Adding a new assay forces dimnames on all existing assays

[LTLA]

Pretty much as it says in the title - if I add a new assay, all of the existing assays are modified with the SE dimnames slapped on top:

library(SummarizedExperiment)

se <- SummarizedExperiment(list(foo = matrix(runif(200), ncol=10)))
rownames(se) <- LETTERS[1:20]
rownames(se) <- letters[1:10]

is.null(rownames(assay(se, "foo", withDimnames=FALSE)))
## [1] TRUE

another <- matrix(runif(200), ncol=10)
dimnames(another) <- dimnames(se)
assay(se, "bar") <- another

is.null(rownames(assay(se, "foo", withDimnames=FALSE)))
## [1] FALSE 

Similar behavior when removing an assay, which forces dimnames on all remaining assays:

library(SummarizedExperiment)

se <- SummarizedExperiment(list(foo = matrix(runif(200), ncol=10), bar = matrix(runif(200), ncol=10)))
rownames(se) <- LETTERS[1:20]
rownames(se) <- letters[1:10]

is.null(rownames(assay(se, "foo", withDimnames=FALSE)))
## [1] TRUE

assay(se, "bar") <- NULL

is.null(rownames(assay(se, "foo", withDimnames=FALSE)))
## [1] FALSE 

This is mostly problematic when saving objects as it unnecessarily duplicates information. Also, previously pristine DelayedArray objects are now wrapped with a DelayedSetDimnames, which interferes with some optimizations that try to operate directly on the delayed seed.

I'd wager that there's an assays() call somewhere inside assay<- that didn't set withDimnames=FALSE.

Session information

R version 4.6.0 Patched (2026-05-01 r89994)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.5 LTS

Matrix products: default
BLAS:   /home/luna/Software/R/R-4-6-branch-copy/lib/libRblas.so 
LAPACK: /home/luna/Software/R/R-4-6-branch-copy/lib/libRlapack.so;  LAPACK version 3.12.1

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Australia/Sydney
tzcode source: system (glibc)

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

other attached packages:
 [1] SummarizedExperiment_1.43.0 Biobase_2.73.2             
 [3] GenomicRanges_1.65.1        Seqinfo_1.3.0              
 [5] IRanges_2.47.2              S4Vectors_0.51.6           
 [7] BiocGenerics_0.59.10        generics_0.1.4             
 [9] MatrixGenerics_1.25.0       matrixStats_1.5.0          

loaded via a namespace (and not attached):
 [1] SparseArray_1.13.2  Matrix_1.7-6        lattice_0.22-9     
 [4] abind_1.4-8         S4Arrays_1.13.0     XVector_0.53.0     
 [7] grid_4.6.0          DelayedArray_0.39.3 compiler_4.6.0     
[10] tools_4.6.0