[BioC] problems loading the Rgraphviz package
Florian Hahne
fhahne at fhcrc.org
Thu May 8 21:30:38 CEST 2008
Jenny Drnevich wrote:
> Hi Martin,
>
> I just ran into this problem myself, and I'm a little confused as to
> your response. I was looking at all the documentation/vignettes for
> Rgraphviz, and it's not very clear or explicit either. First of all,
> there is very little mention of needing graphviz in Rgraphviz; In
> Details it does say SystemRequirements - Graphviz version >= 2.2 ,
> but that's all. It would be useful if in one or both of the vignettes
> at the beginning there was a description that an external program was
> needed, and where to go to download it. The only mention of it all in
> either vignette is at the end in the SessionInfo section, which has
> hard-coded "together with version 2.12 of graphviz."
>
Hi Jenny,
I am not sure that installation instructions for a package should be in
the vignette. First, you will not be able to read it unless you are able
to install the package (of course you can always download the pdf from
somewhere), and second, the main point of a vignette in a Bioconductor
package is to give a short introduction to the functionality provided
and, if possible, a simple use case. With the source code of the package
comes a README file that tells you about all the system requirements and
contains a detailed instruction how to install the package on Windows,
and that seems to be the standard way of documenting these things in the
software world.
> My other confusion is what version of graphviz is needed. The
> SystemRequirements says >= 2.2. The hard-coded 2.12 in the vignettes
> is obviously wrong and a hold-over from the previous version.
That should indeed be fixed. I will take a look at this.
> You say
> below Rgraphviz is built with graphviz 2.16. However, the graphviz
> website (http://www.graphviz.org/Download_windows.php) shows two
> stable versions, 2.16.1.static and 2.18. The SystemRequirements is
> obviously wrong since the developmental version is only 2.19. And I
> wasn't sure what you were referring to below when you said
>
>
>> The version of graphviz installed on your computer has to match the
>> version used to build Rgraphviz, so 2.18 will not work.
>>
>
> I assume the 2.18 is referring to the graphviz 2.18 and not a typo of
> Rgraphviz 1.18? There wasn't any mention of a higher version of
> graphviz in your e-mail, but now it makes since after visiting the
> graphviz website and noticing the ARCHIVE in the link you posted. So
> I guess that after all, I need to have graphviz 2.16 installed (AND
> in my path - another point for the vignette) ? I just wanted to
> point out that this information is apparently not associated with
> Rgraphviz at all, except for this post, and will likely cause other
> users problems.
>
> Oh, and I just noticed this Note to Windows users on the graphviz page:
>
> Meanwhile, if you get error messages like:
> "The application has failed to start because somefilename.dll was not
> found. Re-installing the application may fix this problem."
> please click this
> <http://www.microsoft.com/downloads/details.aspx?familyid=32bc1bee-a3f9-4c13-9c99-220b62a191ee&displaylang=en>link
> and install Microsoft Visual C++ 2005 Redistributable Package (x86).
>
This is also in the README file... It would be helpful if one could
point to this file directly on the Bioc packages webpage. There already
is the yellow box containing the default
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("Rgraphviz")
message, and I wonder if there is a way to customize its content.
Cheers,
Florian
> I had that problem as well. Good to see how to fix it. Overall, a
> VERY difficult packages for (windows) users to get running.
>
>
> Thanks,
> Jenny
>
> At 08:02 AM 5/8/2008, Martin Morgan wrote:
>
>> Hi --
>>
>> The Rgraphviz currently available for Windows with biocLite is built
>> with graphviz 2.16, so you'll need to install
>>
>> http://www.graphviz.org/pub/graphviz/ARCHIVE/graphviz-win-2.16.1.bin.tar.gz
>>
>> Likely the problem you have below is because the path to graphviz
>> needs to be added to your system PATH variable, e.g., settings -> control
>> panels -> system -> advanced -> Environment Variables and then adding
>> or editing a variable PATH to contain the path to graphviz' bin
>> directory. My path reads in part
>>
>> C:\Program Files\Graphviz2.16\Bin
>>
>> The version of graphviz installed on your computer has to match the
>> version used to build Rgraphviz, so 2.18 will not work.
>>
>> Martin
>>
>>
>> LiGang <luzifer.li at gmail.com> writes:
>>
>>
>>> I have problems loading the Rgraphviz package under Windows
>>>
>> with the newest
>>
>>> version of R.
>>>
>>> I installed Rgraphviz package using biocLite("Rgraphviz") method and the
>>> package version of Rgraphviz is 1.18.0.(Also, I have installed the
>>> "Rgraphviz" version 1.16.0 with no trouble at all)
>>>
>>>
>>>
>>> Here is the error message I am getting:
>>>
>>> ----
>>> Error in inDL(x, as.logical(local), as.logical(now), ...) :
>>> unable to load shared library
>>> 'C:/PROGRA~1/R/R-27~1.0RC/library/Rgraphviz/libs/Rgraphviz.dll':
>>> LoadLibrary failure: The specified module could not be found.
>>>
>>> Error : .onLoad failed in 'loadNamespace' for 'Rgraphviz'
>>> Error: package/namespace load failed for 'Rgraphviz'
>>> -----
>>>
>>> The version of Bioconductor is 2.2.
>>>
>>> And here is the session info:
>>> ############
>>> R version 2.7.0 (2008-04-22)
>>> i386-pc-mingw32
>>>
>>> locale:
>>> LC_COLLATE=Chinese_People's Republic of China.936;LC_CTYPE=Chinese_People's
>>> Republic of China.936;LC_MONETARY=Chinese_People's Republic of
>>> China.936;LC_NUMERIC=C;LC_TIME=Chinese_People's Republic of China.936
>>>
>>> attached base packages:
>>> [1] grid stats graphics grDevices utils datasets methods
>>> base
>>>
>>> other attached packages:
>>> [1] graph_1.18.0
>>>
>>> loaded via a namespace (and not attached):
>>> [1] cluster_1.11.10 tools_2.7.0
>>> ############
>>>
>>> Thanks!
>>>
>>> ---
>>> LiGang
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
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>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>> --
>> Martin Morgan
>> Computational Biology / Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N.
>> PO Box 19024 Seattle, WA 98109
>>
>> Location: Arnold Building M2 B169
>> Phone: (206) 667-2793
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
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>>
>
> Jenny Drnevich, Ph.D.
>
> Functional Genomics Bioinformatics Specialist
> W.M. Keck Center for Comparative and Functional Genomics
> Roy J. Carver Biotechnology Center
> University of Illinois, Urbana-Champaign
>
> 330 ERML
> 1201 W. Gregory Dr.
> Urbana, IL 61801
> USA
>
> ph: 217-244-7355
> fax: 217-265-5066
> e-mail: drnevich at uiuc.edu
> [[alternative HTML version deleted]]
>
> _______________________________________________
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>
--
Florian Hahne, PhD
Computational Biology Program
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-3148
fhahne at fhcrc.org
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