I got an error message *AND* R becomes unusable and had to be restarted. Using dependency walker it seems to be complaining about R.dll so I copied all of my ...\R\bin\R*.dll files to .. ...\win-library\2.10\Rgraphviz\libs.
Then it complained about IESHIMS.dll so I copied \Program Files\Internet Explorer\IESHIMS.dll to ...\win-library\2.10\Rgraphviz\libs. Looking at dependency walker these DLLs: LIBCDT-4.DLL, LIBGRAPH-4.DLL, and LIBGVC-4.DLL all seem to point to correct place. I still have this message in dependency walker: Warning: At least one module has an unresolved import due to a missing export function in a delay-load dependent module. There is a red mark beside: c:\windows\system32\IEFRAME.DLL but its not missing. I also tried reinstalling R using the latest R 2.10.1. I am still getting the same result, namely I can run the indicated code up to but not including plot(g1) but if I run plot(g1) R crashes and must be restarted. On Wed, Mar 31, 2010 at 12:54 PM, Martin Morgan <mtmor...@fhcrc.org> wrote: > On 03/31/2010 08:18 AM, Gabor Grothendieck wrote: >> By the way, just in case you did not read the entire message R crashed > > I think you mean that you got an error message, not that R became > unusable? More below... > >> when I tried to run the code from the vignette. >> >> On Wed, Mar 31, 2010 at 10:52 AM, Gabor Grothendieck >> <ggrothendi...@gmail.com> wrote: >>> Based on your success I thought I would try again. I am not sure why I >>> had more success this time but this time I got this far even though I >>> did not change my path at all or make any system changes from what I >>> had before. I did reinstall Rgraphviz but used the previously >>> installed graphviz. I tried this code taken from the Rgrpahviz >>> vignette: >>> >>>> library("Rgraphviz") >>> Loading required package: graph >>> Loading required package: grid >>>> set.seed(123) >>>> V <- letters[1:10] >>>> M <- 1:4 >>>> g1 <- randomGraph(V, M, 0.2) >>>> g1 >>> A graphNEL graph with undirected edges >>> Number of Nodes = 10 >>> Number of Edges = 16 >>> >>> >>> but when I tried to plot it R crashed. >>> >>>> plot(g1) >>> >>> It did produce this message on the Windows console (not the R console): >>> >>> Error: Layout type: "dot" not recognized. Use one of: > > In the past this has come about when accessing incorrect graphviz DLLs. > The gory detail (if I remember correctly) is that a FILE* gets allocated > in Rgraphviz and passed to graphviz, and if there is a compiler mismatch > then there are no guarantees about FILE* representation. > > The implication is that your Rgraphviz and graphiz are at least partly > out of sync, but it could also be that I am 'getting lucky'. When you > say (quoting from above)... > >>> did not change my path at all or make any system changes from what I > > the implication is that your PATH was already set to include a > graphviz2.20\\bin directory; I'd encourage you to confirm that. Yes, My path is: PATH=C:\Graphviz2.20\bin;...more stuff... > > And recognizing that you might justifiably be willing to put this on the > shelf, you might also use Dependency Walker > (http://www.dependencywalker.com/) to open the Rgraphviz DLL > (R_HOME/libraries/Rgraphviz/libs/Rgraphviz.dll), right click on the > RGRAPHVIZ.DLL showing up in the top left panel, and choose 'Full paths', > and verify that LIBCDT-4.DLL, LIBGRAPH-4.DLL, and LIBGVC-4.DLL all point > to Graphviz2.20\bin. > > Martin > > >>> There was nothing after the of: >>> >>>> R.version.string >>> [1] "R version 2.10.1 Patched (2010-03-10 r51276)" >>>> win.version() >>> [1] "Windows Vista (build 6002) Service Pack 2" >>>> packageDescription("Rgraphviz")$Version >>> [1] "1.24.0" >>>> graphvizVersion() >>> $installed_version >>> [1] ‘2.20.3’ >>> >>> $build_version >>> [1] ‘2.20.3’ >>> >>> >>> >>> >>> On Wed, Mar 31, 2010 at 9:56 AM, HU,ZHENGJUN <h...