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

[Mao Jianfeng]

Thanks a lot. I will try it.

Jian-Feng,



2011/2/7 Vincent Carey <stvjc at channing.harvard.edu>:
> 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
>>
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>>
>



-- 
Jian-Feng, Mao

the Institute of Botany,
Chinese Academy of Botany,