[Bioc-devel] Migration of many scater utilities to scuttle

Aaron Lun |n||n|te@monkey@@w|th@keybo@rd@ @end|ng |rom gm@||@com
Thu Jun 4 07:46:28 CEST 2020

Dear list,

scater's functions have now been split into two packages: the plotting 
functions stay in scater while many of the non-plotting utilities (QC, 
normalization, aggregation) move into the new scuttle package.

This has been done to prune the dependency tree by removing 
visualization-related packages that are not necessary for downstream 
packages relying only on the utilities. Some estimates put the reduction 
in the number of dependencies to be almost 40 packages due to the 
removal of the ggplot2 stack and its various accessories.

All migrated functions in scuttle have been re-exported in scater so no 
action is required from users or developers. The re-exported functions 
in the scater namespace should be considered to be soft-deprecated; 
developers should start to import from scuttle instead, even though a 
hard deprecation will not be done in the forseeable future. Proactive 
developers may also consider switching their Imports: from scater to 
scuttle in order to prune their own dependency trees.

Note that there was a bug in the re-exporting for 1.17.1, so some of 
scater's downstream packages may observe build failures in tomorrow's 
reports. This has been fixed in 1.17.2 so just sit tight.


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