[Bioc-devel] Unexpected behaviour with Assays and Vector classes

Hervé Pagès hpages at fredhutch.org
Wed Nov 18 19:54:03 CET 2015


On 11/16/2015 11:39 PM, Hervé Pagès wrote:
> Hi Aaron,
> On 11/16/2015 09:39 AM, Hervé Pagès wrote:
>> Anyway, you convinced me that we should not try to follow too closely
>> the names model for how we treat metadata columns. If nobody objects,
>> I'll change the behavior of the various "replaceROWS" methods in the
>> S4Vectors stack and make sure that they all transfer the metadata
>> columns from 'value' to 'x'.
> This is done in S4Vectors 0.9.9 and IRanges 2.5.6 in devel, and in
> S4Vectors 0.8.3 and IRanges 2.4.2 in release.

Just a heads-up that while making these changes to IRanges, I broke
subsetting of DNAStringSet objects (and other XStringSet derivatives).
So please refrain from updating IRanges today. This is now fixed in
IRanges 2.4.3 (release) and 2.5.7 (devel) but the fix won't become
available via biocLite() before tomorrow.

Sorry for the inconvenience,


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 fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

More information about the Bioc-devel mailing list