[BioC] Rgraphviz, R 2.7.0 and Windows XP
Jenny Drnevich
drnevich at illinois.edu
Tue Jun 3 21:12:01 CEST 2008
>
> > 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.
> >
>
>At least on my Macbook pro, this is true (at least it works for me without
>failing). Jenny, if
>you use biocLite, make sure that you set the type="source" to build it from
>source.
Using the archived Graphviz 2.16 didn't change anything - still same
errors. Also, I'm deliberately not building Rgraphviz from source,
but instead trying to get the Windows binary to work. If it can't be
made to work, perhaps the Windows binary should be removed?
Thanks,
Jenny
> >
> > 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 don't have access to a windows machine at the moment, but this also
>happened on my mac a few months back (always with the agopen and agwrite).
>After I grab the lastest X-code (with the latest compliers) and built both
>graphviz and Rgraphviz from source on the (also following Martin's advice to
>make sure that all previous incarnations of graphviz were completely removed
>before building graphviz again), this problem seems to have gone away.
>
>
> >
> > 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.
> >
>
>I should say ditto for me too now!
>
>
> >
> > 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
> >>> >
> >>> > _______________________________________________
> >>> > 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]]
> >>>
> >>> _______________________________________________
> >>> 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
> >>>
> >>
> >> 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
> >> 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
> >>
> >
> >
> > --
> > 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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>
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