[BioC] Rgraphviz, R 2.7.0 and Windows XP - SOLVED!

Jenny Drnevich drnevich at illinois.edu
Wed Jun 11 17:24:58 CEST 2008 

HI Sebastien,

It would be more helpful if you let us know at what point during the 
vignette code your Rgui crashed. I also was not able to get through 
the vignette - I got up through page 9, and the crash occurred when I called

 > showSigOfNodes(GOdata, score(resultFis), firstTerms = 5,
+ useInfo = "all")

Stepping through the showSigOfNodes function, the problem occurs with 
the (internal?) function plotFunction():

 >complete.dag <- plotFunction(dag, sigNodes = sigNodes, genNodes = 
names(sigTerms),
         wantedNodes = wantedNodes, showEdges = showEdges, 
useFullNames = useFullNames,
         oldSigNodes = oldSigNodes, nodeInfo = nodeInfo)

It's not easy to figure out what plotFunction is doing, and that's 
all the time I have for it now. It may be the same known problem that causes

 > example(agwrite)

to also crash R. For the life of me, I can't remember exactly what 
the problem is, and don't have time to search through the archives to 
find the post by the wonderful person who pointed it out!

Below is my sessionInfo(), right before showSigOfNodes() is called. 
showSigOfNodes() does require Rgraphviz...

Cheers,
Jenny

 > allRes <- GenTable(GOdata, classic = resultFis, KS = resultKS,
+ elim = resultElim, weight = resultWeight, orderBy = "weight",
+ ranksOf = "classic", topNodes = 20)
 > 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] splines   tools     stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
  [1] multtest_1.20.0     genefilter_1.20.0   survival_2.34-1
  [4] hgu95av2.db_2.2.0   ALL_1.4.3           topGO_1.8.1
  [7] SparseM_0.78        GO.db_2.2.0         AnnotationDbi_1.2.0
[10] RSQLite_0.6-8       DBI_0.2-4           Biobase_2.0.1
[13] graph_1.18.1

loaded via a namespace (and not attached):
[1] annotate_1.18.0 cluster_1.11.10
 >

At 08:56 PM 6/10/2008, Sebastien Gerega wrote:
>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
> >>
> >> _______________________________________________
> >> 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
> >>
> >
> > 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
> >
>
>         [[alternative HTML version deleted]]
>
>_______________________________________________
>Bioconductor mailing list
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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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