Hi All - I've downloaded Graphviz 2.8 (and graphviz 2.9 intel) and the new intel Macs (I have OSX 10.4.7) have issues with the library of the package (it automatically goes to i386, but I need it to go to /usr/local/lib/graphviz). Here's the error message I get when I try to load Rgraphviz: Loading required package: Ruuid Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library '/Library/Frameworks/R.framework/Versions/2.3/Resources/library/Rgraph viz/libs/i386/Rgraphviz.so': dlopen(/Library/Frameworks/R.framework/Versions/2.3/Resources/librar y/Rgraphviz/libs/i386/Rgraphviz.so, 6): Symbol not found: _agfstnode Referenced from: /Library/Frameworks/R.framework/Versions/2.3/Resources/library/Rgraphv iz/libs/i386/Rgraphviz.so Expected in: flat namespace Error: .onLoad failed in 'loadNamespace' for 'Rgraphviz' Error: package/namespace load failed for 'Rgraphviz' Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library '/Library/Frameworks/R.framework/Versions/2.3/Resources/library/Rgraph viz/libs/i386/Rgraphviz.so': dlopen(/Library/Frameworks/R.framework/Versions/2.3/Resources/librar y/Rgraphviz/libs/i386/Rgraphviz.so, 6): Symbol not found: _agfstnode Referenced from: /Library/Frameworks/R.framework/Versions/2.3/Resources/library/Rgraphv iz/libs/i386/Rgraphviz.so Expected in: flat namespace Error: .onLoad failed in 'loadNamespace' for 'Rgraphviz' Error: package/namespace load failed for 'Rgraphviz' How do I get around the library problem? Thanks, Jen -- Jennifer E. Buhay, Ph.D. Indiana University Department of Biology 1001 East Third Street Bloomington IN 47405 jenbuhay at indiana.edu

Hi Jen, "Jen Buhay" <jenbuhay at="" gmail.com=""> writes: > Hi All - > I've downloaded Graphviz 2.8 (and graphviz 2.9 intel) So which version do you have? How and where did you install it? > intel Macs (I have OSX 10.4.7) And an intel mac, yes? > /usr/local/lib/graphviz). Here's the error message I get when I try > to load Rgraphviz: How did you install Rgraphviz? For that matter, how did you install R? It looks like you are using an R 2.3.x from the error messages, but did you build from source, install the binary from CRAN, or ??? With a few more details, we may be able to provide some guidance. Basically, if you are using the CRAN binary version of R.app, then you should follow these instructions: 1. Install the _graphviz_ binary from http://r.research.att.com/. [First, remove any other graphviz installs.] 2. Install the _binary_ version of the BioC Rgraphviz package: source("http://bioconductor.org/biocLite.R") biocLite("Rgraphviz") + seth

[cc'd the list for the archives, etc] "Jen Buhay" <jenbuhay at="" gmail.com=""> writes: > Hi Seth - > I have R 1.16 (3198) which I downloaded from r-project.org. My Mac is > an intel. We took off the previous downloads and installed the binary > version you listed below.... same problem. For some reason, R can't > find Rgraphviz. The error message is below. Got any more > suggestions? Did you install the graphviz binary before installing Rgraphviz with biocLite? If so, then I'm somewhat at a lost as to how to help. I would recommend posting to the r-sig-mac email list. Simon, the volunteer who builds the BioC binary packages for the Mac might have some suggestions... + seth > Thanks, Jen > >> source("http://bioconductor.org/biocLite.R"); >> biocLite("Rgraphviz") > Running getBioC version 0.1.8 with R version 2.3.1 > Running biocinstall version 1.8.5 with R version 2.3.1 > Your version of R requires version 1.8 of Bioconductor. > trying URL 'http://bioconductor.org/packages/1.8/bioc/bin/macosx/i38 6/contrib/2.3/Rgraphviz_1.10.0.tgz' > Content type 'application/x-gzip' length 568248 bytes > opened URL > ================================================== > downloaded 554Kb > > > The downloaded packages are in > /tmp/RtmpzS94Lh/downloaded_packages > Warning messages: > 1: number of rows of result > is not a multiple of vector length (arg 2) in: cbind(1, res0, > Repository = repos) > 2: cannot create HTML package index in: make.packages.html() > Loading required package: graph > Loading required package: Ruuid > Error in dyn.load(x, as.logical(local), as.logical(now)) : > unable to load shared library > '/Library/Frameworks/R.framework/Versions/2.3/Resources/library/Rgra phviz/libs/i386/Rgraphviz.so': > dlopen(/Library/Frameworks/R.framework/Versions/2.3/Resources/libra ry/Rgraphviz/libs/i386/Rgraphviz.so, > 6): Symbol not found: _agfstnode > Referenced from: > /Library/Frameworks/R.framework/Versions/2.3/Resources/library/Rgrap hviz/libs/i386/Rgraphviz.so > Expected in: flat namespace > Error: .onLoad failed in 'loadNamespace' for 'Rgraphviz' > Error: package/namespace load failed for 'Rgraphviz' > > > On 9/26/06, Seth Falcon <sfalcon at="" fhcrc.org=""> wrote: >> Hi Jen, >> >> "Jen Buhay" <jenbuhay at="" gmail.com=""> writes: >> > Hi All - >> > I've downloaded Graphviz 2.8 (and graphviz 2.9 intel) >> >> So which version do you have? How and where did you install it? >> >> > intel Macs (I have OSX 10.4.7) >> >> And an intel mac, yes? >> >> > /usr/local/lib/graphviz). Here's the error message I get when I try >> > to load Rgraphviz: >> >> How did you install Rgraphviz? For that matter, how did you install >> R? It looks like you are using an R 2.3.x from the error messages, >> but did you build from source, install the binary from CRAN, or ??? >> >> With a few more details, we may be able to provide some guidance. >> >> Basically, if you are using the CRAN binary version of R.app, then you >> should follow these instructions: >> >> 1. Install the _graphviz_ binary from http://r.research.att.com/. >> [First, remove any other graphviz installs.] >> >> 2. Install the _binary_ version of the BioC Rgraphviz package: >> >> source("http://bioconductor.org/biocLite.R") >> biocLite("Rgraphviz") >> >> + seth >> > > > > -- > Jennifer E. Buhay, Ph.D. > Indiana University > Department of Biology > 1001 East Third Street > Bloomington IN 47405 > jenbuhay at indiana.edu > -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org