> ======= >>> >>> Nov 4, 2008 >>> >>> Here are the steps to build Rgraphviz on Windows: >>> >>> o. install graphviz ***2.20.3*** Windows ***binary*** distribution from >>> http://www.graphviz.org/pub/graphviz/stable/windows/graphviz -2.20.3.msi >>> , say, in dir $DIR. We use the following as an example: >>> C:\Graphviz-2.21 >>> . 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:\Graphviz-2.21) >>> GRAPHVIZ_INSTALL_MAJOR (e.g., 2) >>> GRAPHVIZ_INSTALL_MINOR (e.g., 20) >>> >>> Notice the way "\/" are used for the paths above. >>> >>> (b) add to user variable 'path': $GRAPHVIZ_INSTALL_DIR/bin >>> e.g., C:\Graphviz-2.21\bin >>> >>> o. run "R CMD INSTALL ...Rgraphviz" as usual >>> >> The specific version of graphviz is different for R-2.7.*. >> >> Martin >> >> >>> Cheers >>> Raffaele >>> >>> >>>> Dear Raffaele, >>>> >>>> I have had the same problem on my Macintosh computer. I sent an e-mail to the list last Thursday, but I have not yet received a reply. >>>> >>>> One question for you - have you downloaded Graphviz? Rgraphviz will not work without Graphviz. The website is www.graphiviz.org. >>>> >>>> I downloaded Graphiviz, and it didn't solve my problem, but it may solve yours. >>>> >>>> Good Luck! >>>> Monnie >>>> >>>> >>>> Message: 1 >>>> Date: Sun, 16 Nov 2008 16:39:14 +0100 >>>> From: rcaloger <raffaele.calogero at="" gmail.com=""> >>>> Subject: [BioC] Rgraphviz error under Windows >>>> To: bioconductor at stat.math.ethz.ch >>>> Message-ID: <49203EA2.7030403 at unito.it> >>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >>>> >>>> HI, >>>> I installed Rgraphviz_1.20.2.zip without error on Windows Vista 32 bits >>>> Centrino duo with 2Gb RAM. >>>> But when I tryed to load the library: >>>> library(Rgraphviz) >>>> I got the following error: >>>> Error in get(hookname, envir = env, inherits = FALSE) : >>>> cannot allocate memory block of size 2.2 Gb >>>> Error: package/namespace load failed for 'Rgraphviz' >>>> >>>> This happens on an clean R session without anything loaded. >>>> When I tryed to install the Rgraphviz from Bioconductor 2.2 >>>> Rgraphviz_1.18.1.zip, instllation succeded but the loading of the >>>> library produced an other error: >>>> > 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:/R/R-2.8.0/library/Rgraphviz/libs/Rgraphviz.dll': >>>> LoadLibrary failure: Unable to find the specified module. >>>> >>>> Error : .onLoad failed in 'loadNamespace' for 'Rgraphviz' >>>> Error: package/namespace load failed for 'Rgraphviz' >>>> >>>> Loading of the Rgraphviz lib was instead successful using >>>> Rgraphviz_1.16.0.zip from Bioconductor 2.1 >>>> >>>> Any suggestion how to solve Rgraphviz loading problem? >>>> Raffaele >>>> >>> >>> >> -- >> 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 >> > > -- > 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 > > _______________________________________________ > 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 >