I bet there is a lot of code that depends on having the hits (conveniently) ordered by query,subject index, so we should try to restore the previous behavior.
On Wed, Jan 14, 2015 at 8:00 PM, Dario Strbenac <dstr7...@uni.sydney.edu.au> wrote: > Hello, > > For an identical query, the matrix results are in a different order. > Consider the subject hits of the last two rows : > > > mapping # R Under development (unstable) (2015-01-13 r67453) and > IRanges 2.1.35 > queryHits subjectHits > [1,] 1 1 > [2,] 1 4 > [3,] 2 2 > [4,] 4 1 > [5,] 4 4 > [6,] 6 7 > [7,] 6 6 > > > mapping # R Under development (unstable) (2015-01-13 r67453) and > IRanges 2.0.1 > queryHits subjectHits > [1,] 1 1 > [2,] 1 4 > [3,] 2 2 > [4,] 4 1 > [5,] 4 4 > [6,] 6 6 > [7,] 6 7 > > This causes some values to be extracted in a different order by our > annotationLookup function, and causes an error for the development version > of Repitools on a test case which uses all.equal to compare a list to a > correct list, but not for the release version which uses the release > version of IRanges. Should I update the test case to have a new expected > result, or is this new characteristic of findOverlaps likely to revert to > the previous output soon ? > > The two sets of intervals to produce this result are anno and probesGR, > defined in the tests.R file in the Repitools package. > > -------------------------------------- > Dario Strbenac > PhD Student > University of Sydney > Camperdown NSW 2050 > Australia > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel