[BioC] Rgraphviz, R 2.7.0 and Windows XP
Robert Gentleman
rgentlem at fhcrc.org
Tue Jun 3 21:29:41 CEST 2008
Jenny Drnevich wrote:
>
>>
>> > 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?
In the short - and likely even medium term that may be the only
solution. There do not seem to be easy ways to build a DLL that is
compliant (which is why the very old one was retained for such a long
time) and it requires a substantial effort with every new version of
Graphviz that comes out - given competing needs for scarce resources, I
am afraid that this is likely to be a month or more.
best wishes
Robert
>
> 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
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>> >> 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
>> >
>>
>> [[alternative HTML version deleted]]
>>
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>
> _______________________________________________
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--
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org
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