[BioC] installation of Rgraphviz

ravi rv15i at yahoo.se
Thu Apr 30 17:18:44 CEST 2009


Hi,
Thanks to Sim, Patrick and Kasper. Thank you very much for your enthusiastic willingness to help.
Here are some extra details which can help in your troubleshooting :
I have Graphviz2.22.2. I will try my luck with version 2.20.3.1 and report.
Yes, I have the dll at the following location :
'C:/Program/R/R-2.9.0/library/Rgraphviz/libs/Rgraphviz.dll'

I get the following mesage during the installation of Rgraphviz :
> source("http://bioconductor.org/biocLite.R")
> biocLite("Rgraphviz") 
Running biocinstall version 2.4.10 with R version 2.9.0 
Your version of R requires version 2.4 of Bioconductor.
Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/windows/contrib/2.9
trying URL 'http://bioconductor.org/packages/2.4/bioc/bin/windows/contrib/2.9/Rgraphviz_1.22.0.zip'
Content type 'application/zip' length 1084292 bytes (1.0 Mb)
opened URL
downloaded 1.0 Mb
package 'Rgraphviz' successfully unpacked and MD5 sums checked

On running the command, library(Rgraphviz), I get an error message in a
separate window saying that libcdt-4.dll cannot be found. 
Further, I get the following message in R.
> 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:/Program/R/R-2.9.0/library/Rgraphviz/libs/Rgraphviz.dll':
  LoadLibrary failure:  Det går inte att hitta den angivna modulen.


Error : .onLoad failed in 'loadNamespace' for 'Rgraphviz'
Error: package/namespace load failed for 'Rgraphviz'
> 

> Sys.getenv("PATH")
PATH
"C:\\GTK\\bin;c:\\Rtools\\bin;c:\\Rtools\\perl\\bin;c:\\Rtools\\MinGW\\bin;C:\\Program\\MiKTeX
2.7\\miktex\\bin;C:\\WINDOWS\\system32;C:\\WINDOWS;C:\\WINDOWS\\System32\\Wbem;C:\\Program\\Delade
filer\\Roxio Shared\\DLLShared\\;C:\\Program\\Delade filer\\Roxio
Shared\\10.0\\DLLShared\\;C:\\Program\\DISKEE~1\\DISKEE~1\\;C:\\Program\\QuickTime\\QTSystem\\;C:\\Program\\Delade
filer\\Adobe\\AGL;C:\\Program\\MATLAB\\R2007b\\bin;C:\\Program\\MATLAB\\R2007b\\bin\\win32;C:\\Program\\Java\\jdk1.6.0_11\\bin;C:\\Program\\Graphviz2.22\\bin;C:\\Program\\ggobi" 

Please let me know if you need any extra information.
Thanking You,
Ravi


----- Original Message ----
From: Patrick Aboyoun <paboyoun at fhcrc.org>
To: Kasper Daniel Hansen <khansen at stat.berkeley.edu>
Cc: "Sim, Fraser" <Fraser_Sim at urmc.rochester.edu>; ravi <rv15i at yahoo.se>; bioconductor at stat.math.ethz.ch
Sent: Wednesday, 29 April, 2009 23:32:05
Subject: Re: [BioC] installation of Rgraphviz

One other thing, if you edited your PATH environment variable and had an R session running, you need to either restart R or make a system call from R that refreshes the environment variables. I googled for the later command and couldn't find out what it is. If anybody knows, please share.


Patrick


Patrick Aboyoun wrote:
> Kasper,
> I see what you mean. The error translates to English as "Cannot find the specified module." Ravi, can you provide more information? Does the dll exist at the location 'C:/Program/R/R-2.9.0/library/Rgraphviz/libs/Rgraphviz.dll'?
> 
> 
> Patrick
> 
> 
> Kasper Daniel Hansen wrote:
>> Patrick, Fraser
>> 
>> You are more familiar with Windows error messages. Isn't the error Ravi gets something else? It looks like it cannot find the dll.
>> 
>> Kasper
>> 
>> On Apr 29, 2009, at 10:31 , Patrick Aboyoun wrote:
>> 
>>> Ravi,
>>> As Fraser mentioned, graphviz is a moving target that we often have difficulty linking into. The Windows binary BioC 2.4 (R 2.9) package on bioconductor.org has been build using a Windows build of the previous stable release of graphviz (version 2.20.3.1) located at
>>> 
>>> http://www.graphviz.org/pub/graphviz/stable/windows/graphviz-2.20.3.1.msi 
>>> 
>>> I have tried using a Windows build of the current stable release of graphviz (version 2.22.2)
>>> 
>>> http://www.graphviz.org/pub/graphviz/stable/windows/graphviz-2.22.2.msi
>>> 
>>> but I had trouble linking into the graphviz container data type library (cdt.dll). I was experiencing an unresolved symbol in the Microsoft Visual C++ run-time library (msvcrt.dll) related to object destruction on a machine running Windows Server 2003 (with Microsoft Visual Studio 2008 Express Edition installed). Time permitting, I'll look into where in the cdt.dll graphviz library things are going awry. If others have success with the current stable release of graphviz, please share with the group.
>>> 
>>> 
>>> Cheers,
>>> Patrick
>>> 
>>> 
>>> Sim, Fraser wrote:
>>>> Hi Ravi,
>>>> 
>>>> There are often problem with graphviz and Rgraphviz based on version changes. Graphviz changes very frequently. Could you send the details of the version of graphviz you are using? I had difficulty using the latest msi file from the website and reverted to an older version with success.
>>>> 
>>>> Cheers,
>>>> Fraser
>>>> 
>>>> -----Original Message-----
>>>> From: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of ravi
>>>> Sent: Wednesday, April 29, 2009 3:32 AM
>>>> To: bioconductor at stat.math.ethz.ch
>>>> Subject: [BioC] installation of Rgraphviz
>>>> 
>>>> 
>>>> Hi all,
>>>> I have followed the instructions for installing Rgraphviz (on a win XP pc with R2.9.0) at the following link :
>>>> http://genetics.agrsci.dk/~sorenh/Rpackages-SHD.html
>>>> But I get the following error message (after apparently successfully installing Rgraphviz) :
>>>> 
>>>> 
>>>>> 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:/Program/R/R-2.9.0/library/Rgraphviz/libs/Rgraphviz.dll':
>>>>  LoadLibrary failure:  Det går inte att hitta den angivna modulen.
>>>> 
>>>> 
>>>> Error : ..onLoad failed in 'loadNamespace' for 'Rgraphviz'
>>>> Error: package/namespace load failed for 'Rgraphviz'
>>>> 
>>>> Can you see what the problem is? Is there any way of fixing it?
>>>> I have checked and confirmed that Graphviz is on the path on the environment variable window.
>>>> 
>>>> Thanking you,
>>>> Ravi
>>>> 
>>>> _______________________________________________
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>>>> 
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>>> 
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>> 
> 
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