Unreliable value when using the future package

[AlbertoFabbri93]

When I run Seurat::FindClusters using the future package I get the following warning:

> breast_cancer_patients_tumor_cells <- FindClusters(
+   breast_cancer_patients_tumor_cells,
+   resolution = seq_res,
+   cluster.name = tumor_cluster_seq_res,
+   random.seed = 5,
+   verbose = TRUE)
Warning: NAs produced by integer overflowModularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 38284
Number of edges: 1432724

Running Louvain algorithm...
Maximum modularity in 10 random starts: 0.9574
Number of communities: 8
Elapsed time: 5 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 38284
Number of edges: 1432724

Running Louvain algorithm...
Maximum modularity in 10 random starts: 0.9455
Number of communities: 12
Elapsed time: 6 seconds
Warning: UNRELIABLE VALUE: One of the ‘future.apply’ iterations (‘future_lapply-2’) unexpectedly generated random numbers without declaring so. There is a risk that those random numbers are not statistically sound and the overall results might be invalid. To fix this, specify 'future.seed=TRUE'. This ensures that proper, parallel-safe random numbers are produced via the L'Ecuyer-CMRG method. To disable this check, use 'future.seed = NULL', or set option 'future.rng.onMisuse' to "ignore".Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 38284
Number of edges: 1432724

Running Louvain algorithm...
Maximum modularity in 10 random starts: 0.9348
Number of communities: 13
Elapsed time: 6 seconds
Warning: UNRELIABLE VALUE: One of the ‘future.apply’ iterations (‘future_lapply-3’) unexpectedly generated random numbers without declaring so. There is a risk that those random numbers are not statistically sound and the overall results might be invalid. To fix this, specify 'future.seed=TRUE'. This ensures that proper, parallel-safe random numbers are produced via the L'Ecuyer-CMRG method. To disable this check, use 'future.seed = NULL', or set option 'future.rng.onMisuse' to "ignore".Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 38284
Number of edges: 1432724

Running Louvain algorithm...
Maximum modularity in 10 random starts: 0.9243
Number of communities: 13
Elapsed time: 5 seconds
Warning: UNRELIABLE VALUE: One of the ‘future.apply’ iterations (‘future_lapply-4’) unexpectedly generated random numbers without declaring so. There is a risk that those random numbers are not statistically sound and the overall results might be invalid. To fix this, specify 'future.seed=TRUE'. This ensures that proper, parallel-safe random numbers are produced via the L'Ecuyer-CMRG method. To disable this check, use 'future.seed = NULL', or set option 'future.rng.onMisuse' to "ignore".

At the top of my Quarto file I set the future.seed option:

# Replace this future symbols with others because they conflict with the zeallot package
library (future, exclude = c("%->%", "%<-%"));
`%<--%` = future::`%<-%` ;
`%-->%` = future::`%->%` ;
# Parallelize the computation with several worker processes that will run in their own R session
plan("multisession", workers = 6)
# Set the maximum size of the future globals
options(future.globals.maxSize = 6.5 * 2^30)
# Ensure proper random number seeding globally
options(future.seed = TRUE)

> sessionInfo()
R version 4.4.2 (2024-10-31)
Platform: aarch64-apple-darwin20
Running under: macOS Sequoia 15.1

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

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/Stockholm
tzcode source: internal

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

other attached packages:
 [1] conflicted_1.2.0       org.Hs.eg.db_3.19.1    AnnotationDbi_1.66.0   IRanges_2.38.1         S4Vectors_0.42.1      
 [6] Biobase_2.64.0         BiocGenerics_0.50.0    clusterProfiler_4.12.6 pals_1.9               RColorBrewer_1.1-3    
[11] ggforce_0.4.2          clustree_0.5.1         ggraph_2.2.1           ggpubr_0.6.0           patchwork_1.3.0       
[16] Matrix_1.7-1           abind_1.4-8            presto_1.0.0           data.table_1.16.2      Rcpp_1.0.13-1         
[21] glmGamPoi_1.16.0       EBImage_4.46.0         dittoSeq_1.16.0        InSituType_2.0         here_1.0.1            
[26] glue_1.8.0             zeallot_0.1.0          tidyr_1.3.1            tibble_3.2.1           readr_2.1.5           
[31] readxl_1.4.3           ggplot2_3.5.1          dplyr_1.1.4            future_1.34.0          Seurat_5.1.0          
[36] SeuratObject_5.0.2     sp_2.1-4              

