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Bioconductor
DelayedMatrixStats no longer supports scalar `center=` arguments
PeteHaitch/DelayedMatrixStats@9048f3e7a24035f3526a2ac0455598138e0c8480 causes
https://github.com/Bioconductor/DelayedArray/blob/700cfdc38e0f97a67942963c1555d0fd83a7bc41/R/DelayedArray-utils.R#L868
to fail, for example:
library(DelayedArray)
mat <- DelayedArray(matrix(runif(500), 25, 20))
scale(mat)
## Error in blockfun(x, ..., useNames = useNames) :
## length(center) == nrow(x) is not TRUE
Simple fix is to just do center=numeric(nrow(x)).
Session info
R Under development (unstable) (2024-04-10 r86396)
Platform: aarch64-apple-darwin22.6.0
Running under: macOS Ventura 13.6.4
Matrix products: default
BLAS: /Users/luna/Software/R/trunk/lib/libRblas.dylib
LAPACK: /Users/luna/Software/R/trunk/lib/libRlapack.dylib; LAPACK version 3.12.0
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: America/Los_Angeles
tzcode source: internal
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] DelayedArray_0.29.9 SparseArray_1.3.5 S4Arrays_1.3.7
[4] abind_1.4-5 IRanges_2.37.1 S4Vectors_0.41.6
[7] MatrixGenerics_1.15.0 matrixStats_1.3.0 BiocGenerics_0.49.1
[10] Matrix_1.7-0
loaded via a namespace (and not attached):
[1] DelayedMatrixStats_1.25.2 sparseMatrixStats_1.15.0
[3] zlibbioc_1.49.3 lattice_0.22-6
[5] XVector_0.43.1 grid_4.5.0
[7] compiler_4.5.0 tools_4.5.0
[9] Rcpp_1.0.12 crayon_1.5.2
@PeteHaitch Would you be open to the possibility of keeping length-1 centers valid in DelayedMatrixStats, at least for a little bit longer? Length-1 centers in DelayedArray, SparseArray and sparseMatrixStats have been supported for a while and they didn't start issuing warnings recently despite the fact that matrixStats doesn't like them anymore. So having them now cause a hard error in DelayedMatrixStats is inconsistent with DelayedArray, SparseArray and sparseMatrixStats .
Also I can't think of anything wrong with supporting length-1 centers -- they're just a convenience like recycling.
If you agree with this, I'll submit a patch to DelayedMatrixStats. The patch will simply recycle length-1 centers to nrow(x) or ncol(x).
Thanks, H.
Argh sorry for this. I was trying to follow the defunct-ification by Henrik in matrixStats (https://github.com/HenrikBengtsson/matrixStats/issues/254), since we've (mostly) tried to mimic its API. A patch would be welcome (it might just be reverting the most recent commits).
No worries. Working on it. Will also involve patching MatrixGenerics to make things consistent across the board.
PR for DelayedMatrixStats ready: https://github.com/PeteHaitch/DelayedMatrixStats/pull/101
Thanks, @hpages I'm in the midst of resolving OSCA build issues and I'll then turn to this (hopefully Friday).