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

But the behavior has changed for this case:

merge(Seqinfo("chr1"), Seqinfo())

Before it was "each has seqlevels not in the other" but now it is "these
two sets are disjoint". Subtle difference, but I think it's important?

On Sun, Oct 12, 2014 at 11:46 PM, Herv? Pag?s <hpages at fhcrc.org
<mailto:hpages at fhcrc.org>> wrote:

    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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