[R] about the possible errors in Rgraphviz Package
Prof Brian Ripley
ripley at stats.ox.ac.uk
Tue Mar 30 22:56:04 CEST 2010
Let me add that not only do you need to match binary versions, even if
you install from the sources, Rgraphviz does not work with
graphviz-2.26.3.msi which is built with an incompatible compiler.
You need to follow the instructions exactly: they are in the Rgraphviz
source package.
Idealy Rgraphviz would be statically linked against the right version
of graphviz: that looks to be possible but very tricky as graphviz
uses plugins (and Rgraphviz uses those plugins and will crash R if
they are not present).
[Comments derived from the scars acquired in building Rgraphviz for
64-bit Windows: there is a build on CRANextras.]
On Tue, 30 Mar 2010, Duncan Murdoch wrote:
> On 30/03/2010 3:58 PM, HU,ZHENGJUN wrote:
>> Hi Martin,
>>
>> Thank you for the reply and help. I don't think that this is the version
>> problem of Graphviz. All the R packages are installed under
>> 'C:/PROGRA~1/R/R-2.10.1/library' instead of
>> 'C:/PROGRA~1/R/R-210~1.1/library', whereas the error messages are:
>>
>> "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."
>>
>
> Those are the same path. Windows has an ancient DOS compatibility mode.
>
> Duncan Murdoch
>
>> I will contact the Bioconductor mailing list.
>> Thank you again.
>> 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
>>
>
> ______________________________________________
> 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.
>
--
Brian D. Ripley, ripley at stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UK Fax: +44 1865 272595
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