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

Sebastien Gerega seb at gerega.net
Thu Jun 12 02:57:41 CEST 2008


I have uninstalled Graphviz2.18 and attempted using 2.16.1. This results 
in the following error:
"This application has failed to start because cdt.dll was not found. 
Re-installing the application may fix this problem."

The cdt.dll file is located in the Graphviz bin directory - but how do I 
add this path to R?
thanks,
Sebastien

James W. MacDonald wrote:
> 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
>>
>



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