[R] You are right and the problem is solved. Re: about the possible errors in Rgraphviz Package
Martin Morgan
mtmorgan at fhcrc.org
Wed Mar 31 21:29:38 CEST 2010
On 03/31/2010 11:44 AM, Gabor Grothendieck wrote:
> I got an error message *AND* R becomes unusable and had to be restarted.
>
> Using dependency walker it seems to be complaining about R.dll so I
> copied all of my ...\R\bin\R*.dll files to ..
> ...\win-library\2.10\Rgraphviz\libs.
>
> Then it complained about IESHIMS.dll so I copied \Program
> Files\Internet Explorer\IESHIMS.dll to
> ...\win-library\2.10\Rgraphviz\libs.
>
> Looking at dependency walker these DLLs: LIBCDT-4.DLL, LIBGRAPH-4.DLL,
> and LIBGVC-4.DLL all seem to point to correct place.
>
> I still have this message in dependency walker:
> Warning: At least one module has an unresolved import due to a missing
> export function in a delay-load dependent module.
>
> There is a red mark beside:
> c:\windows\system32\IEFRAME.DLL
> but its not missing.
>
> I also tried reinstalling R using the latest R 2.10.1.
>
> I am still getting the same result, namely I can run the indicated
> code up to but not including plot(g1) but if I run plot(g1) R crashes
> and must be restarted.
Wow, I didn't mean to put you through such convolutions, and am sorry
that I can't offer an immediate solution. Martin
>
>
>
> On Wed, Mar 31, 2010 at 12:54 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
>> 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
>>> <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:
>>
>> 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.
>
> Yes, My path is:
>
> PATH=C:\Graphviz2.20\bin;...more stuff...
>
>>
>> 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 <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.
>>>>
>>>
>>> ______________________________________________
>>> 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
>>
--
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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