[BioC] About KEGGgraph supplementary information

[Jitao Zhang]

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Hi dear Alper,

  I don't know this problem before and it seems to me rather that this
is caused by the Rgraphviz library. Could you please try

  > library(Rgraphviz)

  If it prints the same error codes, please follow the suggestions it
gives (for example to change PATH variable). If the problem still
exists, please feel free to write to bioconductor mail-list (I have
cc-ed there). People in the Rgraphviz group will definitely like to help.

  Best wishes,
David

Uzun, Alper wrote:
> Hi David,
> 
> Thank you very much for your swift response.
> 
> Actually I need to ask one more question, when I try to load the library (> library(KEGGgraph) )
> It gives an error. By the way I already installed Graphviz program. I guess It cant find the the program
> what is your suggestion to solve it?
> 
> Error is pasted below;
> Thank you
> Alper
> **************************************************************
>> library(KEGGgraph)
> Loading required package: XML
> Loading required package: graph
> 
> Attaching package: 'graph'
> 
> The following object(s) are masked from 'package:XML':
> 
>     addNode
> 
> Loading required package: Rgraphviz
> Loading required package: grid
> Error : .onLoad failed in loadNamespace() for 'Rgraphviz', details:
>   call: value[[3L]](cond)
>   error: unable to load shared object 'C:/PROGRA~1/R/R-212~1.0/library/Rgraphviz/libs/i386/Rgraphviz.dll':
>   LoadLibrary failure:  The specified module could not be found.
> 
>   Check that (1) graphviz is installed on your system; (2) the
>   installed version of graphviz matches '2.20.3'; 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
> 
> **************************************************************
> 
> 
> 
> 
> 
> -----Original Message-----
> From: Jitao Zhang [mailto:j.zhang at dkfz-heidelberg.de]
> Sent: Wednesday, November 10, 2010 4:26 AM
> To: Uzun, Alper
> Subject: Re: About KEGGgraph supplementary information
> 
> Hi dear Alper,
> 
>   Thanks for your notification. The file is attached. It was for the version published in 2008 and since then some codes had to be changed due to the KEGG upgrade. Please turn to the KEGGgraph documentation for any questions and don't hesitate to contact me in case further questions exist.
> 
>   Best wishes,
> David
> 
> Uzun, Alper wrote:
>> Dear Dr. Zhang,
> 
>> I was reading your article and try to reach supplementary information at Bioinformatics Journal, but unfortunately it is not reachable (The link says "not found").
>> Could you please send me this supplementary information at your convenience?
> 
>> Thank you
>> Alper
> 
>> -------------------------------------------------------------------
>> Alper Uzun, Ph.D.
>> Women & Infants Hospital, Department of Pediatrics.
>> Brown University, Center for Computational Molecular Biology.
>> Alpert Medical School, Bio-Med Pediatrics.
>> Providence, RI, USA
>> -------------------------------------------------------------------
>> http://www.womenandinfants.org/<blocked::http://www.womenandinfants.or
>> g/> http://www.brown.edu/<blocked::http://www.brown.edu/>
> 
> 
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> 
> 

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- --
PLEASE BE GREEN, THINK BEFORE YOU PRINT

Jitao David Zhang
Computational Biology/Biostatistics Ph.D. Candidate
Division of Molecular Genome Analysis, DKFZ
Im Neuenheimer Feld 580,
Heidelberg D-69120
Germany

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