Hi all,
I have now succeeded in installing Rgraphviz correctly now with
version 2.20 of Graphviz.
I found that the problem, this time, was the absence of Graphviz in
the path.
On adding it to the path, I could run the library(Rgraphviz) command
without getting any error messages.
I checked in the following folder : C:\Program\Graphviz2.20\bin and
found that it contained libcdt-4.dll.
(Strangely enough, it was version 2.20 and not 2.21 as shown in the
Start->All Programs tab).
This confirms your experience that the installation works with version
2.20 of Graphviz.
As Sim says, it was most probably the absence of libcdt-4.dll in
version 2.22.2 of Graphviz that was the culprit.
Thanking you,
Ravi
----- Original Message ----
From: ravi <rv15i@yahoo.se>
To: "Sim, Fraser" <fraser_sim at="" urmc.rochester.edu="">; 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 17:46:10
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@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@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/cont
rib/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 g?r 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\\System
32\\Wbem;C:\\Program\\Delade
filer\\Roxio Shared\\DLLShared\\;C:\\Program\\Delade filer\\Roxio
Shared\\10.0\\DLLShared\\;C:\\Program\\DISKEE~1\\DISKEE~1\\;C:\\Progra
m\\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@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 g?r 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:
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>>>>
>>>> _______________________________________________
>>>> Bioconductor mailing list
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>>>>
https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>
>>>
>>> _______________________________________________
>>> 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
>>
>
> _______________________________________________
> Bioconductor mailing list
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>
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