See my new post on How to install Rgraphviz on Windows - REALLY! https://stat.ethz.ch/pipermail/bioconductor/2008-June/022838.html Thanks Sebastien for figuring this out! Jenny At 10:05 PM 6/11/2008, Sebastien Gerega wrote: >Following advice from another BioC user I ran the command > >strsplit(Sys.getenv('PATH'), ";") > >and found that the Graphviz path was incorrectly set to: > >"\"C:\\Program Files\\Graphviz2.16\\Bin\"" > >After making the necessary changes to the path in the windows system >settings the same command produces the following path: > >"C:\\Program Files\\Graphviz2.16\\Bin" > >I can now load Rgraphviz without any errors and the topGO functions >that were previously crashing R now work. >The problem is resolved for me - how about for other people? > >Sebastien > > >Sebastien Gerega wrote: >>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.htm l >>>>> >>>>>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.cond uctor >>>>>>>>>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.condu ctor >>>>>>>> >>>>>>>>-- >>>>>>>>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.conduct or >>>>>> >>>>>>-- >>>>>>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.conducto r >>>>> >>>>>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 >> >> 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