[BioC] problems loading the Rgraphviz package

Martin Morgan mtmorgan at fhcrc.org
Thu May 8 21:33:33 CEST 2008 

Hi Jenny (and Kasper, and ...) --

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."
> 
> 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. 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

Version numbers are confusing but 2.2 < 2.16 (i.e. version 2.16 is more 
recent than 2.2) because 2 < 16.

>> 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 

yep, only graphviz 2.16 will work with Rgraphviz 1.18 installed with 
biocLite.

> 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 link 
> <http://www.microsoft.com/downloads/details.aspx?familyid=32bc1bee-a3f9-4c13-9c99-220b62a191ee&displaylang=en> 
> and install Microsoft Visual C++ 2005 Redistributable Package (x86).
> 
> I had that problem as well. Good to see how to fix it. Overall, a VERY 
> difficult packages for (windows) users to get running.
> 

Yep, I agree. It's also a bit of a nightmare from the package maintainer 
perspective, because there are all these places (which you point out) 
where the information needs to be kept current, and the correct 
information depends on the machine used to build the package (i.e., not 
under the maintainer's control).

We'll try to work with the maintainer to arrive at some more robust 
solution.

Martin

> 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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>> > Bioconductor at stat.math.ethz.ch
>> > https://stat.ethz.ch/mailman/listinfo/bioconductor
>> > Search the archives: 
>> 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
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>> 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
> 


-- 
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

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