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BatchtoolsParam handles reduce.in.order differently from others

Aperta
#286 1 commento 0 reazioni 0 assegnatari Vedi su GitHub

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Valutazione

Difficoltà
3/5
Tempo stimato
1-2 giorni
Idoneità per principianti
65/100
Tipo di issue
Bug
Chiarezza
Abbastanza chiara
Stato di attività
Tranquilla
Stack tecnologico
r

Direzione di ricerca

Start at R/BatchtoolsParam-class.R around line 465 and trace the bpiterate handling for BatchtoolsParam when reduce.in.order=TRUE. Reproduce the supplied BatchtoolsParam example, compare it with SerialParam, MulticoreParam, and SnowParam, and verify that the same call works without REDUCE or INIT.

Scritto dal modello di indicizzazione a partire dal testo della issue.

Descrizione

Most BPPARAM objects handle the reduce.in.order argument of bpiterate without requiring REDUCE and INIT arguments. However, BatchtoolsParam objects cannot handle this case, which means that some uses of bpiterate can work with some valid BPPARAM arguments but fail with others. This is highly unintuitive. Reprex below:

library(BiocParallel)
library(assertthat)
library(batchtools)

expected_result <- lapply(1:10, sqrt)

assert_that(identical(expected_result, bpiterate(bpiterateAlong(1:10), sqrt, reduce.in.order=TRUE, BPPARAM = SerialParam())))
#> [1] TRUE
assert_that(identical(expected_result, bpiterate(bpiterateAlong(1:10), sqrt, reduce.in.order=TRUE, BPPARAM = MulticoreParam(2))))
#> [1] TRUE
assert_that(identical(expected_result, bpiterate(bpiterateAlong(1:10), sqrt, reduce.in.order=TRUE, BPPARAM = SnowParam(2))))
#> [1] TRUE
## This one fails
assert_that(identical(expected_result, bpiterate(bpiterateAlong(1:10), sqrt, reduce.in.order=TRUE, BPPARAM = BatchtoolsParam(2, cluster = "multicore"))))
#> Error in `.local()`:
#> ! REDUCE must be provided when 'reduce.in.order = TRUE'
## Needs additional arguments to work, although these specific
## arguments may not work in every case
assert_that(identical(expected_result, bpiterate(bpiterateAlong(1:10), sqrt, reduce.in.order=TRUE, BPPARAM = BatchtoolsParam(2, cluster = "multicore"), init = list(), REDUCE = c))) #
#> Submitting 10 jobs in 2 chunks using cluster functions 'Multicore' ...
#> [1] TRUE

Created on 2026-05-28 with reprex v2.1.1

BatchtoolsParam seems to be the odd one out here. Is it possible to bring BatchtoolsParam in line with the other param classes here?

Session info:

> sessionInfo()
R version 4.5.3 (2026-03-11)
Platform: aarch64-apple-darwin24.6.0
Running under: macOS Sequoia 15.7.4

Matrix products: default
BLAS:   /opt/homebrew/Cellar/openblas/0.3.32/lib/libopenblasp-r0.3.32.dylib 
LAPACK: /opt/homebrew/Cellar/r/4.5.3/lib/R/lib/libRlapack.dylib;  LAPACK version 3.12.1

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/New_York
tzcode source: internal

attached base packages:
[1] graphics  grDevices utils     datasets  stats     methods   base     

other attached packages:
 [1] batchtools_0.9.18   assertthat_0.2.1    BiocParallel_1.44.0 tidyr_1.3.2         future_1.68.0       devtools_2.4.6      usethis_3.2.1       openxlsx_4.2.8.1    magrittr_2.0.5      dplyr_1.2.1         rex_1.2.1           glue_1.8.1          stringr_1.6.0       ggplot2_4.0.1       colorout_1.3-2     

loaded via a namespace (and not attached):
 [1] gtable_0.3.6       xfun_0.57          remotes_2.5.0      processx_3.8.6     callr_3.7.6        vctrs_0.7.3        tools_4.5.3        pak_0.9.1          ps_1.9.1           generics_0.1.4     base64url_1.4      parallel_4.5.3     tibble_3.3.1       pkgconfig_2.0.3    data.table_1.18.4  checkmate_2.3.4   
[17] RColorBrewer_1.1-3 S7_0.2.2           lifecycle_1.0.5    compiler_4.5.3     farver_2.1.2       progress_1.2.3     codetools_0.2-20   htmltools_0.5.9    snow_0.4-4         yaml_2.3.12        pillar_1.11.1      crayon_1.5.3       ellipsis_0.3.2     cachem_1.1.0       sessioninfo_1.2.3  parallelly_1.45.1 
[33] brew_1.0-10        tidyselect_1.2.1   zip_2.3.3          digest_0.6.39      stringi_1.8.7      purrr_1.2.2        listenv_0.10.0     fastmap_1.2.0      grid_4.5.3         cli_3.6.6          dichromat_2.0-0.1  pkgbuild_1.4.8     clipr_0.8.0        withr_3.0.2        prettyunits_1.2.0  scales_1.4.0      
[49] backports_1.5.1    rappdirs_0.3.4     rmarkdown_2.31     globals_0.18.0     otel_0.2.0         hms_1.1.4          evaluate_1.0.5     memoise_2.0.1      knitr_1.51         rlang_1.2.0        Rcpp_1.1.1-1.1     reprex_2.1.1       pkgload_1.4.1      rstudioapi_0.17.1  R6_2.6.1           fs_2.1.0          

As you can see, I'm not running this test on the latest R/Bioconductor versions, but looking in the code I see that the error message is still there: https://github.com/Bioconductor/BiocParallel/blob/devel/R/BatchtoolsParam-class.R#L465

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