Hi Sim,
I have now checked out the installation of Graphviz 2.22 and confirmed that it does not have libcdt-4.dll in the C:\Program\Graphviz2.20\bin folder.
/Ravi
----- Original Message ----
From: "Sim, Fraser" <Fraser_Sim at URMC.Rochester.edu>
To: ravi <rv15i at yahoo.se>; Patrick Aboyoun <paboyoun at fhcrc.org>; Kasper Daniel Hansen <khansen at stat.berkeley.edu>
Cc: bioconductor at stat.math.ethz.ch
Sent: Thursday, 30 April, 2009 18:05:02
Subject: RE: [BioC] installation of Rgraphviz
Hi Ravi,
You've probably already done this but I just want to double check. Did you uninstall version 2.22 first? Was the PATH variable reset to 2.20? If not you may still be trying to load the newer version in R.
Also, could you check whether libcdt-4.dll is present in the bin folder of Graphviz2.20? It is in 2.21 but not in 2.22.
Cheers,
Fraser
-----Original Message-----
From: ravi [mailto:rv15i at yahoo.se]
Sent: Thursday, April 30, 2009 11:46 AM
To: Sim, Fraser; Patrick Aboyoun; Kasper Daniel Hansen
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] installation of Rgraphviz
Hi all,
I repeated the installation procedure after downloading and installing from the link provided by Patrick :
http://www.graphviz.org/pub/graphviz/stable/windows/graphviz-2.20.3.1.msi
Instead of version 2.20.3.1, I see that it is Graphviz 2.21 on the newly installed program on the Start->All Programs tab.
Unfortunately, I get exactly the same error message as before that libcdt-4.dll cannot be found.
Even with the older version of Graphviz.
The plot thickens now!
Thanking you,
Ravi
----- Original Message ----
From: "Sim, Fraser" <Fraser_Sim at URMC.Rochester.edu>
To: ravi <rv15i at yahoo.se>; Patrick Aboyoun <paboyoun at fhcrc.org>; Kasper Daniel Hansen <khansen at stat.berkeley.edu>
Cc: bioconductor at stat.math.ethz.ch
Sent: Thursday, 30 April, 2009 17:32:25
Subject: RE: [BioC] installation of Rgraphviz
Hi all,
I wanted to confirm the problem with 2.22.2 on my Vista 64-bit box.
I downloaded 2.22.2 msi and installed as usual. Updated the environment setting to indicate the new dir and minor version. Built RGraphviz 1.21.11 from source without error (see end of email for output).
Then tried to load the library in R 2.9.0. The following dialog appears, the application failed to start because libcdt-4.dll was not found.
R reports the following 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:/Users/FSIM/R/win-library/2.9/Rgraphviz/libs/Rgraphviz.dll':
LoadLibrary failure: The specified module could not be found.
Error : .onLoad failed in 'loadNamespace' for 'Rgraphviz'
Error: package/namespace load failed for 'Rgraphviz'
> sessionInfo()
R version 2.9.0 (2009-04-17)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] grid stats graphics grDevices datasets utils methods
[8] base
other attached packages:
[1] graph_1.21.7 rcom_2.1-3 rscproxy_1.3-1
loaded via a namespace (and not attached):
[1] cluster_1.11.13 tools_2.9.0
####
I switched back to graphviz versions 2.21.20090302.545 and it works fine.
I checked the two graphviz installs and it appears that libcdt-4.dll is not longer present in version 2.22. Hope that helps diagnose the problem?
Cheers,
Fraser
-----Original Message-----
From: ravi [mailto:rv15i at yahoo.se]
Sent: Thursday, April 30, 2009 11:19 AM
To: Patrick Aboyoun; Kasper Daniel Hansen
Cc: Sim, Fraser; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] installation of Rgraphviz
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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>>>>
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
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>>
>
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