Hi,

I got "negative widths are not allowed" error when I use findOverlaps. Could anybody help me to figure this out? Thanks. Here is the code:

> library("IRanges")
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from ‘package:stats’:

    xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
    duplicated, eval, Filter, Find, get, intersect, lapply, Map,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff,
    sort, table, tapply, union, unique, unlist

> Ranges1 <- sort(IRanges(start=c(3123260, 167889600), end=c(3123360, 167893599), names=c("Site5", "Site12")))
> Ranges2 <- sort(IRanges(start=c(312326, 3123260, 167888600), end=c(312586, 3123470, 167888999), names=c("t11", "t5", "t17")))
> tree = IntervalTree(Ranges2)
> findOverlaps(tree, query = Ranges1, maxgap = 1000, minoverlap = 20, select = "first")
Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") :
  solving row 2: negative widths are not allowed
> traceback()
11: .Call(.NAME, ..., PACKAGE = PACKAGE)
10: .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
9: solveUserSEW0(start = start, end = end, width = width)
8: IRanges(pmax.int(qstart, sstart), pmin.int(send, qend))
7: .local(x, ...)
6: ranges(result, unsortedQuery, subject)
5: ranges(result, unsortedQuery, subject)
4: .postProcess_findOverlaps_result(result, unsortedQuery, origQuery,
       subject, type, minoverlap, maxgap, origSelect)
3: .local(query, subject, maxgap, minoverlap, type, select, ...)
2: findOverlaps(tree, query = Ranges1, maxgap = 1000, minoverlap = 20,
       select = "first")
1: findOverlaps(tree, query = Ranges1, maxgap = 1000, minoverlap = 20,
       select = "first")
> sessionInfo()
R Under development (unstable) (2013-04-30 r62697)
Platform: x86_64-apple-darwin12.3.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] IRanges_1.19.19    BiocGenerics_0.7.3

loaded via a namespace (and not attached):
[1] stats4_3.1.0


Yours sincerely,

Jianhong Ou

LRB 670A
Program in Gene Function and Expression
364 Plantation Street Worcester,
MA 01605

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