Fix ordered BatchtoolsParam iteration without reduction - #288
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LeonidasZhak wants to merge 1 commit into
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Fix ordered BatchtoolsParam iteration without reduction#288LeonidasZhak wants to merge 1 commit into
LeonidasZhak wants to merge 1 commit into
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Summary
Allow
bpiterate(..., reduce.in.order = TRUE)to return ordered results withBatchtoolsParamwhen noREDUCEfunction is supplied.Thanks to maintainers
Thanks to the BiocParallel maintainers for maintaining the parallel backends and for the guidance in #286.
Issue or motivation
Fixes #286.
SerialParam,MulticoreParam, andSnowParamaccept this combination, butBatchtoolsParamrejected it before the shared reducer could collect the results.Root cause
The BatchtoolsParam-specific
bpiterate()method unconditionally stopped whenREDUCEwas missing andreduce.in.orderwasTRUE. The sharedIterateReduceralready supports ordered collection without reduction.Change
Remove that extra rejection and add regression coverage for the multicore and socket Batchtools backends. The existing error for supplying
initwithoutREDUCEremains unchanged.Tests
R CMD INSTALL: passed.R CMD build --no-build-vignettes: passed.R CMD check --no-examples --no-manual --ignore-vignettes --no-build-vignettes: no errors, with 1 existing WARNING and 3 existing NOTEs.Rsamtoolscannot be installed on this R 4.6.1 environment.Scope
This changes only the BatchtoolsParam
bpiterate()guard and its unit tests. It does not change reduction behavior for suppliedREDUCEfunctions,initvalidation, other backends, or batchtools scheduling.