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DESCRIPTION file and Rd examples

6 messages · Dario Strbenac, Uwe Ligges, Simon Urbanek +3 more

Original
Dario Strbenac
# 
I have a confusing error from R CMD check that I don't get when running the example manually by hand.

In the \examples section of an Rd file, I create a GRanges object, then I call a function with the GRanges object, whose first 2 lines are

    require(GenomicRanges)
    annoDF <- as.data.frame(anno) # anno is the GRanges object.

and that second line gives:

Error in as.data.frame.default(anno) : 
  cannot coerce class 'structure("GRanges", package = "GenomicRanges")' into a data.frame
Calls: annoGR2DF ... annoGR2DF -> .local -> as.data.frame -> as.data.frame.default

I have GenomicRanges listed in my Imports: field, and IRanges in the Suggests: of the DESCRIPTION file (it's require()d elsewhere). I'm trying to avoid putting packages in Depends: , so my package loads fast. Any tips of what I'm not understanding properly ?

Thanks.

--------------------------------------
Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia
Uwe Ligges
# 
It would probably be helpful if you could point us to the source version 
of your package so that we can take a look what happens.
Which version of R, and the other required packages are you talking about?

Uwe Ligges
On 15.04.2011 05:00, Dario Strbenac wrote:
Simon Urbanek
#
On Apr 14, 2011, at 11:00 PM, Dario Strbenac wrote:

            

      
      
      
    

        
require() is doesn't guarantee that the package will load, so I think what you meant to write was more

if (require(GenomicRanges, quietly=TRUE)) {
 ...

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Martin Morgan
    

    

      
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On 04/15/2011 11:18 AM, Simon Urbanek wrote:

            

      
      
      
    

        
Try IRanges::as.data.frame(anno)

I'm guessing that your call finds base::as.data.frame, perhaps because 
some earlier example has already require'd GenomicRanges, and that it's 
definition of as.data.frame has been masked some time in between.

It's too complicated to debug in detail; R CMD check produces a file 
<pkg>.Rcheck/<pkg>-Ex.R that contains the compiled example code, and it 
is in the evaluation of this file that the error occurs. So you could 
dissect it to discover the gory details.

Martin

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    
2 days later

    

      
      

        


  

        

      Shawna JOB
    

    

      
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Does anyone have any pointers on troubleshooting an R installation on a Windows 2008 server?  I had it running on a Windows 2003 server after many permissions updates to the server, but I'm stumped on getting it to run on 2008.

--The error I'm getting when I run the StatConnector Test is:
Loading StatConnector Server... Done
Initializing R...Function call failed
  Code: -2147221485
  Text: installation problem: unable to load connector
Releasing StatConnector Server...Done

--With a popup that just says:   "Method '~' of object '~' failed"

--I've run through all the documented troubleshooting I can find - no change.   I've verified the %R_HOME%, registry key corresponding to your R installation, and %PATH% mentioned in the documentation already.
--I've also tried reinstalling from scratch twice just in case.


Any suggestions would be appreciated


Shawna Job
Sr. Systems Analyst
PSOB Desk: 971-673-0128
OIS/AMS

  
  


  


      

    

    

      
      

        


  

        

      Brian Ripley
    

    

      
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This isn't 'R fails', it is 'StatConnector' fails.  That project is 
nothing to do with this list, so please don't ask here for free 
consultancy on it (and fail to give any of the information asked for 
in our posting guide).

        
On Mon, 18 Apr 2011, Shawna JOB wrote: