[BioC] Rgraphviz, R 2.7.0 and Windows XP - SOLVED!
James W. MacDonald
jmacdon at med.umich.edu
Wed Jun 11 22:25:31 CEST 2008
Yeah I remember seeing that and assuming I had already installed
Graphviz at some point in time. However, upon inspection of my comp I
don't see any evidence that I have done so.
I usually build R from source because I think zlib works better that way
(or some such reason that I have forgotten by now), and I then put it
right in C:\ (e.g., C:\R-2.7.0 or whatever). I wonder if the path matters?
Jim
Jenny Drnevich wrote:
> 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
--
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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