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Compatibity with DelayedArray 0.31.7 #110
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The following breaking changes happened between DelayedArray < 0.31.5 and 0.31.7: The OLD_extract_sparse_array() generic and SparseArraySeed objects are now deprecated in favor of the new extract_sparse_array() generic defined in the SparseArray package. Methods for the new extract_sparse_array() generic are expected to return a SparseArray derivative, typically an SVT_SparseArray object but COO_SparseArray objects are ok. This commit restores compatibility with DelayedArray 0.31.7.
@LTLA FWIW the only thing I did to beachmat in order to succesfully run
Of course more changes are needed in order to make beachmat fully compatible with DelayedArray 0.31.7 but that's a start. |
Thanks for so proactively making this change. SparseArray 1.5.19 is required in the DESCRIPTION for this patch, but it is not (yet) available on Bioc devel. I notice that DelayedArray has a version requirement only of 1.5.18 at the moment in its github repo. Is this version 1.5.19 something I should wait for before merging this, or is it a typo? |
Ooops, it's a version I have locally on my laptop but that I never pushed, sorry. Just pushed it now: Bioconductor/SparseArray@3a9d9fa Anyways, SparseArray 1.5.19 doesn't contain any meaningful change compared to 1.5.18 so I adjusted the patch to only require the latter. H. |
The soft-deprecation of The problem should be addressed in DelayedArray 0.31.9 (see Bioconductor/DelayedArray@5afb60e). FWIW DropletUtils 1.25.1 passes H. |
The following breaking changes happened between DelayedArray < 0.31.5 and 0.31.7:
The
OLD_extract_sparse_array()
generic and SparseArraySeed objects are now deprecated in favor of the newextract_sparse_array()
generic defined in the SparseArray package. Methods for the newextract_sparse_array()
generic are expected to return a SparseArray derivative, typically an SVT_SparseArray object but COO_SparseArray objects are ok.This commit restores compatibility with DelayedArray 0.31.7.
IMPORTANT NOTE: Some unit tests in DropletUtils won't pass until the beachmat package is modified as follow:
whichNonZero()
method for COO_SparseArray objects.whichNonZero()
method for DelayedMatrix objects.Best,
H.