Rgraphviz, R 2.7.0 and Windows XP - SOLVED!
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Jenny Drnevich ★ 2.0k
@jenny-drnevich-2812
Last seen 25 days ago
United States
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 (yes, 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
Rgraphviz Rgraphviz • 1.1k views
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Jenny Drnevich ★ 2.0k
@jenny-drnevich-2812
Last seen 25 days ago
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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(yes > , 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
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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;L C_MONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Austral ia.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(yes , >> 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
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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;L C_MONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Austral ia.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
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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. 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_Austr alia.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
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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_Austr alia.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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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.12 52;LC_MONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Aus tralia.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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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.1 252;LC_MONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Au stralia.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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At 03:52 PM 6/11/2008, 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? Could be... Early on in this long thread, it was said that Graphviz 2.16.1 specifically was needed, because that's what was used to make the Windows binary of Rgraphviz. However, when I tried it on the first virgin PC yesterday, I was still getting a Windows error saying "The application has failed to start because somefilename.dll was not found..." Then I uninstalled Graphviz 2.16.1 and installed Graphviz 2.18.1 and that seemed to work. Then I did everything, including installing R 2.7.0 from scratch, on another PC and only ever installed Graphviz 2.18.1 and was able to load the Rgraphviz library without any Windows or R errors. But I guess it's still not working correctly. SIGH. What now? Jenny >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.1 252;LC_MONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Au stralia.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.conduc tor >>>>>>>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.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.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 > >_______________________________________________ >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
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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_A ustralia.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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Entering edit mode
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.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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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
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@sebastien-gerega-2229
Last seen 8.1 years ago
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_M ONETARY=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@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(yes, 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@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@illinois.edu > > _______________________________________________ > Bioconductor mailing list > Bioconductor@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]]
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@john-barrett-jzb-2848
Last seen 8.1 years ago
Dear Jenny using your instructions I can get Rgraphviz to load with no problems (2.16 or 2.18)! But like Sebastian when I try and plot ,R crashes with no error messages. Could this be something simple like missing/incorrect environmental variable?? John ________________________________ From: sgerega@gmail.com on behalf of Sebastien Gerega Sent: Wed 11/06/2008 02:56 To: Jenny Drnevich Cc: Li Long; Robert Gentleman; John Barrett [jzb]; Myroslav Sypa; bioconductor@stat.math.ethz.ch Subject: Re: [BioC] Rgraphviz, R 2.7.0 and Windows XP - SOLVED! 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_M ONETARY=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@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 (yes, 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@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@illinois.edu _______________________________________________ Bioconductor mailing list Bioconductor@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]]
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Jenny Drnevich ★ 2.0k
@jenny-drnevich-2812
Last seen 25 days ago
United States
At 02:37 AM 6/12/2008, John Barrett [jzb] wrote: >Dear Jenny >using your instructions I can get Rgraphviz to load with no problems >(2.16 or 2.18)! But like Sebastian when I try and plot ,R crashes >with no error messages. Could this be something simple like >missing/incorrect environmental variable?? >John Hi John, See my new post (https://stat.ethz.ch/pipermail/bioconductor/2008-June/022838.html) about removing the quotes from around graphviz2.16.1\bin in your PATH. It will be interesting to see if you still have problems if both Graphviz 2.16.1 and 2.18.1 are present. Let me know, Jenny >________________________________ > >From: sgerega at gmail.com on behalf of Sebastien Gerega >Sent: Wed 11/06/2008 02:56 >To: Jenny Drnevich >Cc: Li Long; Robert Gentleman; John Barrett [jzb]; Myroslav Sypa; >bioconductor at stat.math.ethz.ch >Subject: Re: [BioC] Rgraphviz, R 2.7.0 and Windows XP - SOLVED! > > >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 > (yes, 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
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