[Bioc-devel] do SummarizedExperiments really need colnames?

While on the topic of SummarizedExperiment colnames, the circumstances in
which these are stripped from the assays and overridden by colData is
confusing to me, particularly case 2 below (a warning in case 3 might be
useful too).

m1 <- matrix(1:10, ncol = 2)
m2 <- m1
colnames(m2) <- c("A", "B")

se1 <- SummarizedExperiment(m1, colData = DataFrame(row.names = c("A",

"B")))

se2 <- SummarizedExperiment(m2)
se3 <- SummarizedExperiment(m2, colData = DataFrame(row.names = c("C",

"D")))

# colnames correctly set to c("A", "B") and stripped from assays
colnames(se1)

[1] "A" "B"

se1 at assays[[1]]

[,1] [,2]
[1,] 1 6
[2,] 2 7
[3,] 3 8
[4,] 4 9
[5,] 5 10

# colnames correctly set to c("A", "B") set and but not stripped from

assays

colnames(se2)

[1] "A" "B"

se2 at assays[[1]]

A B
[1,] 1 6
[2,] 2 7
[3,] 3 8
[4,] 4 9
[5,] 5 10

# colnames set to c("C", "D") (without warning about mismatch) and

stripped

# from assays
se3 at assays[[1]]

[,1] [,2]
[1,] 1 6
[2,] 2 7
[3,] 3 8
[4,] 4 9
[5,] 5 10

sessionInfo()

R Under development (unstable) (2015-11-28 r69714)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.5 (Yosemite)

locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base

other attached packages:
[1] SummarizedExperiment_1.1.5 Biobase_2.31.1
[3] GenomicRanges_1.23.4 GenomeInfoDb_1.7.3
[5] IRanges_2.5.9 S4Vectors_0.9.11
[7] BiocGenerics_0.17.2

loaded via a namespace (and not attached):
[1] zlibbioc_1.17.0 XVector_0.11.1