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Question: Error with Rgraphviz
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gravatar for Mayte Suarez-Farinas
12.5 years ago by
Mayte Suarez-Farinas300 wrote:
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
ADD COMMENTlink modified 12.5 years ago by Seth Falcon7.4k • written 12.5 years ago by Mayte Suarez-Farinas300
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gravatar for Seth Falcon
12.5 years ago by
Seth Falcon7.4k
Seth Falcon7.4k wrote:
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
ADD COMMENTlink written 12.5 years ago by Seth Falcon7.4k
0
gravatar for Mayte Suarez-Farinas
12.5 years ago by
Mayte Suarez-Farinas300 wrote:
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
ADD COMMENTlink written 12.5 years ago by Mayte Suarez-Farinas300
On Tue, 24 May 2005, Mayte Suarez-Farinas wrote: > In fact that was the first thing we did when I got the error and > it didn't work. Another hint ? > > 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 Sorry, I somehow missed the original message. Rgraphviz wouldn't install if Graphviz was not available. The most likely problem here is that you don't have the path to the graphviz libraries in your LD_LIBRARY_PATH environment variable.
ADD REPLYlink written 12.5 years ago by Jeff Gentry3.9k
0
gravatar for Seth Falcon
12.5 years ago by
Seth Falcon7.4k
Seth Falcon7.4k wrote:
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 > > ------------------------------
ADD COMMENTlink written 12.5 years ago by Seth Falcon7.4k
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