[BioC] (no subject)

Mon Nov 17 18:17:58 CET 2008

Dear Martin,

Thank you.  What are the steps for Macintosh?  I've copied in the error and my sessionInfo below.  

As far as I can tell, the version of Graphviz that I downloaded for the Mac (Version 2.20 (2.20.3)) does not have a README file.  Do I need to download that from the Graphviz website, also?

Thanks,
Monnie

##### Error I received ######
> library(Rgraphviz)
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared library '/Library/Frameworks/R.framework/Resources/library/Rgraphviz/libs/i386/Rgraphviz.so':
  dlopen(/Library/Frameworks/R.framework/Resources/library/Rgraphviz/libs/i386/Rgraphviz.so, 6): Library not loaded: /usr/local/lib/libgvc.3.dylib
  Referenced from: /Library/Frameworks/R.framework/Resources/library/Rgraphviz/libs/i386/Rgraphviz.so
  Reason: image not found
Error : .onLoad failed in 'loadNamespace' for 'Rgraphviz'
Error: package/namespace load failed for 'Rgraphviz'

### Session Info #####
> sessionInfo()
R version 2.7.2 (2008-08-25) 
i386-apple-darwin8.11.1 

locale:
en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] tools     grid      stats     graphics  grDevices utils     datasets  methods  
[9] base     

other attached packages:
[1] Rintact_1.2.0       hypergraph_1.12.0   XML_1.96-0          yeastExpData_0.9.11
[5] RBGL_1.16.0         RColorBrewer_1.0-2  Biobase_2.0.1       graph_1.18.1       

loaded via a namespace (and not attached):
[1] cluster_1.11.11
> 
________________________________________
From: Martin Morgan [mtmorgan at fhcrc.org]
Sent: Monday, November 17, 2008 5:10 PM
To: Raffaele calogero
Cc: McGee, Monnie; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] (no subject)

Raffaele calogero wrote:
> On Mon, Nov 17, 2008 at 4:59 PM, McGee, Monnie <mmcgee at mail.smu.edu> wrote:
> Dear Monnie,
> thank you for your answer.
> I Rgraphviz is always somehow problematic on windows computers.
> I do not think I have to download Graphviz since it was never
> necessary before on  packages compiled for windows. The strange point
> is that I can load and use without problems the Bioconductor 2.1
> Rgraphviz version.

Windows versions of Rgraphviz working with R 2.7.* or 2.8.* require that
you have graphviz installed. It must be a specific version of Graphviz.
The README file for the CURRENT version (for use with R-2.8.*) of
Rgraphviz says

> Windows
> =======
>
> Nov 4, 2008
>
> Here are the steps to build Rgraphviz on Windows:
>
> o. install graphviz ***2.20.3*** Windows ***binary*** distribution from
>       http://www.graphviz.org/pub/graphviz/stable/windows/graphviz-2.20.3.msi
>    , say, in dir $DIR.  We use the following as an example:
>          C:\Graphviz-2.21
>    .  If you install it in other dir, just use your dir correspondingly.
>
> o. set the following Windows environment variables accordingly
>    (control panel -> systems -> Advanced -> Environment Variables ):
>    (a) create new user variables:
>      GRAPHVIZ_INSTALL_DIR   (e.g., C:\Graphviz-2.21)
>      GRAPHVIZ_INSTALL_MAJOR (e.g., 2)
>      GRAPHVIZ_INSTALL_MINOR (e.g., 20)
>
>      Notice the way "\/" are used for the paths above.
>
>    (b) add to user variable 'path': $GRAPHVIZ_INSTALL_DIR/bin
>      e.g., C:\Graphviz-2.21\bin
>
> o. run "R CMD INSTALL ...Rgraphviz" as usual

The specific version of graphviz is different for R-2.7.*.

Martin

> Cheers
> Raffaele
>
>> Dear Raffaele,
>>
>> I have had the same problem on my Macintosh computer.  I sent an e-mail to the list last Thursday, but I have not yet received a reply.
>>
>> One question for you - have you downloaded Graphviz?  Rgraphviz will not work without Graphviz.  The website is www.graphiviz.org.
>>
>> I downloaded Graphiviz, and it didn't solve my problem, but it may solve yours.
>>
>> Good Luck!
>> Monnie
>>
>>
>> Message: 1
>> Date: Sun, 16 Nov 2008 16:39:14 +0100
>> From: rcaloger <raffaele.calogero at gmail.com>
>> Subject: [BioC] Rgraphviz error under Windows
>> To: bioconductor at stat.math.ethz.ch
>> Message-ID: <49203EA2.7030403 at unito.it>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>> HI,
>> I installed Rgraphviz_1.20.2.zip without error on Windows Vista 32 bits
>> Centrino duo with 2Gb RAM.
>> But when I tryed to load the library:
>> library(Rgraphviz)
>> I got the following error:
>> Error in get(hookname, envir = env, inherits = FALSE) :
>>  cannot allocate memory block of size 2.2 Gb
>> Error: package/namespace load failed for 'Rgraphviz'
>>
>> This happens on an clean R session without anything loaded.
>> When I tryed to install the Rgraphviz from Bioconductor 2.2
>> Rgraphviz_1.18.1.zip, instllation succeded but the loading of the
>> library produced an other error:
>>  > library(Rgraphviz)
>> Loading required package: graph
>> Loading required package: grid
>> Error in inDL(x, as.logical(local), as.logical(now), ...) :
>>  unable to load shared library
>> 'C:/R/R-2.8.0/library/Rgraphviz/libs/Rgraphviz.dll':
>>  LoadLibrary failure:  Unable to find the specified module.
>>
>> Error : .onLoad failed in 'loadNamespace' for 'Rgraphviz'
>> Error: package/namespace load failed for 'Rgraphviz'
>>
>> Loading of the Rgraphviz lib was instead successful using
>> Rgraphviz_1.16.0.zip from Bioconductor 2.1
>>
>> Any suggestion how to solve Rgraphviz loading problem?
>> Raffaele
>
>
>

--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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PO Box 19024 Seattle, WA 98109

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