[BioC] Rgraphviz, R 2.7.0 and Windows XP - SOLVED!
Jenny Drnevich
drnevich at illinois.edu
Thu Jun 12 18:18:11 CEST 2008
At 02:37 AM 6/12/2008, John Barrett [jzb] wrote:
>Dear Jenny
>using your instructions I can get Rgraphviz to load with no problems
>(2.16 or 2.18)! But like Sebastian when I try and plot ,R crashes
>with no error messages. Could this be something simple like
>missing/incorrect environmental variable??
>John
Hi John,
See my new post
(https://stat.ethz.ch/pipermail/bioconductor/2008-June/022838.html)
about removing the quotes from around graphviz2.16.1\bin in your
PATH. It will be interesting to see if you still have problems if
both Graphviz 2.16.1 and 2.18.1 are present.
Let me know,
Jenny
>________________________________
>
>From: sgerega at gmail.com on behalf of Sebastien Gerega
>Sent: Wed 11/06/2008 02:56
>To: Jenny Drnevich
>Cc: Li Long; Robert Gentleman; John Barrett [jzb]; Myroslav Sypa;
>bioconductor at stat.math.ethz.ch
>Subject: Re: [BioC] Rgraphviz, R 2.7.0 and Windows XP - SOLVED!
>
>
>Hi,
>I followed these instructions and am now able to load Rgraphviz
>without error. However, when I attempt to use it R crashes.
>I am not directly using Rgraphviz but am using the topGO package
>which is calling it. I am basically just running through the example
>in the topGO vignette when R crashes.
>
>Here is my sessionInfo():
>R version 2.7.0 (2008-04-22)
>i386-pc-mingw32
>
>locale:
>LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_MONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252
>
>attached base packages:
>[1] grid tools stats graphics grDevices
>utils datasets methods base
>
>other attached packages:
> [1]
> Rgraphviz_1.18.1 topGO_1.8.1 SparseM_0.77
> GO.db_2.2.0 AnnotationDbi_1.2.0 RSQLite_0.6-8 DBI_0.2-4
> [8] graph_1.18.0 arrayQuality_1.18.0
> RColorBrewer_1.0-2 gridBase_0.4-3 hexbin_1.14.0
> lattice_0.17-6 convert_1.16.0
>[15]
>Biobase_2.0.0 marray_1.18.0 limma_2.14.4 GDD_0.1-12
>
>loaded via a namespace (and not attached):
>[1] cluster_1.11.10
>
>thanks,
>Sebastien
>
>
>
>
>On Wed, Jun 11, 2008 at 3:03 AM, Jenny Drnevich <drnevich at illinois.edu> wrote:
>
>
> Hi everyone,
>
> I finally got Rgraphviz to work from the Windows binary.
> For some reason, Graphviz versions that didn't seem to work last
> week are working this week! I just tried the following on two
> "virgin" Windows machines, and it seems to work:
>
> 1. Download and install Microsoft Visual C++ 2005 SP1
> Redistributable Package:
> http://www.microsoft.com/downloads/details.aspx?familyid=200B2FD9-AE1A-4A14-984D-389C36F85647&displaylang=en
>
> 2. Download and install the current stable release for
> Windows of Graphviz 2.18.1:
> http://www.graphviz.org/pub/graphviz/ARCHIVE/graphviz-2.18.1.exe
> (yes, I know before we were saying 2.16.1 was needed, but for some
> reason 2.18.1 is working this week!)
>
>
> 3. From within R, download and install Rgraphviz using:
> > source("http://bioconductor.org/biocLite.R")
> > biocLite("Rgraphviz")
>
> 4. If everything goes well, this should work:
> > library(Rgraphviz)
>
> I'm not having any troubles now, at least in loading the
> package! Special thanks to Martin Morgan and Tony Chiang for
> helping me sort this out off-list.
>
> Cheers,
> Jenny
>
> BTW - there's a known bug in graphviz-2.18.exe that the
> uninstall.exe file doesn't work. Won't matter until you try to
> uninstall it! They said to install the development release to the
> same folder and start menu and then uninstall.
>
>
> At 03:51 AM 6/4/2008, Li Long wrote:
>
>
> >
> > 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
> >
>
> Hi,
>
> Graphviz releases are also not as stable as one would hope:
>
> (1) graphviz 2.16 didn't contain some required
> .dlls as graphviz 2.15,
> which causes a lot of confusions, it seems like
> graphviz 2.18 contains all
> the .dlls needed and it works ok in linking; the
> README was written when
> testing was done for graphviz 2.15, assuming
> graphviz releases are
> somewhat stable...
>
> (2) graphviz built on Windows uses Microsoft Visual
> Studio, not minGW or
> any thing Linux-like, and the developers strongly discourage
> build-your-own approach; when mixing the .obj from
> these different
> sources, things are pretty nasty, and we (me and
> graphviz developers)
> haven't found a way out; it seems that the
> suggestion from graphviz users
> and developers is to use .dlls;
>
> It's not without trying...
>
> Li
>
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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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