[BioC] Rgraphviz, R 2.7.0 and Windows XP - SOLVED! - SOLVED AGAIN!
Jenny Drnevich
drnevich at illinois.edu
Thu Jun 12 18:14:33 CEST 2008
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.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
>>
>>
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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