[Bioc-devel] [BioC] Bioconductor1.6(Rgraphviz etc.) install pro blem with red hat9.0

[xinan yang]

Hi Ellis,

I tried the graphviz-2.6.0, the default installed path is still 
"/usr/local/lib/graphviz". and the worse is Rgraphviz-1.8.0 "unable to 
load shared library '/usr/local/lib/R/library/ 
Rgraphviz/libs/Rgraphviz.so': " again.

Then I re-tried graphviz-2.2 as mentioned in last email, it works, but 
need to type the path for R.
Where is the deault path for graphviz as Rgraphviz looks for?

need more help to simplify that.


xinan


Byron Ellis wrote:

> Yes, you've chosen to install graphviz in a place not specified in  
> the default library path so you need to set an environment variable.  
> Why is this a surprise?
>
> On Nov 22, 2005, at 8:13 AM, xinan yang wrote:
>
>> Hi Robert and Byron,
>>
>> Thanks for your prompt reply.  It seems work  using "sudo make  
>> install" !
>> because, in the shell, it "R CMD INSTALL" works, which did not work  
>> before:
>>
>> %whereis graphviz
>> graphviz: /usr/local/lib/graphviz
>>
>> %export LD_LIBRARY_PATH=/usr/local/lib/graphviz
>> %R CMD REMOVE Rgraphviz
>> % R CMD INSTALL Rgraphviz
>>
>> Then I can load the package.
>>
>>
>> But , after open a new shell, it still doesn"t work!
>> %R
>> > library(Rgraphviz)
>> Loading required package: graph
>> Loading required package: cluster
>> Loading required package: Ruuid
>> Creating a new generic function for 'print' in 'Ruuid'
>> Error in dyn.load(x, as.logical(local), as.logical(now)) :
>>        unable to load shared library '/usr/local/lib/R/library/ 
>> Rgraphviz/libs/Rgraphviz.so':
>>  libdotneato.so.0: cannot open shared object file: No such file or  
>> directory
>> Error: .onLoad failed in 'loadNamespace' for 'Rgraphviz'
>> Error: package/namespace load failed for 'Rgraphviz'
>> > sessionInfo()
>> R version 2.2.0, 2005-10-06, i686-pc-linux-gnu
>>
>> attached base packages:
>> [1] "methods"   "stats"     "graphics"  "grDevices" "utils"      
>> "datasets"
>> [7] "base"
>>
>> other attached packages:
>>   graph    Ruuid  cluster
>> "1.8.0"  "1.5.3" "1.10.2"
>>
>>
>> I must re-type "export LD_LIBRARY_PATH=/usr/local/lib/graphviz" to  
>> let it works!
>>
>>
>> BTW,
>> What should I do if I want to update the graphviz-2.2 to graphviz 2.6?
>> Simply download the graphviz-2.2.0, then "./configure","make","sudo  
>> make install" in the directory of graphviz-2.6?
>> Should I uninstall the previous one?
>>
>> The same question for R, How to install R-2.2.0 while keep the old  
>> version?
>>
>>
>> Thanks!
>>
>> Xinan
>>