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

Hervé Pagès hpages at fhcrc.org
Mon Oct 13 08:46:47 CEST 2014

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 
     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.


> Michael
> 	[[alternative HTML version deleted]]
> _______________________________________________
> Bioc-devel at r-project.org mailing list
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Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
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