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HenrikBengtsson / matrixStats

R package: Methods that Apply to Rows and Columns of Matrices (and to Vectors)
https://cran.r-project.org/package=matrixStats
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CLEANUP: Make `useNames = NA` defunct in R-devel (after October 2023) #235

Closed HenrikBengtsson closed 8 months ago

HenrikBengtsson commented 1 year ago

Since matrixStats 1.0.0 (2023-06-02), useNames = TRUE is the new default. For legacy reasons, and backward compatible reasons, the default used to be useNames = NA. However, no one should use useNames = NA going forward; it's already deprecated, e.g.

> x <- matrix(rnorm(20), nrow = 5, ncol = 4)
> y <- rowMedians(x, useNames = NA)
Warning message:
useNames = NA is deprecated. Instead, specify either useNames = TRUE or useNames = TRUE.

Everyone should either use useNames = TRUE or useNames = FALSE.

Action

Next, matrixStats should:

Because several core packages in Bioconductor release version 3.17 (2023-04-26 -- 2023-10-24) still use useNames = NA to preserve their API, we need to wait until the next Bioconductor release cycle on October 25, 2023 to make it defunct.

HenrikBengtsson commented 9 months ago

Bioconductor 3.18 was released on 2023-10-25, meaning we should be able to move forward with this.

HenrikBengtsson commented 9 months ago

Starting by making useNames = NA defunct on R-devel (>= 4.4.0)