[R] You are right and the problem is solved. Re: about the possible errors in Rgraphviz Package
HU,ZHENGJUN
hhu at ufl.edu
Wed Mar 31 15:56:49 CEST 2010
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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