[Bioc-devel] warning when merging disjoint sets of seqlevels

Hi Michael,


On 10/12/2014 02:02 PM, Michael Lawrence wrote:

This recently became a warning, and I am not sure why. Yes, in the overlap
case, that might be something to worry about. But a perfectly reasonable
use case of merge,Seqinfo is to merge two disjoint sets of seqlevels. Now
we're forced to use suppressWarnings() for that.

For that use case, nothing has changed, we've always had a warning and
we still have it.

With BioC 2.14:

  > merge(Seqinfo("chr1"), Seqinfo("chr2"))

  Seqinfo of length 2
  seqnames seqlengths isCircular genome
  chr1             NA         NA   <NA>
  chr2             NA         NA   <NA>
  Warning message:
  In .Seqinfo.mergexy(x, y) :
    Each of the 2 combined objects has sequence levels not in the other:
    - in 'x': chr1
    - in 'y': chr2
    Make sure to always combine/compare objects based on the same reference
    genome (use suppressWarnings() to suppress this warning).

With BioC 3.0:

  > merge(Seqinfo("chr1"), Seqinfo("chr2"))

  Seqinfo object with 2 sequences from an unspecified genome; no
seqlengths:
    seqnames seqlengths isCircular genome
    chr1             NA         NA   <NA>
    chr2             NA         NA   <NA>
  Warning message:
  In .Seqinfo.mergexy(x, y) :
    The 2 combined objects have no sequence levels in common. (Use
    suppressWarnings() to suppress this warning.)

It's just that the warning is different. The intention was to make
the new warning more to the point.

H.

Michael

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