[Bioc-devel] setdiff error (GenomicRanges)

[Michael Stadler]

Dear masters of genomic ranges,

Since a few days, I am getting an error in Bioc 2.13 when comparing two
GRanges objects by setdiff():

chrs <- c(chr1=20, chr2=20)
grA <- GRanges("chr1", IRanges(1,10), strand="*", seqlengths=chrs)
grB <- GRanges("chr2", IRanges(11,15), strand="*", seqlengths=chrs)
setdiff(grA, grB)

Warning messages:
1: In ans[] <- x :
  number of items to replace is not a multiple of replacement length
2: In ans[] <- x :
  number of items to replace is not a multiple of replacement length
Error in gaps(union(gaps(x, end = seqlengths), y), end = seqlengths) :
  error in evaluating the argument 'x' in selecting a method for
function 'gaps': Error in union(gaps(x, end = seqlengths), y) :
  error in evaluating the argument 'x' in selecting a method for
function 'union': Error in Rle(strand(listNameMatrix[2L, ]), k) :
  error in evaluating the argument 'values' in selecting a method for
function 'Rle': Error in .local(x, ...) : strand values must be in '+'
'-' '*'

This is in:
sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] C

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

other attached packages:
[1] GenomicRanges_1.13.38 XVector_0.1.0         IRanges_1.19.27
[4] BiocGenerics_0.7.4    RColorBrewer_1.0-5

loaded via a namespace (and not attached):
[1] stats4_3.0.1


The same code runs fine for Bioc 2.12:
chrs <- c(chr1=20, chr2=20)
grA <- GRanges("chr1", IRanges(1,10), strand="*", seqlengths=chrs)
grB <- GRanges("chr2", IRanges(11,15), strand="*", seqlengths=chrs)
setdiff(grA, grB)

GRanges with 1 range and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]     chr1   [1, 10]      *
  ---
  seqlengths:
   chr1 chr2
     20   20

for:
sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] C

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

other attached packages:
[1] GenomicRanges_1.12.4 IRanges_1.18.2       BiocGenerics_0.7.0
[4] RColorBrewer_1.0-5

loaded via a namespace (and not attached):
[1] stats4_3.0.1


Would anybody have an idea what could be wrong?

Kind regards,
Michael