[R] about the possible errors in Rgraphviz Package
HU,ZHENGJUN
hhu at ufl.edu
Wed Mar 31 00:06:06 CEST 2010
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.
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
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