HU,ZHENGJUN
2010-Mar-31 13:56 UTC
[R] You are right and the problem is solved. Re: about the possible errors in Rgraphviz Package
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 <mtmorgan at 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 >> <mtmorgan at 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 >>>> <mtmorgan at 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 >>>>>> <murdoch at 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 at 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 at 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
Gabor Grothendieck
2010-Mar-31 14:52 UTC
[R] You are right and the problem is solved. Re: about the possible errors in Rgraphviz Package
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) > g1A 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 <hhu at 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 <mtmorgan at 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 <mtmorgan at 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 <mtmorgan at 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 >>>>>>> <murdoch at 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 at 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 at 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 > >
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