[BioC] Rgraphviz package can not be invoked in Mac OS X

[Vincent Carey]

before attempting installation of Rgraphviz again, be sure you have
installed graphviz from www.graphviz.org

to ensure that you have a good installation, be sure that you have
sufficient infrastructure to perform the following in a terminal:

bash-3.2$ pkg-config --modversion libgvc
2.24.0  # that's the answer you need to see

this would involve suitably setting the PKG_CONFIG_PATH environment
variable, perhaps in ~/.bashrc


On Mon, Feb 7, 2011 at 4:36 AM, Mao Jianfeng <jianfeng.mao at gmail.com> wrote:
> Dear listers,
>
> I need you help on invoking Rgraphviz package in Mac OS X. It can be
> installed, but I failed to invoke it.
>
> Thanks in advance.
>
> Jian-Feng,
>
> #############(1) install#################################
>> source("http://bioconductor.org/biocLite.R")
> BioC_mirror = http://www.bioconductor.org
> Change using chooseBioCmirror().
>> biocLite("Rgraphviz")
> Using R version 2.12.1, biocinstall version 2.7.4.
> Installing Bioconductor version 2.7 packages:
> [1] "Rgraphviz"
> Please wait...
>
> trying URL 'http://www.bioconductor.org/packages/2.7/bioc/bin/macosx/leopard/contrib/2.12/Rgraphviz_1.28.0.tgz'
> Content type 'application/x-gzip' length 779320 bytes (761 Kb)
> opened URL
> ==================================================
> downloaded 761 Kb
>
>
> The downloaded packages are in
>        /var/folders/Ic/IcbLL0ELH9uqwZPaFP9Nz++++TQ/-Tmp-//Rtmpa2ilQU/downloaded_packages
>
>
>
> #############(2) invoke#################################
>> library(Rgraphviz)
> Error : .onLoad failed in loadNamespace() for 'Rgraphviz', details:
>  call: value[[3L]](cond)
>  error: unable to load shared object
> '/Library/Frameworks/R.framework/Versions/2.12/Resources/library/Rgraphviz/libs/x86_64/Rgraphviz.so':
>  dlopen(/Library/Frameworks/R.framework/Versions/2.12/Resources/library/Rgraphviz/libs/x86_64/Rgraphviz.so,
> 6): Library not loaded: /usr/local/lib/libgvc.5.dylib
>  Referenced from:
> /Library/Frameworks/R.framework/Versions/2.12/Resources/library/Rgraphviz/libs/x86_64/Rgraphviz.so
>  Reason: image not found
>
>  Check that (1) graphviz is installed on your system; (2) the
>  installed version of graphviz matches '2.24.0'; this is the version
>  used to build this Rgraphviz package; (3) graphviz is accessible to
>  R, e.g., the path to the graphviz 'bin' directory is in the system
>  'PATH' variable.  See additional instructions in the 'README' file of
>  the Rgraphviz 'source' distribution, available at
>
>  http://bioconductor.org/packages/release/bioc/html/Rgraphviz.html
>
>  Ask further questions on the Bioconductor mailing list
>
>  http://bioconductor.org/docs/mailList.html
>
>
> Error: package/namespace load failed for 'Rgraphviz'
>
>
> #############(3) sessionInfo and version#################################
>> version
>               _
> platform       x86_64-apple-darwin9.8.0
> arch           x86_64
> os             darwin9.8.0
> system         x86_64, darwin9.8.0
> status
> major          2
> minor          12.1
> year           2010
> month          12
> day            16
> svn rev        53855
> language       R
> version.string R version 2.12.1 (2010-12-16)
>> sessionInfo()
> R version 2.12.1 (2010-12-16)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] C/UTF-8/C/C/C/C
>
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] graph_1.28.0
>
> loaded via a namespace (and not attached):
> [1] tools_2.12.1
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>