[BioC] shared library 'Rgraphviz' not found

[Martin Morgan]

On 02/18/2010 01:01 AM, Gustavo Lacerda wrote:
>> Hi Gustavo --
>>
>> yes, your PATH needs to include something like
>>
>>  c:\Program Files\Graphviz2.20\bin
> 
> 
> Thanks!
> 
> In the meantime, things stopped working again due to a system
> restore... While I did lose my modified PATH variable, I suspect
> something else is responsible this time.
> 
> Now when I do:  library(Rgraphviz)
> My error is:  there is no package called 'Rgraphviz'
> 
> When I do
>  strsplit(Sys.getenv("PATH"), ";")
> 
> I get :
> $PATH
> ...
>  [3] "C:\\Progra~1\\Graphviz2.20\\bin"
> 

Can you confirm that this points to the correct place? what does

  list.files("C:\\Progra~1\\Graphviz2.20\\bin")

display?

> 
> The only slightly weird thing is that when I call library(),  I get:
> 
> << Packages in library 'C:/PROGRA~1/R/R-29~1.1/library': >>
> 
> which is a non-existent directory: the correct name is "R-2.9.1".

this is the Windows short name of the file. In a DOS shell try

  DIR/x "c:\Program Files\R"

to see. Nothing to be concerned about.

> 
> Yet I can load other packages. Only Rgraphviz isn't working...
> 
> Upon further investigation, there was a weird folder named
> "file1eb26e9", containing another copy of the Rgraphviz folder. The
> only apparent difference between them is that the latter has 5 files
> which seem to be necessary for being an R library: CONTENTS,
> DESCRIPTION, INDEX, MD5, NAMESPACE.
> 
> Putting this in the place of "Rgraphviz" (after renaming the orig. inal
> to "Rgraphviz-broken"), has the effect that library() can now see
> Rgraphviz.  However, there is still an error:

Was file1eb260 in the c:\Program Files\R\R-2.9.1\library directory? If
so, remove it. Also remove the version that you renamed as Rgraphviz,
and you might as well remove Rgraphiz-broken while you're at it. Do this
using Windows; no need to involve R. Likely these are left-overs from a
failed installation attempt.

>> library(Rgraphviz)
> Loading required package: graph
> Loading required package: grid
> Error in library.dynam(lib, package, package.lib) :
>   shared library 'Rgraphviz' not found
> In addition: Warning message:
> package 'Rgraphviz' was built under R version 2.9.2
> Error: package/namespace load failed for 'Rgraphviz'
> 
> 
> What does this mean,  "shared library 'Rgraphviz' not found" ?
> 
> I'd be happy to reinstall Rgraphviz... but I do *NOT* want to upgrade
> from 1.22.2, because that sounds like more headache.

With your cleaned up R, and with your PATH variable set correctly. What
happens when you ask to install Rgraphviz using biocLite

  source('http://bioconductor.org/biocLite.R')
  biocLite('Rgraphviz')

?

> 
> Cheers,
> 
> Gustavo
> 
> 
> 
>>>
>>> Error in inDL(x, as.logical(local), as.logical(now), ...) :
>>>  unable to load shared library
>>> 'c:/PROGRA~1/R/R-2.9.1/library/Rgraphviz/libs/Rgraphviz.dll':
>>>  LoadLibrary failure:  The specified module could not be found.
>>>
>>> In addition: Warning message:
>>> package 'Rgraphviz' was built under R version 2.9.2
>>> Error: package/namespace load failed for 'Rgraphviz'
>>
>> You shouldn't see this message if you install using biocLite(). If you
>> do, then please let us know; you might want to visit
>>
>>  http://bioconductor.org/docs/install
>>
>> and follow the directions for updating packages.
>>
>> Martin
>>>
>>> _______________________________________________
>>> 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 M1 B861
>> Phone: (206) 667-2793
>>


-- 
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