Disjoin bug ======== It seems to have a bug when there are names on the IRanges: library(IRanges) ir = IRanges(start = 1:3, end = 2:4) disjoin(ir) ## Correct names(ir) = c("a", "b", "c") disjoin(ir) ## Wrong IRanges of length 3 start end width names [1] 1 1 1 a [2] 2 2 1 b [3] 3 3 1 c Warning messages: 1: In x at start[] <- numeric2integer(value) : number of items to replace is not a multiple of replacement length 2: In width(x) + numeric2integer(value) : longer object length is not a multiple of shorter object length 3: In width(x) + numeric2integer(value) - end(x) : longer object length is not a multiple of shorter object length 4: In x at width[] <- width(x) + numeric2integer(value) - end(x) : number of items to replace is not a multiple of replacement length The last range from 4 to 4 is not included in the output. c behaviour ========= It seems to behave strangely in connection with do.call and a named list: ir = IRanges(start = 1:3, end = 2:4) do.call(c, list(ir, ir)) ## What I expect, a single IRange with 6 entries. do.call(c, list(ir1 = ir, ir2 = ir)) ## This I don't get $ir1 IRanges of length 3 start end width [1] 1 2 2 [2] 2 3 2 [3] 3 4 2 $ir2 IRanges of length 3 start end width [1] 1 2 2 [2] 2 3 2 [3] 3 4 2 My guess is that this is something with c and method dispatching and do.call. Using fresh IRanges 1.5.36 from devel. Kasper

On Fri, Jan 29, 2010 at 10:31 AM, Kasper Daniel Hansen < khansen@stat.berkeley.edu> wrote: > Disjoin bug > ======== > > It seems to have a bug when there are names on the IRanges: > > library(IRanges) > ir = IRanges(start = 1:3, end = 2:4) > disjoin(ir) ## Correct > > names(ir) = c("a", "b", "c") > disjoin(ir) ## Wrong > > IRanges of length 3 > start end width names > [1] 1 1 1 a > [2] 2 2 1 b > [3] 3 3 1 c > Warning messages: > 1: In x@start[] <- numeric2integer(value) : > number of items to replace is not a multiple of replacement length > 2: In width(x) + numeric2integer(value) : > longer object length is not a multiple of shorter object length > 3: In width(x) + numeric2integer(value) - end(x) : > longer object length is not a multiple of shorter object length > 4: In x@width[] <- width(x) + numeric2integer(value) - end(x) : > number of items to replace is not a multiple of replacement length > > The last range from 4 to 4 is not included in the output. > > Thanks, I just fixed this. > > c behaviour > ========= > > It seems to behave strangely in connection with do.call and a named list: > > ir = IRanges(start = 1:3, end = 2:4) > do.call(c, list(ir, ir)) ## What I expect, a single IRange with 6 entries. > do.call(c, list(ir1 = ir, ir2 = ir)) ## This I don't get > > $ir1 > IRanges of length 3 > start end width > [1] 1 2 2 > [2] 2 3 2 > [3] 3 4 2 > > $ir2 > IRanges of length 3 > start end width > [1] 1 2 2 > [2] 2 3 2 > [3] 3 4 2 > > My guess is that this is something with c and method dispatching and > do.call. > > Yes, it is known that there is strange behavior here. The combination of dispatching on a .Primitive and the "..." signature pushes things a bit too far. > Using fresh IRanges 1.5.36 from devel. > > Kasper > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]