[R] Reserve and biobase

[Martin Morgan]

Wild speculation on my part, but I wonder if the 'graphics window'
that pops up is the 'welcome' message in Biobase? This is invoked by a
call to 'message' in the .onAttach function...

.onAttach <- function(libname, pkgname) {
   message(paste("\nWelcome to Bioconductor\n",
   [etc]

If so,

suppressMessages(library(Biobase))

might help. It would be great to hear confirmation of this as the
problem. If not, a completely streamlined example (no extra packages
loaded / actions taken) would aid in debugging.

Martin
-- 
Bioconductor

Robert Gentleman <rgentlem at fhcrc.org> writes:

> You should ask questions about Bioconductor software on the Bioconductor 
> list, you might also read the posting guide and provide version numbers 
> for all packages you are using (the output of sessionInfo is useful).
>
> Biobase does not do any plotting, so where ever the action is coming 
> from it is unlikely to be Biobase that is doing it. I don't use Rserve 
> so I cannot comment on how that might interact with other software. I 
> have no idea what you are trying to do, but somehow you seem to be doing 
> a lot more than just loading Biobase - so why not try just doing that 
> and leave out all the other code opening devices (and why open two 
> postscript devices and then close them?).
>
> Robert
>
>
> saeedeh maleki wrote:
>> Hi 
>>    
>>   I am using Rserve for R2.3.1.  every time after I load Biobase
>>   library, a new Graphics window frame pops up. Could any onw know
>>   how can avoid it.
>>    
>>   Best
>>   Saeede 
>>    
>>   class testReserve {
>>     public static void main(String[] args) {
>>     RServeConnection rsCon = null;
>>     Rconnection c = null;
>>     Process proc = null;
>>       try {
>>       Runtime rt = Runtime.getRuntime();
>>       proc = rt.exec(generalMetaData.rserveDir);
>>       try {
>>         c = new Rconnection();
>>         c.eval("library(grDevices)");
>> //        c.eval("graphics.off()");
>>         c.eval("postscript()");
>>         //load library
>>         c.eval("library(tools)");
>>         System.out.println(" load library tools");
>>         c.eval(" postscript('foo2.ps')");
>>         c.eval(" library(Biobase)");
>>         c.eval("graphics.off()");
>>         System.out.println(" load library Biobase");
>>        
>>         }
>>       catch (RSrvException ex1) {
>>         System.out.println(ex1.getMessage());
>>       }
>>       }
>>     catch (Exception e) {
>>       System.out.print("cannot run rserve");
>>     }
>>     //end of testing
>>     }
>> }
>>    
>> 
>>  		
>> ---------------------------------
>> 
>> 	[[alternative HTML version deleted]]
>> 
>> ______________________________________________
>> R-help at stat.math.ethz.ch mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>> 
>
> -- 
> Robert Gentleman, PhD
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M2-B876
> PO Box 19024
> Seattle, Washington 98109-1024
> 206-667-7700
> rgentlem at fhcrc.org
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.