Error when merging a large number of cells.

[jmzhang1911]

Hello, developer!
I encountered an error while using merge to combine multiple Seurat objects (a total of 315,177 * 315,658). My server has 1TB of memory, which should be sufficient to handle this data. The error message is as follows:

    seob_list <- list()

    for(file in input_files){
        seob <- readRDS(file)
        sample = seob$sample_id %>% unique()
        cat('making ', sample, '\n')
        print(seob)
        seob_list[[sample]] = seob
    }

    seob <- merge(
        x = seob_list[[1]],
        y = seob_list[-1],
        add.cell.ids = names(seob_list)
    )

Error in cbind.Matrix(x, y, deparse.level = 0L) : 
  p[length(p)] cannot exceed 2^31-1

> sessionInfo()
R version 4.2.3 (2023-03-15)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /share/zhangjm/software/miniconda3/envs/scverse2/lib/libopenblasp-r0.3.25.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
 [1] reticulate_1.34.0    GenomicRanges_1.50.2 GenomeInfoDb_1.34.9
 [4] IRanges_2.32.0       S4Vectors_0.36.2     BiocGenerics_0.44.0
 [7] SeuratWrappers_0.3.5 lubridate_1.9.3      forcats_1.0.0
[10] stringr_1.5.1        dplyr_1.1.4          purrr_1.0.2
[13] readr_2.1.5          tidyr_1.3.1          tibble_3.2.1
[16] ggplot2_3.4.2        tidyverse_2.0.0      Signac_1.14.0
[19] Seurat_5.0.3         SeuratObject_5.0.2   sp_2.1-2

loaded via a namespace (and not attached):
  [1] spam_2.10-0            fastmatch_1.1-4        plyr_1.8.9
  [4] igraph_2.0.2           lazyeval_0.2.2         splines_4.2.3
  [7] RcppHNSW_0.5.0         BiocParallel_1.32.6    listenv_0.9.0
 [10] scattermore_1.2        digest_0.6.35          htmltools_0.5.8.1
 [13] fansi_1.0.6            magrittr_2.0.3         tensor_1.5
 [16] cluster_2.1.6          ROCR_1.0-11            remotes_2.4.2.1
 [19] tzdb_0.4.0             globals_0.16.2         Biostrings_2.66.0
 [22] matrixStats_1.1.0      R.utils_2.12.3         timechange_0.3.0
 [25] spatstat.sparse_3.0-3  colorspace_2.1-0       ggrepel_0.9.4
 [28] crayon_1.5.2           RCurl_1.98-1.14        jsonlite_1.8.8
 [31] progressr_0.14.0       spatstat.data_3.0-3    survival_3.5-7
 [34] zoo_1.8-12             glue_1.7.0             polyclip_1.10-6
 [37] gtable_0.3.4           zlibbioc_1.44.0        XVector_0.38.0
 [40] leiden_0.4.3.1         future.apply_1.11.1    abind_1.4-5
 [43] scales_1.3.0           spatstat.random_3.2-2  miniUI_0.1.1.1
 [46] Rcpp_1.0.12            viridisLite_0.4.2      xtable_1.8-4
 [49] rsvd_1.0.5             dotCall64_1.1-1        htmlwidgets_1.6.4
 [52] httr_1.4.7             RColorBrewer_1.1-3     ellipsis_0.3.2
 [55] ica_1.0-3              pkgconfig_2.0.3        R.methodsS3_1.8.2
 [58] uwot_0.1.16            deldir_2.0-2           utf8_1.2.4
 [61] tidyselect_1.2.1       rlang_1.1.3            reshape2_1.4.4
 [64] later_1.3.2            munsell_0.5.0          tools_4.2.3
 [67] cli_3.6.2              generics_0.1.3         ggridges_0.5.4
 [70] fastmap_1.1.1          goftest_1.2-3          fitdistrplus_1.1-11
 [73] RANN_2.6.1             pbapply_1.7-2          future_1.33.1
 [76] nlme_3.1-164           mime_0.12              R.oo_1.26.0
 [79] RcppRoll_0.3.1         compiler_4.2.3         plotly_4.10.3
 [82] png_0.1-8              spatstat.utils_3.1-0   stringi_1.8.3
 [85] RSpectra_0.16-1        lattice_0.22-5         Matrix_1.6-4
 [88] vctrs_0.6.5            pillar_1.9.0           lifecycle_1.0.4
 [91] BiocManager_1.30.22    spatstat.geom_3.2-7    lmtest_0.9-40
 [94] RcppAnnoy_0.0.21       data.table_1.15.4      cowplot_1.1.2
 [97] bitops_1.0-7           irlba_2.3.5.1          httpuv_1.6.15
[100] patchwork_1.1.3        R6_2.5.1               promises_1.3.0
[103] KernSmooth_2.23-22     gridExtra_2.3          parallelly_1.36.0
[106] codetools_0.2-19       fastDummies_1.7.3      MASS_7.3-60
[109] withr_3.0.0            sctransform_0.4.1      Rsamtools_2.14.0
[112] GenomeInfoDbData_1.2.9 parallel_4.2.3         hms_1.1.3
[115] grid_4.2.3             Rtsne_0.16             spatstat.explore_3.2-5
[118] shiny_1.8.0