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. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ > -- 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. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/
