I've noticed that the parallelVectorNames function definition in
S4Vectors has changed at commit 113621, from:
setMethod("parallelVectorNames", "ANY", function(x) character())
... to:
setMethod("parallelVectorNames", "ANY",
function(x) colnames(as.data.frame(new(class(x)))))
This ends up breaking some of my code at makeFixedColumnEnv(), as it
assumes that an accessor method exists with the same name as each entry
of parallelVectorNames(), which is not the case. (Specifically, for my
genomic interactions class, I have two GRanges representing pairs of
anchor regions, and as.data.frame yields a data.frame with column names
of seqnames1, start1, end1, ... and seqnames2, start2, end2, etc. that
do not have corresponding accessor methods.)
What is the recommended course of action here? Defining an accessor for
seqnames1, etc. is not impossible, but it seems a bit excessive given
that those functions would rarely ever be used. Is it okay to restate
the old definition for the affected class in my package, i.e.:
setMethod("parallelVectorNames", "GInteractions",
function(x) character())
... or is there something extra that it should return? I don't really
know what parallelVectorNames() is designed for, so it's hard to tell.
Cheers,
Aaron
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
