Re: [aroma.affymetrix] Function Clash With IRanges

[Dario Strbenac]

Thanks for this. I tried it before, but I think the reason that it didn't work 
for me previously is that I didn't start a new R session. It works now that I 
did it in a new session.

- Dario.

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Re: [aroma.affymetrix] Function Clash With IRanges

[Henrik Bengtsson]

Hi,

thanks for this.  The issue with the trim() clash with IRanges was
(supposed to be) dealt with in aroma.core v1.0.6 [2009-05-14]:

o BUG FIX: Now aroma.core works with the IRanges and grid packages,
  regardless on the order they were loaded.

and the comments in the code show that this especially done regarding
trim(). The fix is that aroma.core makes sure IRanges will always come
after R.oo in the search() path.  So, I'm interesting in getting more
details about your case.  Could you please:

1. Produce a minimum example that gives this error.
2. Show exactly what error you get.
3. Report your sessionInfo() after you get the error.

Thanks,

Henrik


On Fri, Sep 2, 2011 at 2:00 AM, Dario Strbenac dario.gar...@gmail.com wrote:
 When loading aroma.affymetrix, then calling a function that has
 require(GenomicRanges) in it, that has AromaCellPositionFile
 $byChipType(getChipType(cdf)), I get an error because IRanges has a
 trim method too, and the aroma method eventually calls trim(tags).

 Should this be R.oo::trim(tags) in the next release ?

 I have IRanges 1.10.6, aroma.affymetrix 2.1.9 and R.oo_1.8.1 in R
 2.13.0.

 --
 When reporting problems on aroma.affymetrix, make sure 1) to run the latest 
 version of the package, 2) to report the output of sessionInfo() and 
 traceback(), and 3) to post a complete code example.


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-- 
When reporting problems on aroma.affymetrix, make sure 1) to run the latest 
version of the package, 2) to report the output of sessionInfo() and 
traceback(), and 3) to post a complete code example.


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