By the way, just in case you did not read the entire message R crashed 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: > > 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.