[BioC] Rgraphviz, R 2.7.0 and Windows XP - SOLVED! - SOLVED AGAIN!
Sebastien Gerega
seb at gerega.net
Thu Jun 12 05:05:27 CEST 2008
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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