[BioC] installation of Rgraphviz
Martin Morgan
mtmorgan at fhcrc.org
Fri May 1 18:33:19 CEST 2009
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
>>>>>>
>>>>>> _______________________________________________
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>>>>>> _______________________________________________
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>>>>>>
>>>>>
>>>>> _______________________________________________
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