[BioC] Rgraphviz, R 2.7.0 and Windows XP
Jenny Drnevich
drnevich at illinois.edu
Tue Jun 3 20:45:44 CEST 2008
Hi Tony,
I got your other e-mail - thanks for working on trying to figure out
what's wrong. For others following this post, there is a lot of
confusion over versions. Rgraphviz's current version is 1.18.1, which
was build using Graphviz 2.16.1. To make matters worse, there is also
a stable Graphviz 2.18 version.
Jenny
At 01:33 PM 6/3/2008, Tony Chiang wrote:
>Sorry Jenny,
>
>I forgot to ask...you mention that you were using Rgraphviz_1.18.1 but then
>say you installed 2.16.1, why is that?
>
>On Tue, Jun 3, 2008 at 7:27 PM, Tony Chiang <tchiang at fhcrc.org> wrote:
>
> > Hi Jenny,
> >
> > Someone had the same error and posted the question to the mailing list.
> > Martin had a suggestion about setting the path correctly (as Li also
> > mentioned). Here is Martin's reply:
> >
> > The Rgraphviz currently available for Windows with biocLite is built
> >> with graphviz 2.16, so you'll need to install
> >>
> >> http://www.graphviz.org/pub/graphviz/ARCHIVE/graphviz
> >> -win-2.16.1.bin.tar.gz
> >>
> >> Likely the problem you have below is because the path to graphviz
> >> needs to be added to your system PATH variable, e.g., settings -> control
> >> panels -> system -> advanced -> Environment Variables and then adding
> >> or editing a variable PATH to contain the path to graphviz' bin
> >> directory. My path reads in part
> >>
> >> C:\Program Files\Graphviz2.16\Bin
> >>
> >> The version of graphviz installed on your computer has to match the
> >> version used to build Rgraphviz, so 2.18 will not work.
> >>
> >> Martin
> >
> >
> > I use google mail, so I can search in my folders for past post fairly
> > easily. There are quite a few posts about Rgraphviz, and I
> understand it has
> > been hard for people to get things working. I use a mac almost exclusively,
> > and had a rough time with it as well.
> >
> > But searching the archives and (if there is no reasonable answers there)
> > letting us know what went wrong will let us better help.
> >
> > cheers,
> > --tony
> >
> > On Tue, Jun 3, 2008 at 7:14 PM, Jenny Drnevich <drnevich at illinois.edu>
> > 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.
> >>
> >> 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
> >>> >
> >>>
> >>> [[alternative HTML version deleted]]
> >>>
> >>> _______________________________________________
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> >>> Bioconductor at stat.math.ethz.ch
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> >>> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>>
> >>
> >> 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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>
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