[BioC] Rgraphviz, R 2.7.0 and Windows XP - SOLVED!
Jenny Drnevich
drnevich at illinois.edu
Wed Jun 11 21:59:44 CEST 2008
At 02:39 PM 6/11/2008, James W. MacDonald wrote:
>I just updated to Rgraphviz_1.18.1 (the binary version) and it still
>works for me. Plus, I have never installed Graphviz on this box, nor
>the Visual Studio redistributable.
REALLY!?! Some of us were having problems getting the binary to work
back in April after switching to R 2.7.0. Here's Martin's original
post saying it was because we needed to install Graphviz:
https://stat.ethz.ch/pipermail/bioconductor/2008-April/022026.html
I'll have to see if I can find another virgin PC to test... good
thing I work in a core lab :)
Jenny
>I haven't followed this thread closely since biocLite("Rgraphviz")
>has always worked for me out of the box, but is it really necessary
>to have these extras installed for the binary version?
>
>Jim
>
>
>
>Jenny Drnevich wrote:
>>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
>>>>>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
>>_______________________________________________
>>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
>
>_______________________________________________
>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
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