reduce_dimension error : address (nil), cause 'memory not mapped'

[Donbbit]

Describe the bug
Thank you for creating such great software.
I performed pseudotime analysis using monocle3, but I got an error when I did reduce_dimension. Here is the code :

library(monocle3)
library(Seurat)
library(Matrix)
library(data.table)
library(dplyr)
library(ggplot2)

obj <- readRDS("../res_0.7_harmony.rds")

data <- GetAssayData(obj, assay = 'RNA', slot = 'counts')
cell_metadata <- [email protected]
gene_annotation <- data.frame(gene_short_name = rownames(data))
rownames(gene_annotation) <- rownames(data)
cds <- new_cell_data_set(data,
cell_metadata = cell_metadata,
gene_metadata = gene_annotation)
pc_variance_plot <- plot_pc_variance_explained(cds)

cds <- reduce_dimension(cds, preprocess_method = "PCA")

To Reproduce
The code that produced the bug:
cds <- reduce_dimension(cds, preprocess_method = "PCA")

traceback()
After the error, run traceback() in R and post the output:
Traceback:
1: .Primitive(".Call")("eigs_shift_sym", new("dgCMatrix", i = c(0L, 1L, 2L, 3L, 313L, 520L, 614L, 670L, 2561L, 3035L, 5441L, 6515L, 8325L, 10557L, 22451L, 26556L, 0L, 1L, 2L, 3L, 520L, 614L, 670L, 3813L, 5950L, 7548L, 7803L, 8588L,....
2: do.call(.Call, args = dot_call_args)
3: eigs_real_sym(A, nrow(A), k, which, sigma, opts, mattype = "sym_dgCMatrix", extra_args = list(use_lower = as.logical(lower)))
4: eigs_sym.dgCMatrix(L, k = k, which = "LM", sigma = 0, opt = opt)
5: RSpectra::eigs_sym(L, k = k, which = "LM", sigma = 0, opt = opt)
6: doTryCatch(return(expr), name, parentenv, handler)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: tryCatchList(expr, classes, parentenv, handlers)
9: tryCatch(RSpectra::eigs_sym(L, k = k, which = "LM", sigma = 0, opt = opt), error = function(c) { NULL})
10: withCallingHandlers(expr, warning = function(w) if (inherits(w, classes)) tryInvokeRestart("muffleWarning"))
11: suppressWarnings(res <- tryCatch(RSpectra::eigs_sym(L, k = k, which = "LM", sigma = 0, opt = opt), error = function(c) { NULL}))
12: rspectra_eigs_sym(L, ndim, verbose = verbose)
13: rspectra_normalized_laplacian_init(A, ndim, verbose = FALSE)
14: spectral_init(V, ndim = n_components, verbose = verbose)
15: uwot(X = X, n_neighbors = n_neighbors, n_components = n_components, metric = metric, n_epochs = n_epochs, alpha = learning_rate, scale = scale, init = init, init_sdev = init_sdev, spread = spread, min_dist = min_dist,
16: uwot::umap(as.matrix(preprocess_mat), n_components = max_components, metric = umap.metric, min_dist = umap.min_dist, n_neighbors = umap.n_neighbors, fast_sgd = umap.fast_sgd, n_threads = cores, verbose = verbose, nn_m
17: reduce_dimension(cds, preprocess_method = "PCA")

sessionInfo():
Run sessionInfo() in R and post the output
R version 4.3.2 (2023-10-31)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /home/envs/ClusterGVis/lib/libopenblasp-r0.3.24.so; LAPACK version 3.11.0

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

time zone: Asia/Shanghai
tzcode source: system (glibc)

