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

James W. MacDonald jmacdon at med.umich.edu
Wed Jun 11 22:52:34 CEST 2008


Martin just helped me figure out where I am missing things. I _do_ have 
Graphviz_2.16.1 'installed' in my program files directory. I say 
'installed' because I evidently just stuck it in there and put it in my 
path.

I wonder if your problem has to do with the version of Graphviz then?

Jim



James W. MacDonald wrote:
> 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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