[BioC] Rgraphviz, R 2.7.0 and Windows XP - SOLVED!
James W. MacDonald
jmacdon at med.umich.edu
Wed Jun 11 19:14:58 CEST 2008
What version of Rgraphviz is this? I don't have any problem running
Sweave on the topGO vignette:
> Sweave("topGO.Rnw")
Writing to file topGO.tex
Processing code chunks ...
1 : term verbatim
2 : echo term hide
3 : echo term verbatim
4 : echo term verbatim
5 : echo term verbatim
Loading required package: survival
Loading required package: splines
6 : echo term hide
7 : echo term verbatim
8 : echo term verbatim
9 : echo term verbatim
10 : echo term hide
11 : echo term hide
Loading required package: multtest
12 : term verbatim eps pdf
13 : echo term hide
14 : echo term verbatim
15 : echo term hide
16 : echo term hide
17 : echo term hide
18 : echo term hide
19 : echo term hide
20 : echo term hide
21 : echo term verbatim
22 : echo term hide
23 : echo term hide
24 : echo term verbatim
25 : echo term verbatim
26 : echo term verbatim
27 : echo term verbatim
28 : echo term verbatim
29 : echo term verbatim
30 : term verbatim
31 : term tex
Loading required package: xtable
32 : echo term hide
Loading required package: Rgraphviz
Loading required package: grid
33 : term hide
34 : echo term verbatim
35 : echo term verbatim
36 : term tex
You can now run LaTeX on 'topGO.tex'
> 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
[7] datasets utils methods base
other attached packages:
[1] Rgraphviz_1.18.0 xtable_1.5-2 multtest_1.20.0
[4] genefilter_1.20.0 survival_2.34-1 hgu95av2.db_2.2.0
[7] ALL_1.4.3 topGO_1.8.1 SparseM_0.77
[10] GO.db_2.2.0 AnnotationDbi_1.2.0 RSQLite_0.6-8
[13] DBI_0.2-4 Biobase_2.0.1 graph_1.18.1
loaded via a namespace (and not attached):
[1] annotate_1.18.0 cluster_1.11.10
>
Jenny Drnevich wrote:
> 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
>> 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
--
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
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