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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LeonidasZhak
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September 10, 2026 07:58
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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
devel: reproduced the originalREDUCE must be provided when 'reduce.in.order = TRUE'error.R CMD INSTALL --no-multiarch --with-keep.source .: passed.R CMD build .: passed, including vignette creation._R_CHECK_FORCE_SUGGESTS_=true R CMD check --no-manual BiocParallel_1.47.0.tar.gz: passed with 1 existing WARNING and 2 existing NOTEs.R CMD check --as-cran --no-manual; it fails on existing examples/tests because CRAN's_R_CHECK_LIMIT_CORES_cap conflicts with existingMulticoreParam(3)/larger-worker examples, outside this PR's diff.Scope
This changes only the BatchtoolsParam
bpiterate()guard and its unit tests. It does not change reduction behavior for suppliedREDUCEfunctions,initvalidation, other backends, batchtools scheduling, documentation, or vignettes.