@ufl.edu> wrote: >>>> Hi Martin, >>>> >>>> It is really a 'PATH' problem. After adding C:\Program >>>> Files\Graphviz2.20\bin to the 'PATH' environment variable, the Rgraphviz >>>> package can be loaded without any error messages. >>>> >>>> Sorry that I ONLY set my 'PATH' environment variable correctly for R but >>>> not for Graphviz. >>>> >>>> Thank you and Duncan so much for your great help. >>>> Howard >>>> >>>> >>>> On Tue Mar 30 18:12:54 EDT 2010, Martin Morgan <mtmor...@fhcrc.org> wrote: >>>> >>>>> On 03/30/2010 03:06 PM, HU,ZHENGJUN wrote: >>>>>> >>>>>> Hi Martin, >>>>>> >>>>>> I am 100% sure that I set my 'PATH' environment variable correctly >>>>>> because all other packages can loaded correctly as well as because R can >>>>>> be run correctly under both MS DOS and MS Windows XP. Also, I can create >>>>>> some simple R packages correctly. >>>>> >>>>> The PATH must be set correctly to include graphviz, as in my example >>>>> below. Copy and paste the output of >>>>> >>>>> strsplit(Sys.getenv("PATH"), ";") >>>>> >>>>> and >>>>> >>>>> list.files(strsplit(Sys.getenv("PATH"), ";")[[1]][[14]], "dll") >>>>> >>>>> Martin >>>>> >>>>>> >>>>>> Thanks. >>>>>> Howard >>>>>> >>>>>> >>>>>> On Tue Mar 30 16:58:55 EDT 2010, Martin Morgan <mtmor...@fhcrc.org> >>>>>> wrote: >>>>>> >>>>>>> On 03/30/2010 01:13 PM, HU,ZHENGJUN wrote: >>>>>>>> >>>>>>>> Hi Martin, >>>>>>>> >>>>>>>> I uninstalled graphviz-2.26.3.msi and then installed >>>>>>>> graphviz-2.20.3.1.msi. Then installed the >>>>>>>> Rgraphviz package again. As expected, I got the same error messages as >>>>>>>> before: >>>>>>>> >>>>>>>> "Error in inDL(x, as.logical(local), as.logical(now), ...) : >>>>>>>> unable to load shared library >>>>>>>> 'C:/PROGRA~1/R/R-210~1.1/library/Rgraphviz/libs/Rgraphviz.dll': >>>>>>>> LoadLibrary failure: The specified module could not be found." >>>>>>> >>>>>>> 'LoadLibrary' is being vague, the 'specified modules' are the DLLs from >>>>>>> graphviz. >>>>>>> >>>>>>> Have you checked that your 'PATH' environment variable is set correctly? >>>>>>> In R >>>>>>> >>>>>>> > strsplit(Sys.getenv("PATH"), ";") >>>>>>> $PATH >>>>>>> ... >>>>>>> [14] "C:\\Program Files\\Graphviz2.20\\bin" >>>>>>> ... >>>>>>> >>>>>>> The relevant files in this directory might look like >>>>>>> >>>>>>>> list.files(strsplit(Sys.getenv("PATH"), ";")[[1]][[14]], "dll") >>>>>>> >>>>>>> [1] "iconv.dll" "intl.dll" >>>>>>> [3] "jpeg62.dll" "libcairo-2.dll" >>>>>>> [5] "libcdt-4.dll" "libcgraph-4.dll" >>>>>>> [7] "libexpat.dll" "libfontconfig-1.dll" >>>>>>> [9] "libfreetype-6.dll" "libgdk_pixbuf-2.0-0.dll" >>>>>>> [11] "libglib-2.0-0.dll" "libgmodule-2.0-0.dll" >>>>>>> [13] "libgobject-2.0-0.dll" "libgraph-4.dll" >>>>>>> [15] "libgvc-4.dll" "libgvplugin_core-5.dll" >>>>>>> [17] "libgvplugin_dot_layout-5.dll" "libgvplugin_gd-5.dll" >>>>>>> [19] "libgvplugin_neato_layout-5.dll" "libgvplugin_pango-5.dll" >>>>>>> [21] "libltdl-3.dll" "libpango-1.0-0.dll" >>>>>>> [23] "libpangocairo-1.0-0.dll" "libpangoft2-1.0-0.dll" >>>>>>> [25] "libpangowin32-1.0-0.dll" "libpathplan-4.dll" >>>>>>> [27] "libpng12.dll" "libxml2.dll" >>>>>>> >>>>>>> Martin >>>>>>> >>>>>>>> >>>>>>>> Thank you. >>>>>>>> Howard >>>>>>>> >>>>>>>> >>>>>>>> On Tue Mar 30 15:36:05 EDT 2010, Martin Morgan <mtmor...