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

other attached packages:
[1] ggplot2_3.5.1 dplyr_1.1.4
[3] data.table_1.14.8 Matrix_1.6-1.1
[5] Seurat_5.0.0 SeuratObject_5.0.0
[7] sp_2.1-1 monocle3_1.3.1
[9] SingleCellExperiment_1.22.0 SummarizedExperiment_1.30.2
[11] GenomicRanges_1.52.0 GenomeInfoDb_1.36.1
[13] IRanges_2.34.1 S4Vectors_0.38.1
[15] MatrixGenerics_1.12.2 matrixStats_1.0.0
[17] Biobase_2.60.0 BiocGenerics_0.46.0

loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-3 jsonlite_1.8.7 magrittr_2.0.3
[4] spatstat.utils_3.0-5 nloptr_2.0.3 zlibbioc_1.46.0
[7] vctrs_0.6.4 ROCR_1.0-11 spatstat.explore_3.2-5
[10] minqa_1.2.6 RCurl_1.98-1.13 base64enc_0.1-3
[13] terra_1.7-55 htmltools_0.5.7 S4Arrays_1.0.4
[16] sctransform_0.4.1 parallelly_1.36.0 KernSmooth_2.23-22
[19] htmlwidgets_1.6.2 ica_1.0-3 plyr_1.8.9
[22] plotly_4.10.3 zoo_1.8-12 uuid_1.1-1
[25] igraph_1.4.3 mime_0.12 lifecycle_1.0.3
[28] pkgconfig_2.0.3 R6_2.5.1 fastmap_1.1.1
[31] GenomeInfoDbData_1.2.10 fitdistrplus_1.1-11 future_1.33.0
[34] shiny_1.7.5.1 digest_0.6.33 colorspace_2.1-0
[37] patchwork_1.2.0 tensor_1.5 RSpectra_0.16-1
[40] irlba_2.3.5.1 progressr_0.14.0 spatstat.sparse_3.0-3
[43] fansi_1.0.5 polyclip_1.10-6 abind_1.4-5
[46] httr_1.4.7 compiler_4.3.2 withr_3.0.0
[49] fastDummies_1.7.3 MASS_7.3-60 DelayedArray_0.26.6
[52] tools_4.3.2 lmtest_0.9-40 httpuv_1.6.12
[55] future.apply_1.11.0 goftest_1.2-3 glue_1.7.0
[58] nlme_3.1-163 promises_1.2.1 grid_4.3.2
[61] pbdZMQ_0.3-10 Rtsne_0.16 cluster_2.1.4
[64] reshape2_1.4.4 generics_0.1.3 spatstat.data_3.0-3
[67] gtable_0.3.4 tidyr_1.3.1 utf8_1.2.4
[70] XVector_0.40.0 spatstat.geom_3.2-7 RcppAnnoy_0.0.21
[73] ggrepel_0.9.5 RANN_2.6.1 pillar_1.9.0
[76] stringr_1.5.0 spam_2.10-0 IRdisplay_1.1
[79] RcppHNSW_0.5.0 later_1.3.1 splines_4.3.2
[82] lattice_0.22-5 deldir_1.0-9 survival_3.5-7
[85] tidyselect_1.2.0 miniUI_0.1.1.1 pbapply_1.7-2
[88] gridExtra_2.3 scattermore_1.2 stringi_1.7.12
[91] lazyeval_0.2.2 boot_1.3-28.1 evaluate_0.23
[94] codetools_0.2-19 tibble_3.2.1 cli_3.6.1
[97] uwot_0.1.16 IRkernel_1.3.2 xtable_1.8-4
[100] reticulate_1.34.0 repr_1.1.6 munsell_0.5.0
[103] Rcpp_1.0.11 spatstat.random_3.2-1 globals_0.16.2
[106] png_0.1-8 parallel_4.3.2 ellipsis_0.3.2
[109] dotCall64_1.1-0 bitops_1.0-7 lme4_1.1-35
[112] listenv_0.9.0 viridisLite_0.4.2 scales_1.3.0
[115] ggridges_0.5.4 leiden_0.4.3 purrr_1.0.2
[118] crayon_1.5.2 rlang_1.1.4 cowplot_1.1.1

I truly appreciate any help you can provide！