Hi! I got an error using GOstats vignete example. I am afraid is something related with my Rgraphviz but althought we reinstalled it, I continue to get the same error (see below). I will appreciate if somebody can advice me what to do. best regards, Mayte Errors... g1 <- oneGOGraph("GO:0003680", GOMFPARENTS) > g2 <- oneGOGraph("GO:0003701", GOMFPARENTS) > g3 <- join(g1, g2) > > g4 <- GOGraph(c("GO:0003680", "GO:0003701"), GOMFPARENTS) > if( require("Rgraphviz") && interactive() ) + plot(g3) Loading required package: Rgraphviz Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library "/usr/local/R-2.0.1/library/Rgraphviz/libs/Rgraphviz.so": libdotneato.so.0: cannot open shared object file: No such file or directory Error: .onLoad failed in loadNamespace for 'Rgraphviz' > plot(g3) Error in plot.window(xlim, ylim, log, asp, ...) : need finite xlim values In addition: Warning messages: 1: no finite arguments to min; returning Inf 2: no finite arguments to max; returning -Inf 3: no finite arguments to min; returning Inf 4: no finite arguments to max; returning -Inf

Hi Mayte, Mayte Suarez-Farinas <mayte@babel.rockefeller.edu> writes: > I got an error using GOstats vignete example. > I am afraid is something related with my Rgraphviz > but althought we reinstalled it, I continue to > get the same error (see below). > I will appreciate if somebody can advice > me what to > do. > Errors... > Loading required package: Rgraphviz > Error in dyn.load(x, as.logical(local), as.logical(now)) : > unable to load shared library > "/usr/local/R-2.0.1/library/Rgraphviz/libs/Rgraphviz.so": > libdotneato.so.0: cannot open shared object file: No such file or > directory Rgraphviz depends on a library called graphviz --- this is a system-level program and not R-specific. You will need to install graphviz before using Rgraphviz. graphviz is available from www.graphviz.org. PS: Next time, be sure to tell us about the version of R you are using as well as the versions of Bioc packages and your OS! + seth

Hi Seth, In fact that was the first thing we did when I got the error and it didn't work. Another hint ? I am working with: Rgraphviz Version: 1.5.10 GOstats: Version: 1.1.3 R.version _ platform i686-pc-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status major 2 minor 0.1 year 2004 month 11 day 15 language R ------------------------------ Message: 15 Date: Mon, 23 May 2005 09:00:50 -0700 From: Seth Falcon <sfalcon@fhcrc.org> Subject: Re: [BioC] Error with Rgraphviz To: bioconductor@stat.math.ethz.ch Message-ID: <m2is1aj5jh.fsf@macaroni.local> Content-Type: text/plain; charset=us-ascii Hi Mayte, Mayte Suarez-Farinas <mayte@babel.rockefeller.edu> writes: > I got an error using GOstats vignete example. > I am afraid is something related with my Rgraphviz but althought we > reinstalled it, I continue to get the same error (see below). > I will appreciate if somebody can advice me what to do. > Errors... > Loading required package: Rgraphviz > Error in dyn.load(x, as.logical(local), as.logical(now)) : > unable to load shared library > "/usr/local/R-2.0.1/library/Rgraphviz/libs/Rgraphviz.so": > libdotneato.so.0: cannot open shared object file: No such file or > directory Rgraphviz depends on a library called graphviz --- this is a system- level program and not R-specific. You will need to install graphviz before using Rgraphviz. graphviz is available from www.graphviz.org. PS: Next time, be sure to tell us about the version of R you are using as well as the versions of Bioc packages and your OS! + seth

Hi Mayte, Two comments: 1. You appear to be using R 2.0.1 (previous R release) with Bioconductor 1.6 packages. This is not recommened. As it says on the webpage, you must have R 2.1.x to get started with Bioconductor 1.6. 2. You may need to put the graphviz lib dir in your LD_LIBRARY_PATH or edit your system config to pickup the directory into which graphviz was installed. I think the default for graphviz (if installed from source) is to install to /usr/local/lib/graphviz. With such a setup I would try: export LD_LIBRARY_PATH=/usr/local/lib/graphviz Also, what version of graphviz are you using? You should be able to discover this: dotneato-config --version 2.2 HTH, + seth Mayte Suarez-Farinas <mayte@babel.rockefeller.edu> writes: > Hi Seth, > > In fact that was the first thing we did when I got the error and > it didn't work. Another hint ? > > I am working with: > Rgraphviz Version: 1.5.10 > GOstats: Version: 1.1.3 > > R.version > _ > platform i686-pc-linux-gnu > arch i686 > os linux-gnu > system i686, linux-gnu > status > major 2 > minor 0.1 > year 2004 > month 11 > day 15 > language R > > ------------------------------