[Bioc-devel] setdiff error (GenomicRanges)

[Hervé Pagès]

Hi Michael,

I can't reproduce this:

   > library(GenomicRanges)
   > 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

Some core packages have been updated since your original post so that
could explain why the problem is gone now. See my session info below.

Cheers,
H.


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

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=C                 LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] GenomicRanges_1.13.39 XVector_0.1.0         IRanges_1.19.28
[4] BiocGenerics_0.7.4

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


On 08/29/2013 08:48 AM, Michael Stadler wrote:
> 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
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319