[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 17:18:25 CEST 2010 

By the way, just in case you did not read the entire message R crashed
when I tried to run the code from the vignette.

On Wed, Mar 31, 2010 at 10:52 AM, Gabor Grothendieck
<ggrothendieck at 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:
>
> 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
>>
>>
>
> ______________________________________________
> 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.
>

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