@fhcrc.org> >>>>>>>> wrote: >>>>>>>> >>>>>>>>> On 03/30/2010 10:24 AM, HU,ZHENGJUN wrote: >>>>>>>>>> >>>>>>>>>> Hi Duncan, >>>>>>>>>> >>>>>>>>>>> (They are pretty hard to find, but I think you can find them on the >>>>>>>>>>> Bioconductor site.) It is > not enough to install the Rgraphviz >>>>>>>>>>> package, you also need to install Graphviz. >>>>>>>>>> >>>>>>>>>> Yes I did. Before installing the Rgraphviz package successfully, >>>>>>>>>> (1) I >>>>>>>>>> downloaded graphviz-2.26.3.msi for MS Windows (XP) and installed it >>>>>>>>>> successfully and (2) I also installed the packages from >>>>>>>>>> Bioconductor by: >>>>>>>>>> (Note: I use MS Windows XP and R 2.10.1 version) >>>>>>>>> >>>>>>>>> This is a bioconductor package so please ask on the Bioconductor >>>>>>>>> mailing >>>>>>>>> list >>>>>>>>> >>>>>>>>> http://bioconductor.org/docs/mailList.html >>>>>>>>> >>>>>>>>> See the 'README' file in the 'tar.gz' file at >>>>>>>>> >>>>>>>>> >>>>>>>>> http://bioconductor.org/packages/release/Software.html >>>>>>>>> http://bioconductor.org/packages/2.5/bioc/html/Rgraphviz.html >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> http://bioconductor.org/packages/2.5/bioc/src/contrib/Rgraphviz_1.24.0.tar.gz >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> which says >>>>>>>>> >>>>>>>>> >>>>>>>>> o. install Graphviz ***2.20.3.1*** Windows ***binary*** distribution >>>>>>>>> from >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> http://www.graphviz.org/pub/graphviz/stable/windows/graphviz-2.20.3.1.msi >>>>>>>>> >>>>>>>>> >>>>>>>>> you must use this version of graphviz. File paths must be correct. >>>>>>>>> >>>>>>>>> Martin >>>>>>>>> >>>>>>>>> >>>>>>>>>> >>>>>>>>>> source("http://www.bioconductor.org/biocLite.R") >>>>>>>>>> biocLite() >>>>>>>>>> >>>>>>>>>> I got those error messages: >>>>>>>>>> >>>>>>>>>> "Error in inDL(x, as.logical(local), as.logical(now), ...) : >>>>>>>>>> unable to load shared library >>>>>>>>>> 'C:/PROGRA~1/R/R-210~1.1/library/Rgraphviz/libs/Rgraphviz.dll': >>>>>>>>>> LoadLibrary failure: The specified module could not be found." >>>>>>>>>> >>>>>>>>>> Obviously, it seems it is the package problem because it should go >>>>>>>>>> to >>>>>>>>>> 'C:/PROGRA~1/R/R-2.10.1/library/Rgraphviz/libs/Rgraphviz.dll' >>>>>>>>>> instead of >>>>>>>>>> 'C:/PROGRA~1/R/R-210~1.1/library/Rgraphviz/libs/Rgraphviz.dll' >>>>>>>>>> >>>>>>>>>> Thank you for the reply. Howard >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Tue Mar 30 12:50:44 EDT 2010, Duncan Murdoch >>>>>>>>>> <murd...@stats.uwo.ca> >>>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>>> On 30/03/2010 10:44 AM, HU,ZHENGJUN wrote: >>>>>>>>>>>> >>>>>>>>>>>> Hi All, >>>>>>>>>>>> >>>>>>>>>>>> I tried to install the package of Rgraphviz in the following two >>>>>>>>>>>> ways successfully: >>>>>>>>>>>> >>>>>>>>>>>> source("http://bioconductor.org/biocLite.R") >>>>>>>>>>>> biocLite("Rgraphviz") >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> install.packages(pkgs="C:/Progra~1/R/lib_download/Rgraphviz_1.24.0.zip", >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> lib="C:/Progra~1/R/R-2.10.1/library", repos=NULL) >>>>>>>>>>>> >>>>>>>>>>>> but when I loaded the package