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]]
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]]
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
--
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
On 6/13/07, marco.R.help marco.R.help <marco.r.help@gmail.com> 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 !But it's libgvc.so.3 that's missing. Make sure your LD_LIBRARY_PATH environment variable points to the directory containing it. 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]] > > ______________________________________________ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >[[alternative HTML version deleted]]
"marco.R.help marco.R.help" <marco.r.help at gmail.com> writes:> 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 RgraphvizI'm pretty sure that you will have problems with graphviz 2.13 and that you will need to use graphviz 2.12. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org