[BioC] Rgraphviz, R 2.7.0 and Windows XP - SOLVED!
Jenny Drnevich
drnevich at illinois.edu
Wed Jun 11 19:24:08 CEST 2008
Hi Jim,
Rgraphviz_1.18.1 . Did you build Rgraphviz from source? If so, then
the problem may be related to using the Windows binary, not the OS.
Jenny
At 12:14 PM 6/11/2008, James W. MacDonald wrote:
>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(y
>>> es , 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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>>>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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