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
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