Resync the package with the most recent developments in packages SparseArray and DelayedArray

[hpages]

Hi @alanocallaghan,

Even though scater 1.33.2 is mostly green on the BioC 3.20 daily build report, a few things are out of date with the current devel versions of SparseArray and DelayedArray. In particular:

• SparseArraySeed objects are deprecated in DelayedArray >= 0.31.5;
• Sparse blocks are now returned as SparseArray derivatives (either as COO_SparseArray or SVT_SparseArray objects). The latter support many operations (e.g. [, colSums(), colMeans(), etc...) very efficiently, and, for almost all the operations that they support, SVT_SparseArray objects outperform dgCMatrix objects. So most of the time it's preferrable to coerce to SVT_SparseArray than to dgCMatrix.

This patch removes references to the SparseArraySeed class and takes advantage of the efficiency of SVT_SparseArray objects. It also updates a few outdated importFrom statements.

Let me know if you have questions.

Best,
H.

[alanocallaghan]

Thanks!