[BioC] Rgraphviz, R 2.7.0 and Windows XP

Jenny Drnevich drnevich at illinois.edu
Tue Jun 3 20:14:51 CEST 2008 

Hi Tony,

Actually, I have NOT been able to get Rgraphviz to work with R 2.7.0, 
and I've tried two different Windows machines. I'm not sure the 
problem completely lies with Rgraphviz, but maybe with Graphviz as 
well. Even though I want to use the Rgraphviz Windows binary instead 
of building Rgraphviz, I followed the README file found in the 
Rgraphviz_1.18.1.tar.gz source file:

1. I'm not sure how to "make sure your MSVCR80.DLL is from Microsoft 
Visual C++ 2005 SP1 Redistributable Package", but I downloaded and 
installed the package from the link provided, following all their 
instructions and warnings.

2. I downloaded and installed the graphviz-2.16.1.static.exe binary 
from Graphviz.org, which is the only 2.16 version available.

3. I created the new user variables as indicated, and made sure the 
C:\Program Files\graphviz-2.16\bin was added to my path (it was done 
automatically)

4. Then I used biocLite() to install Rgraphviz.

When I tried to load Rgraphviz, I got both a Windows error and an 
error within R; The Windows error message is known to Graphviz 
because it is mentioned on the download page: "The application has 
failed to start because somefilename.dll was not found. Re-installing 
the application may fix this problem."  Graphviz says to install 
Microsoft Visual C++ 2005 Redistributable Package (x86) to fix it, 
but I've already done that!

The R error message is:
 > library(Rgraphviz)
Loading required package: grid
Error in inDL(x, as.logical(local), as.logical(now), ...) :
   unable to load shared library 
'C:/PROGRA~1/R/R-27~1.0/library/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'


Finally, I finished the directions in the README file to safely load 
Rgraphviz but I got another error message:

 > dyn.load("C:/Program Files/graphviz-2.16/bin/gvc.dll")
Error in inDL(x, as.logical(local), as.logical(now), ...) :
   unable to load shared library 'C:/Program Files/graphviz-2.16/bin/gvc.dll':
   LoadLibrary failure:  The specified module could not be found.


So is this gvc.dll file missing from Graphviz? Or would building 
Rgraphviz from source have created it? I'm still having the general 
Windows problem related to the Microsoft Visual C++ 2005 
Redistributable Package (x86), which I have no idea how to fix. I'd 
be very interested in hearing if anyone has gotten the Rgraphviz 
Windows _binary_ working with R 2.7.0 and how they did it. If someone 
knows what I'm doing wrong or have other suggestions to try, please 
let me now! Overall, I doubt that a generic/novice Windows R user 
could be able to get Rgraphviz to work...

Thanks,
Jenny

 > sessionInfo()
R version 2.7.0 (2008-04-22)
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      splines   tools     stats     graphics  grDevices utils
  [8] datasets  methods   base

other attached packages:
  [1] affyQCReport_1.18.0  geneplotter_1.18.0   lattice_0.17-8
  [4] RColorBrewer_1.0-2   simpleaffy_2.16.0    made4_1.14.0
  [7] ade4_1.4-7           affyPLM_1.16.0       affycoretools_1.12.0
[10] annaffy_1.12.0       KEGG.db_2.2.0        gcrma_2.12.0
[13] matchprobes_1.12.0   biomaRt_1.14.0       RCurl_0.8-1
[16] GOstats_2.6.0        Category_2.6.0       genefilter_1.20.0
[19] survival_2.34-1      RBGL_1.16.0          annotate_1.18.0
[22] xtable_1.5-2         GO.db_2.2.0          AnnotationDbi_1.2.0
[25] RSQLite_0.6-8        DBI_0.2-4            graph_1.18.1
[28] limma_2.14.1         affy_1.18.0          preprocessCore_1.2.0
[31] affyio_1.8.0         Biobase_2.0.1        RWinEdt_1.8-0

loaded via a namespace (and not attached):
[1] cluster_1.11.10    KernSmooth_2.22-22 XML_1.94-0.1
 >




At 10:39 AM 6/3/2008, Tony Chiang wrote:
>I am sure that there are plenty of folks with Windows XP and R-2.7.0 who
>have gotten Rgraphviz to work. Unless you let us who what seems to be the
>problem on your end, I would suggest reading the large number of e-mails
>from the archives that deals with the different issues that have come
>up...and maybe it might solve your problems.
>
>tony
>
>On Tue, Jun 3, 2008 at 4:09 PM, Myroslav Sypa <msypa at email.unc.edu> wrote:
>
> > Hello all,
> >
> > I'm creating an application which use rJava to connect with R. But my
> > question is about Rgraphviz. Could you tell me if Rgraphviz will 
> (in nearest
> > future) work with R 2.7.0 as it has been working with R 2.6.*? I mean that
> > for installing Rgraphviz I need just run these two strings in R:
> >
> > /source("http://bioconductor.org/biocLite.R")
> > biocLite("Rgraphviz")
> >
> > /?/
> > /
> >
> > --
> > Best regards, Myroslav
> >
> > _______________________________________________
> > 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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Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at illinois.edu

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