[BioC] Rgraphviz, R 2.7.0 and Windows XP
Martin Morgan
mtmorgan at fhcrc.org
Tue Jun 3 20:36:56 CEST 2008
I'm a little reluctant to add my comments here, which seem to miss the
mark more often than not on this, but..
Jenny Drnevich wrote:
> 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.
Actually, you don't want this static version. Instead go looking here
http://www.graphviz.org/pub/graphviz/ARCHIVE/
Make sure to clean up as completely as possible your previous installation.
I *think*, contrary to previous posts of mine, that you can also use the
recent graphviz (2.18), so long as you're building Rgraphviz yourself.
Once built, your Rgraphviz will still have missing functionality, in
particular it will be unable to read / write graph objects using agopen,
agwrite, etc. This seems to be a complex issue in the interaction
between R and graphviz, tracing I think to the use of different
development tools for the two project. There might be similar surprises
in other functions; these are just the ones that the Bioc build machine
stumbles on when checking the package. You'll encounter missing
functionality in a most unpleasant way, abruptly aborting your session.
I think the rationale for not updating the instructions in the package,
or making some functionality 'optional' on windows, is the hope for a
more robust solution.
Again I seem to have a poor track record on providing reliable
information about this, so please take with a grain of salt.
Martin
> 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
>> >
>> > _______________________________________________
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>> > https://stat.ethz.ch/mailman/listinfo/bioconductor
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>> > http://news.gmane.org/gmane.science.biology.informatics.conductor
>> >
>>
>> [[alternative HTML version deleted]]
>>
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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
>
> _______________________________________________
> Bioconductor mailing list
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--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M2 B169
Phone: (206) 667-2793
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