Re: [R] installing Rgraphviz under fedora 5

From: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>
Date: Wed, 13 Jun 2007 13:15:14 +0100 (BST)

The problem is that libgvc.so.3 is not in your dynamic library search path. That's true by default for FC5, it is in /usr/lib64/graphviz on a x86_64 FC5 box.

The proper solution is to fix the FC5 graphviz installation to tell ld.so about the location. A simpler way is to add /usr/lib64/graphviz to the LD_LIBRARY_PATH: on our servers we have edited R_HOME/etc/ldpaths to do so, so we have

: ${R_LD_LIBRARY_PATH=${R_HOME}/lib:/usr/local/lib64:/opt/export/lib64:/usr/lib6 4/graphviz}

If you don't have permissions to do this, set it in your personal LD_LIBRARY_PATH. BTW, asking questions about installing Bioconductor is best done on their mailing list, not R-help.

On Wed, 13 Jun 2007, marco.R.help marco.R.help wrote:

> Dear list,
>
> I have a lot of troubles installing Rgraphviz.
> I installed graphviz 2.13 from "graphviz-2.13.20061222.0540.tar"
> I installed the library Rgraphviz
>
>> getBioC("Rgraphviz")
> Running biocinstall version 2.0.8 with R version 2.5.0
> Your version of R requires version 2.0 of Bioconductor.
> trying URL '
> http://bioconductor.org/packages/2.0/bioc/src/contrib/Rgraphviz_1.14.0.tar.gz
> '
> Content type 'application/x-gzip' length 1522949 bytes
>
> etc etc....
>
> but when I do: library(Rgraphviz)
>
>> library(Rgraphviz)
> Error in dyn.load(x, as.logical(local), as.logical(now)) :
> unable to load shared library '/home/jke/mazu/SOFTWARE_INST/R-2.5.0
> /library/Rgraphviz/libs/Rgraphviz.so':
> libgvc.so.3: cannot open shared object file: No such file or directory
> Error : .onLoad failed in 'loadNamespace' for 'Rgraphviz'
> Error: package/namespace load failed for 'Rgraphviz'
>
> The path to Rgraphviz.so is correct !
>
> Can someone help with this?
>
> this is the session info ....
>
>
> regards
>
> Marco
>
>
>> sessioninfo()
> Error: could not find function "sessioninfo"
>> sessionInfo()
> R version 2.5.0 (2007-04-23)
> x86_64-unknown-linux-gnu
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] "tools" "stats" "graphics" "grDevices" "datasets" "utils"
> [7] "methods" "base"
>
> other attached packages:
> geneplotter lattice annotate Biobase graph
> "1.14.0" "0.15-4" "1.14.1" "1.14.0" "1.14.2"
>
> [[alternative HTML version deleted]]
>
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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>

-- 
Brian D. Ripley,                  ripley_at_stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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Received on Wed 13 Jun 2007 - 12:35:18 GMT

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