aggregateAcrossCells with `statistics = "median"` produces warnings

[nilseling]

Hi @LTLA

since a week or so the aggregateAcrossCells function produces warnings when setting statistics = "median". This would be a reproducible example:

example_sce <- mockSCE()
ids <- sample(LETTERS[1:5], ncol(example_sce), replace=TRUE)
out <- aggregateAcrossCells(example_sce, ids, statistics = "median")

which produces:

Warning messages:
1: useNames = NA is deprecated. Instead, specify either useNames = TRUE or useNames = TRUE. 
2: useNames = NA is deprecated. Instead, specify either useNames = TRUE or useNames = TRUE. 
3: useNames = NA is deprecated. Instead, specify either useNames = TRUE or useNames = TRUE. 
4: useNames = NA is deprecated. Instead, specify either useNames = TRUE or useNames = TRUE. 
5: useNames = NA is deprecated. Instead, specify either useNames = TRUE or useNames = TRUE.

It's not a huge issue, just a couple of my unit tests fail because of this. Here's my sessionInfo

R version 4.3.0 (2023-04-21)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Big Sur 11.7.4

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

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

time zone: Europe/Zurich
tzcode source: internal

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

other attached packages:
 [1] scuttle_1.10.1              SingleCellExperiment_1.22.0 SummarizedExperiment_1.30.1 Biobase_2.60.0              GenomicRanges_1.52.0       
 [6] GenomeInfoDb_1.36.0         IRanges_2.34.0              S4Vectors_0.38.1            BiocGenerics_0.46.0         MatrixGenerics_1.12.0      
[11] matrixStats_1.0.0          

loaded via a namespace (and not attached):
 [1] crayon_1.5.2              DelayedArray_0.26.3       DelayedMatrixStats_1.22.0 RCurl_1.98-1.12           grid_4.3.0               
 [6] bitops_1.0-7              sparseMatrixStats_1.12.0  compiler_4.3.0            codetools_0.2-19          Rcpp_1.0.10              
[11] XVector_0.40.0            BiocParallel_1.34.2       lattice_0.21-8            parallel_4.3.0            GenomeInfoDbData_1.2.10  
[16] Matrix_1.5-4              tools_4.3.0               beachmat_2.16.0           zlibbioc_1.46.0           S4Arrays_1.0.4   

[LTLA]

This is a consequence of some matrixStats updates, see Bioconductor/MatrixGenerics#32.

[nilseling]

Great thanks! I'll wait for this to be merged.

[nilseling]

Looks like this has been resolved on release and devel.