[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 20:44:23 CEST 2010
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.
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
>
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