It sounds to me that the class definition / structure is updated. You should also have an associated updateObject() method to deal with this; that's tradition. Of course, you may already have addressed this and just not written about it in your email.
On Sun, Feb 16, 2020 at 3:51 AM Aaron Lun < infinite.monkeys.with.keyboa...@gmail.com> wrote: > Dear list, > > As of version 1.9.2, the SingleCellExperiment class structure has been > updated so that "sizeFactors()<-" will store values in a "sizeFactor" > field in the "colData()", rather than the internal metadata. This aims > to improve interoperability of the SCE size factors with functions that > retrieve information from the column metadata; see GitHub for details. > > This change occurs under the hood in the "sizeFactors()" getter and > setter functions, so no action should be required from users who were > already using those functions to manipulate the SCE size factors. > Nonetheless, downstream developers should keep an eye on their unit > tests as some of the more fragile checks may fail, e.g., if they > hard-coded the expected column names of the "colData" of an SCE. > > Version 1.9.2. also removes a bunch of deprecated functionality from the > package, which may cause unrelated failures; though this was pretty > esoteric stuff that didn't see a lot of use in the first place. > > Best, > > -A > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- Best, Kasper [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
