[BioC] Rgraphviz load problem

Li.Long at isb-sib.ch Li.Long at isb-sib.ch
Fri Apr 13 12:33:55 CEST 2007


It certainly sounds like installation-related issue.

I assume your "Rgraphviz" is 1.12.x.

Could you please double-check the following?
(1) Rgraphviz is 1.12.3: this version is updated to handle graphviz 2.12,
(2) new DYLD_LIBRARY_PATH is visible to your R-run (something like "env"
will tell you, if not, you can either log-out/log-back-in or do "source
~/.bashrc" to make it happen)
(3) libs (.so files) from graphviz 2.12 are indeed available in your path

Li


> Dear list,
>
> I am trying to load the package Rgraphviz on Mac OS X 10.4.9, and R
> 2.4.1 using bioC 1.9 and Graphviz 2.12  and am running into the
> following problem:
>
>  > library(Rgraphviz)
> Loading required package: graph
> Loading required package: geneplotter
> Loading required package: annotate
> Loading required package: Biobase
> Loading required package: tools
>
> Welcome to Bioconductor
>
>      Vignettes contain introductory material. To view, type
>      'openVignette()' or start with 'help(Biobase)'. For details
>      on reading vignettes, see the openVignette help page.
>
> KernSmooth 2.22 installed
> Copyright M. P. Wand 1997
> Error in dyn.load(x, as.logical(local), as.logical(now)) :
> 	unable to load shared library '/Users/danielk/Library/R/library/
> Rgraphviz/libs/i386/Rgraphviz.so':
>    dlopen(/Users/danielk/Library/R/library/Rgraphviz/libs/i386/
> Rgraphviz.so, 6): Symbol not found: _agfstnode
>    Referenced from: /Users/danielk/Library/R/library/Rgraphviz/libs/
> i386/Rgraphviz.so
>    Expected in: dynamic lookup
> Error: .onLoad failed in 'loadNamespace' for 'Rgraphviz'
> Error: package/namespace load failed for 'Rgraphviz'
>
> I have seen this problem posted before on the list, with the answer
> to reinstalling the latest binary from bioC. I have tried this and it
> didn't work. I have also seen something about setting the system
> variable DYLD_LIBRARY_PATH, and I tried setting it in ~/.bashrc:
> export DYLD_LIBRARY_PATH=/usr/local/graphviz-2.12/lib
>
> The same error as above still occurs. Does anyone know how to solve
> this problem?
>
>  > sessionInfo()
> R version 2.4.1 (2006-12-18)
> i386-apple-darwin8.8.1
>
> locale:
> en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
>
> attached base packages:
> [1] "tools"     "stats"     "graphics"  "grDevices" "utils"
> "datasets"
> [7] "methods"   "base"
>
> other attached packages:
> geneplotter    annotate     Biobase       graph
>     "1.12.0"    "1.12.0"    "1.12.2"    "1.12.1"
>  >
>
>
> --
>
> Contact information:
>
> Daniel Klevebring
> M. Sc. Eng., Ph.D. Student
> Dept of Gene Technology
> Royal Institute of Technology, KTH
> SE-106 91 Stockholm, Sweden
>
> Visiting address: Roslagstullsbacken 21, B3
> Delivery address: Roslagsvägen 30B, 104 06, Stockholm
> E-mail: daniel at biotech.kth.se
> E-mail: daniel at arrayadvice.se
> Phone: +46 8 5537 8337 (Office)
> Phone: +46 704 71 65 91 (Mobile)
> Web: http://www.ktharray.se/
> Web: http://www.arrayadvice.se/
> Fax: +46 8 5537 8481
> MSN messenger: klevebring at msn.com
>
>
>
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>
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