[R] You are right and the problem is solved. Re: about the possible errors in Rgraphviz Package

Gabor Grothendieck ggrothendieck at gmail.com
Wed Mar 31 16:52:38 CEST 2010 

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 <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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