[BioC] installation of Rgraphviz

Kasper Daniel Hansen khansen at stat.berkeley.edu
Fri May 1 19:01:15 CEST 2009 

Somehow he knew about specifically that libcdt-4.dll was missing. I am  
just wondering how.

We do know that libcdt-4.dll has been renamed. Unfortunately  
libgraph-5.dll has been renamed to libgraph.dll conflicting with the  
Bioconductor package graph, but that has been fixed by Patrick.

It has always been essential that Rgraphviz is used with the same  
version it was build with. I have tried to do somediagnosis of this  
when loading Rgraphviz, but unfortunately (at least on windows), in  
this case (since it is not just a version conflict, but also a case of  
renamed dlls), it bangs out with an error before checks can be run.

This might be fixable, but I will need a some way to test it on  
windows. Guess I need to look into getting a virtual machine. Have  
anyone tried running/building R under Fusion or Parallels on the Mac?

Kasper

On May 1, 2009, at 9:33 , Martin Morgan wrote:

> Kasper Daniel Hansen wrote:
>> 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
>
> The error message printed in R should be interpretted as either 'I  
> am R
> and I tried to load Rgraphviz.dll, and I failed', or 'I am  
> Rgraphviz.dll
> and I tried to load a dependency of mine, and failed'. Since R has
> control over Rgraphviz installation, the usual suspect turns out to be
> the dependency-of-Rgraphviz. The content of the dialog box is of  
> course
> helpful in hind sight.
>
> Having been helpful (hopefully!) on that front, I'll spread
> mis-information by noting that I think libcdt-4.dll (and the other
> graphviz dlls) seem to be renamed with a certain amount of enthusiasm;
> this makes it essential that Rgraphviz is loaded (and checks that for
> same) with the same version of graphviz that it was built with.
>
> Martin
>
>> 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
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>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
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>>>>>>
>>>>>> _______________________________________________
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>>>>>
>>>>
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