loaded via a namespace (and not attached):
  [1] fs_1.6.5                    matrixStats_1.4.1           spatstat.sparse_3.1-0       bitops_1.0-9               
  [5] enrichplot_1.24.4           httr_1.4.7                  tools_4.4.2                 sctransform_0.4.1          
  [9] backports_1.5.0             utf8_1.2.4                  R6_2.5.1                    lazyeval_0.2.2             
 [13] uwot_0.2.2                  withr_3.0.2                 gridExtra_2.3               progressr_0.15.0           
 [17] textshaping_0.4.0           cli_3.6.3                   spatstat.explore_3.3-3      fastDummies_1.7.4          
 [21] scatterpie_0.2.4            labeling_0.4.3              spatstat.data_3.1-2         ggridges_0.5.6             
 [25] pbapply_1.7-2               askpass_1.2.1               systemfonts_1.1.0           yulab.utils_0.1.8          
 [29] gson_0.1.0                  R.utils_2.12.3              DOSE_3.30.5                 dichromat_2.0-0.1          
 [33] parallelly_1.39.0           maps_3.4.2.1                rstudioapi_0.17.1           RSQLite_2.3.7              
 [37] gridGraphics_0.5-1          generics_0.1.3              vroom_1.6.5                 ica_1.0-3                  
 [41] spatstat.random_3.3-2       car_3.1-3                   GO.db_3.19.1                fansi_1.0.6                
 [45] R.methodsS3_1.8.2           lifecycle_1.0.4             yaml_2.3.10                 carData_3.0-5              
 [49] SummarizedExperiment_1.34.0 qvalue_2.36.0               SparseArray_1.4.8           Rtsne_0.17                 
 [53] blob_1.2.4                  grid_4.4.2                  promises_1.3.0              crayon_1.5.3               
 [57] miniUI_0.1.1.1              lattice_0.22-6              cowplot_1.1.3               KEGGREST_1.44.1            
 [61] mapproj_1.2.11              pillar_1.9.0                knitr_1.49                  fgsea_1.30.0               
 [65] GenomicRanges_1.56.2        future.apply_1.11.3         codetools_0.2-20            fastmatch_1.1-4            
 [69] leiden_0.4.3.1              ggfun_0.1.7                 spatstat.univar_3.1-1       treeio_1.28.0              
 [73] vctrs_0.6.5                 png_0.1-8                   spam_2.11-0                 cellranger_1.1.0           
 [77] gtable_0.3.6                cachem_1.1.0                xfun_0.49                   S4Arrays_1.4.1             
 [81] mime_0.12                   tidygraph_1.3.1             survival_3.7-0              SingleCellExperiment_1.26.0
 [85] pheatmap_1.0.12             fitdistrplus_1.2-1          ROCR_1.0-11                 lsa_0.73.3                 
 [89] nlme_3.1-166                ggtree_3.12.0               bit64_4.5.2                 RcppAnnoy_0.0.22           
 [93] GenomeInfoDb_1.40.1         rprojroot_2.0.4             SnowballC_0.7.1             irlba_2.3.5.1              
 [97] KernSmooth_2.23-24          colorspace_2.1-1            DBI_1.2.3                   tidyselect_1.2.1           
[101] bit_4.5.0                   compiler_4.4.2              httr2_1.0.6                 DelayedArray_0.30.1        
[105] plotly_4.10.4               shadowtext_0.1.4            scales_1.3.0                lmtest_0.9-40              
[109] rappdirs_0.3.3              tiff_0.1-12                 stringr_1.5.1               digest_0.6.37              
[113] goftest_1.2-3               fftwtools_0.9-11            spatstat.utils_3.1-1        XVector_0.44.0             
[117] htmltools_0.5.8.1           pkgconfig_2.0.3             jpeg_0.1-10                 umap_0.2.10.0              
[121] sparseMatrixStats_1.16.0    MatrixGenerics_1.16.0       fastmap_1.2.0               rlang_1.1.4                
[125] htmlwidgets_1.6.4           UCSC.utils_1.0.0            shiny_1.9.1                 farver_2.1.2               
[129] zoo_1.8-12                  jsonlite_1.8.9              BiocParallel_1.38.0         mclust_6.1.1               
[133] R.oo_1.27.0                 GOSemSim_2.30.2             RCurl_1.98-1.16             magrittr_2.0.3             
[137] ggplotify_0.1.2             Formula_1.2-5               GenomeInfoDbData_1.2.12     dotCall64_1.2              
[141] munsell_0.5.1               ape_5.8                     viridis_0.6.5               reticulate_1.39.0          
[145] stringi_1.8.4               zlibbioc_1.50.0             MASS_7.3-61                 plyr_1.8.9                 
[149] parallel_4.4.2              listenv_0.9.1               ggrepel_0.9.6               deldir_2.0-4               
[153] Biostrings_2.72.1           graphlayouts_1.2.0          splines_4.4.2               tensor_1.5                 
[157] hms_1.1.3                   locfit_1.5-9.10             igraph_2.1.1                spatstat.geom_3.3-3        
[161] ggsignif_0.6.4              RcppHNSW_0.6.0              reshape2_1.4.4              evaluate_1.0.1             
[165] renv_1.0.11                 BiocManager_1.30.25         tzdb_0.4.0                  tweenr_2.0.3               
[169] httpuv_1.6.15               RANN_2.6.2                  openssl_2.2.2               purrr_1.0.2                
[173] polyclip_1.10-7             scattermore_1.2             broom_1.0.7                 xtable_1.8-4               
[177] tidytree_0.4.6              RSpectra_0.16-2             rstatix_0.7.2               later_1.3.2                
[181] ragg_1.3.3                  viridisLite_0.4.2           aplot_0.2.3                 memoise_2.0.1              
[185] cluster_2.1.6               globals_0.16.3

I saw the other bug reports but none of them seems to have a fix for this.