Hello,

I am encountering a fully reproducible failure when running DESeq2 in parallel using MulticoreParam on macOS (ARM). The error appears to originate inside BiocParallel and occurs even on trivial bplapply() examples.

Below is a complete minimal example, the full traceback, and my sessionInfo().

Minimal reproducible example

library(DESeq2)
library(BiocParallel)
set.seed(1)
dds <- makeExampleDESeqDataSet(n=1000, m=6)
dds <- DESeq(dds, parallel=TRUE, BPPARAM=MulticoreParam(4))

Output:

estimating size factors
estimating dispersions
gene-wise dispersion estimates: 4 workers
mean-dispersion relationship
final dispersion estimates, fitting model and testing: 4 workers
Warning in parallel::mccollect(wait = FALSE, timeout = 1) :
  1 parallel job did not deliver a result
Error in h(simpleError(msg, call)) :
  error in evaluating the argument 'args' in selecting a method for function 'do.call': wrong args for environment subassignment

Independent BiocParallel failure (no DESeq2)

library(BiocParallel)
param <- MulticoreParam(workers = 4)
x <- 1:12
res <- bplapply(X = x, FUN = \(i) i^2, BPPARAM = param)

Produces:

Warning in parallel::mccollect(wait = TRUE) :
  3 parallel jobs did not deliver results
Error in h(simpleError(msg, call)) :
  error in evaluating the argument 'args' in selecting a method for function 'do.call': wrong args for environment subassignment

FULL TRACEBACK (VERBATIM)

Error in h(simpleError(msg, call)) :
error in evaluating the argument 'args' in selecting a method for function 'do.call': wrong args for environment subassignment
12.
.reducer_add(reducer, njob, value)
11.
.reducer_add(reducer, njob, value)
10.
.collect_result(manager, reducer, progress, BPPARAM)
9.
.bploop_impl(ITER = ITER, FUN = FUN, ARGS = ARGS, BPPARAM = BPPARAM,
BPOPTIONS = BPOPTIONS, BPREDO = BPREDO, reducer = reducer,
progress.length = length(redo_index))
8.
bploop.lapply(manager, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS,
...)
7.
bploop(manager, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS, ...)
6.
.bpinit(manager = manager, X = X, FUN = FUN, ARGS = ARGS, BPPARAM = BPPARAM,
BPOPTIONS = BPOPTIONS, BPREDO = BPREDO)
5.
bplapply(levels(idx), function(l) {
objectSub <- estimateDispersionsMAP(object[idx == l, ], dispPriorVar = dispPriorVar,
quiet = TRUE, modelMatrix = modelMatrix)
nbinomWaldTest(objectSub, betaPrior = FALSE, quiet = TRUE, ...
4.
bplapply(levels(idx), function(l) {
objectSub <- estimateDispersionsMAP(object[idx == l, ], dispPriorVar = dispPriorVar,
quiet = TRUE, modelMatrix = modelMatrix)
nbinomWaldTest(objectSub, betaPrior = FALSE, quiet = TRUE, ...
3.
do.call(rbind, bplapply(levels(idx), function(l) {
objectSub <- estimateDispersionsMAP(object[idx == l, ], dispPriorVar = dispPriorVar,
quiet = TRUE, modelMatrix = modelMatrix)
nbinomWaldTest(objectSub, betaPrior = FALSE, quiet = TRUE, ...
2.
DESeqParallel(object, test = test, fitType = fitType, betaPrior = betaPrior,
full = full, reduced = reduced, quiet = quiet, modelMatrix = modelMatrix,
useT = useT, minmu = minmu, BPPARAM = BPPARAM)
1.
DESeq(dds, parallel = TRUE, BPPARAM = MulticoreParam(4))

sessionInfo()

R version 4.5.2 (2025-10-31)
Platform: aarch64-apple-darwin20
Running under: macOS Tahoe 26.1

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/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: Europe/Paris
tzcode source: internal

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] BiocParallel_1.44.0         DESeq2_1.50.2              
 [3] SummarizedExperiment_1.40.0 Biobase_2.70.0             
 [5] MatrixGenerics_1.22.0       matrixStats_1.5.0          
 [7] GenomicRanges_1.62.0        Seqinfo_1.0.0              
 [9] IRanges_2.44.0              S4Vectors_0.48.0           
[11] BiocGenerics_0.56.0         generics_0.1.4             

loaded via a namespace (and not attached):
 [1] Matrix_1.7-4        gtable_0.3.6        BiocManager_1.30.27
 [4] dplyr_1.1.4         compiler_4.5.2      tidyselect_1.2.1   
 [7] Rcpp_1.1.0          parallel_4.5.2      scales_1.4.0       
[10] yaml_2.3.11         fastmap_1.2.0       lattice_0.22-7     
[13] ggplot2_4.0.1       R6_2.6.1            XVector_0.50.0     
[16] S4Arrays_1.10.0     knitr_1.50          tibble_3.3.0       
[19] DelayedArray_0.36.0 pillar_1.11.1       RColorBrewer_1.1-3 
[22] rlang_1.1.6         xfun_0.54           S7_0.2.1           
[25] SparseArray_1.10.2  cli_3.6.5           magrittr_2.0.4     
[28] locfit_1.5-9.12     digest_0.6.39       grid_4.5.2         
[31] rstudioapi_0.17.1   lifecycle_1.0.4     vctrs_0.6.5        
[34] evaluate_1.0.5      glue_1.8.0          farver_2.1.2       
[37] codetools_0.2-20    abind_1.4-8         rmarkdown_2.30     
[40] pkgconfig_2.0.3     tools_4.5.2         htmltools_0.5.8.1

Questions

1. Is this a known issue with MulticoreParam on macOS ARM?

Thank you for your help.

The DESeq2 error makes sense, as we've talked about, given that the simple bplapply isn't working in your setup.

Maybe give the traceback for the bplapply example. Debugging the simple case is always easier.

Still happening in a clean install