[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
> 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.so, 6): Symbol not found: _agfstnode
> Referenced from: /Users/danielk/Library/R/library/Rgraphviz/libs/
> 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)
> attached base packages:
>  "tools" "stats" "graphics" "grDevices" "utils"
>  "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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