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.
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
______________________________________________
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