though library(Rgraphviz) or >>>>>>>>>>>> library("Rgraphviz"), and got the same error message below: >>>>>>>>>>>> >>>>>>>>>>>> "Error in inDL(x, as.logical(local), as.logical(now), ...) : >>>>>>>>>>>> unable to load shared library >>>>>>>>>>>> 'C:/PROGRA~1/R/R-210~1.1/library/Rgraphviz/libs/Rgraphviz.dll': >>>>>>>>>>>> LoadLibrary failure: The specified module could not be found." >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Most likely the problem is that you haven't followed the >>>>>>>>>>> installation >>>>>>>>>>> instructions. (They are pretty hard to find, but I think you can >>>>>>>>>>> find >>>>>>>>>>> them on the Bioconductor site.) It is not enough to install the >>>>>>>>>>> Rgraphviz package, you also need to install Graphviz. >>>>>>>>>>> >>>>>>>>>>> Duncan Murdoch >>>>>>>>>>>> >>>>>>>>>>>> I think that it is the error in the package because it should go to >>>>>>>>>>>> 'C:/PROGRA~1/R/R-2.10.1/library/Rgraphviz/libs/Rgraphviz.dll' >>>>>>>>>>>> instead >>>>>>>>>>>> of 'C:/PROGRA~1/R/R-210~1.1/library/Rgraphviz/libs/Rgraphviz.dll' >>>>>>>>>>>> >>>>>>>>>>>> Could anyone help me to solve to problem? >>>>>>>>>>>> Thank you very much for the help. Howard >>>>>>>>>>>> >>>>>>>>>>>> ______________________________________________ >>>>>>>>>>>> R-help@r-project.org mailing list >>>>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-help >>>>>>>>>>>> PLEASE do read the posting guide >>>>>>>>>>>> http://www.R-project.org/posting-guide.html >>>>>>>>>>>> and provide commented, minimal, self-contained, reproducible code. >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> -- HU,ZHENGJUN >>>>>>>>>> >>>>>>>>>> ______________________________________________ >>>>>>>>>> R-help@r-project.org mailing list >>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-help >>>>>>>>>> PLEASE do read the posting guide >>>>>>>>>> http://www.R-project.org/posting-guide.html >>>>>>>>>> and provide commented, minimal, self-contained, reproducible code. >>>>>>>>> >>>>>>>>> >>>>>>>>> -- Martin Morgan >>>>>>>>> Computational Biology / Fred Hutchinson Cancer Research Center >>>>>>>>> 1100 Fairview Ave. N. >>>>>>>>> PO Box 19024 Seattle, WA 98109 >>>>>>>>> >>>>>>>>> Location: Arnold Building M1 B861 >>>>>>>>> Phone: (206) 667-2793 >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- HU,ZHENGJUN >>>>>>>> >>>>>>> >>>>>>> >>>>>>> -- Martin Morgan >>>>>>> Computational Biology / Fred Hutchinson Cancer Research Center >>>>>>> 1100 Fairview Ave. N. >>>>>>> PO Box 19024 Seattle, WA 98109 >>>>>>> >>>>>>> Location: Arnold Building M1 B861 >>>>>>> Phone: (206) 667-2793 >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> >>>>>> -- HU,ZHENGJUN >>>>>> >>>>> >>>>> >>>>> -- Martin Morgan >>>>> Computational Biology / Fred Hutchinson Cancer Research Center >>>>> 1100 Fairview Ave. N. >>>>> PO Box 19024 Seattle, WA 98109 >>>>> >>>>> Location: Arnold Building M1 B861 >>>>> Phone: (206) 667-2793 >>>>> >>>>> >>>> >>>> >>>> >>>> -- >>>> HU,ZHENGJUN >>>> >>>> >>> >>> ______________________________________________ >>> R-help@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/r-help >>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html >>> and provide commented, minimal, self-contained, reproducible code. >>> >> >> ______________________________________________ >> R-help@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. > > > -- > Martin Morgan > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.