[BioC] installation of Rgraphviz
Kasper Daniel Hansen
khansen at stat.berkeley.edu
Fri May 1 18:21:12 CEST 2009
Ravi
Just for reference for future problems: how did you know that it could
not find libcdt-4.dll. That was not mentioned in the error message you
copied and pasted (and had we known that, the diagnosis would have
been obvious). Was that displayed in some pop-up box or did you just
fail to copy and paste it (twice)?
And we are working on getting Graphviz 2.22 to work on windows.
Kasper
On Apr 30, 2009, at 8:46 , ravi wrote:
>
> 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
>>>>>
>>>>> _______________________________________________
>>>>> Bioconductor mailing list
>>>>> Bioconductor at stat.math.ethz.ch
>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>>
>>>>> _______________________________________________
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>>>>>
>>>>
>>>> _______________________________________________
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>>>
>>
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