[Bioc-devel] [devteam-bioc] Error in findOverlaps

[Hervé Pagès]

Hi,

This fails in Bioc-devel only and the following fix "seems" to address
the problem:

   hpages at thinkpad:~/svn/bioconductor/Rpacks/IRanges$ svn diff 
R/findOverlaps-methods.R
   Index: R/findOverlaps-methods.R
   ===================================================================
   --- R/findOverlaps-methods.R	(revision 78801)
   +++ R/findOverlaps-methods.R	(working copy)
   @@ -142,7 +142,7 @@
                # preprocess query
                preprocRes <- .preProcess_findOverlaps_query(query, 
maxgap, minoverlap)
                origQuery <- preprocRes$origQuery
   -            unsortedQuery <- preprocRes$origQuery
   +            unsortedQuery <- preprocRes$unsortedQuery
                query <- preprocRes$query
                query_ord <- preprocRes$query_ord

However a *real* fix would be to actually clarify what's the meaning of
using 'maxgap' and 'minoverlap' together. Right now the result below
doesn't make much sense to me (using Bioc-release):

   > findOverlaps(IRanges(1, 5), IRanges(7, 10), maxgap=3, minoverlap=2)
   Hits of length 0
   queryLength: 1
   subjectLength: 1

   > findOverlaps(IRanges(1, 5), IRanges(7, 10), maxgap=4, minoverlap=2)
   Hits of length 1
   queryLength: 1
   subjectLength: 1
     queryHits subjectHits
      <integer>   <integer>
    1         1           1

H.


On 07/23/2013 12:08 PM, Maintainer wrote:
> 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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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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