[BioC] problems loading the Rgraphviz package

Thu May 8 21:42:42 CEST 2008

Thanks Martin (and Kasper, and ...),

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

This was just recently pointed out on the list, but my brain did not 
incorporate it! My biological/statistical training see it 
mathematically: 2.2 > 2.16. Maybe now after this second reminder I'll 
remember it...

:)
Jenny

>>>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]]
>>> >
>>> > _______________________________________________
>>> > Bioconductor mailing list
>>> > 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
>>>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
>>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

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