RunLNMF error: "memory not mapped"

[MicTott]

Hi, just want to say thanks for creating RcppML andsinglet packages. They've been a big help and I'm very interested in using them for my analyses, particularly Linked NMF.

Unfortunately I'm currently running into the following issue. Any ideas how to solve this?

Running this below code:

set.seed(123) # for reproducible NMF models
get_pbmc3k_data() %>% NormalizeData %>% RunNMF -> pbmc3k
pbmc3k <- Seurat::RunUMAP(pbmc3k, reduction = "nmf", dims = 1:ncol(pbmc3k@reductions$nmf))

pbmc3k <- RunLNMF(pbmc3k, split.by="cell_type", reduction.use="nmf", link.cutoff=0.7, verbose=FALSE)

Results in the following error:

> pbmc3k <- RunLNMF(pbmc3k, split.by="cell_type", reduction.use="nmf", link.cutoff=0.7, verbose=FALSE)

 *** caught segfault ***
address 0x55d9a1419148, cause 'memory not mapped'

Traceback:
 1: weight_by_split(A, split.by, length(unique(split.by)))
 2: RunLNMF.Seurat(pbmc3k, split.by = "cell_type", reduction.use = "nmf",     link.cutoff = 0.7, verbose = FALSE)
 3: RunLNMF(pbmc3k, split.by = "cell_type", reduction.use = "nmf",     link.cutoff = 0.7, verbose = FALSE)

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace

Session info:

> sessionInfo()
R version 4.3.2 Patched (2024-02-08 r85876)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Rocky Linux 9.2 (Blue Onyx)

Matrix products: default
BLAS:   /jhpce/shared/community/core/conda_R/4.3.x/R/lib64/R/lib/libRblas.so 
LAPACK: /jhpce/shared/community/core/conda_R/4.3.x/R/lib64/R/lib/libRlapack.so;  LAPACK version 3.11.0

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       

time zone: US/Eastern
tzcode source: system (glibc)

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

other attached packages:
 [1] cowplot_1.1.3               patchwork_1.2.0            
 [3] bluster_1.12.0              igraph_2.0.1.9008          
 [5] RColorBrewer_1.1-3          pheatmap_1.0.12            
 [7] scran_1.30.2                Matrix_1.6-4               
 [9] scRNAseq_2.16.0             here_1.0.1                 
[11] ggspavis_1.8.0              scater_1.30.1              
[13] ggplot2_3.4.4               scuttle_1.12.0             
[15] SpatialExperiment_1.12.0    SingleCellExperiment_1.24.0
[17] SummarizedExperiment_1.32.0 Biobase_2.62.0             
[19] GenomicRanges_1.54.1        GenomeInfoDb_1.38.5        
[21] IRanges_2.36.0              S4Vectors_0.40.2           
[23] BiocGenerics_0.48.1         MatrixGenerics_1.14.0      
[25] matrixStats_1.2.0           singlet_0.99.6             
[27] RcppEigen_0.3.3.9.4         dplyr_1.1.4                
[29] RcppML_0.5.6                SeuratObject_5.0.0         
[31] Seurat_4.4.0               

loaded via a namespace (and not attached):
  [1] ProtGenerics_1.34.0           spatstat.sparse_3.0-3        
  [3] bitops_1.0-7                  httr_1.4.7                   
  [5] tools_4.3.2                   sctransform_0.4.1            
  [7] utf8_1.2.4                    R6_2.5.1                     
  [9] lazyeval_0.2.2                uwot_0.1.16                  
 [11] withr_3.0.0                   sp_2.1-3                     
 [13] prettyunits_1.2.0             gridExtra_2.3                
 [15] progressr_0.14.0              cli_3.6.2                    
 [17] spatstat.explore_3.2-5        spatstat.data_3.0-3          
 [19] ggridges_0.5.6                pbapply_1.7-2                
 [21] Rsamtools_2.18.0              parallelly_1.36.0            
 [23] limma_3.58.1                  RSQLite_2.3.5                
 [25] generics_0.1.3                BiocIO_1.12.0                
 [27] ica_1.0-3                     spatstat.random_3.2-1        
 [29] ggbeeswarm_0.7.2              fansi_1.0.6                  
 [31] abind_1.4-5                   lifecycle_1.0.4              
 [33] edgeR_4.0.14                  yaml_2.3.8                   
 [35] SparseArray_1.2.3             BiocFileCache_2.10.1         
 [37] Rtsne_0.17                    grid_4.3.2                   
 [39] blob_1.2.4                    dqrng_0.3.2                  
 [41] promises_1.2.1                ExperimentHub_2.10.0         
 [43] crayon_1.5.2                  miniUI_0.1.1.1               
 [45] lattice_0.22-5                beachmat_2.18.0              
 [47] msigdbr_7.5.1                 GenomicFeatures_1.54.3       
 [49] KEGGREST_1.42.0               magick_2.8.2                 
 [51] metapod_1.10.1                pillar_1.9.0                 
 [53] knitr_1.45                    fgsea_1.28.0                 
 [55] rjson_0.2.21                  future.apply_1.11.0          
 [57] codetools_0.2-19              fastmatch_1.1-4              
 [59] leiden_0.4.3                  glue_1.7.0                   
 [61] data.table_1.15.0             vctrs_0.6.5                  
 [63] png_0.1-8                     spam_2.10-0                  
 [65] gtable_0.3.4                  cachem_1.0.8                 
 [67] xfun_0.42                     S4Arrays_1.2.0               
 [69] mime_0.12                     ggside_0.2.3                 
 [71] survival_3.5-7                statmod_1.5.0                
 [73] interactiveDisplayBase_1.40.0 ellipsis_0.3.2               
 [75] fitdistrplus_1.1-11           ROCR_1.0-11                  
 [77] nlme_3.1-164                  bit64_4.0.5                  
 [79] progress_1.2.3                filelock_1.0.3               
 [81] RcppAnnoy_0.0.22              rprojroot_2.0.4              
 [83] irlba_2.3.5.1                 vipor_0.4.7                  
 [85] KernSmooth_2.23-22            colorspace_2.1-0             
 [87] DBI_1.2.1                     tidyselect_1.2.0             
 [89] bit_4.0.5                     compiler_4.3.2               
 [91] curl_5.2.0                    BiocNeighbors_1.20.2         
 [93] xml2_1.3.6                    DelayedArray_0.28.0          
 [95] plotly_4.10.4                 rtracklayer_1.62.0           
 [97] scales_1.3.0                  lmtest_0.9-40                
 [99] rappdirs_0.3.3                stringr_1.5.1                
[101] digest_0.6.34                 goftest_1.2-3                
[103] spatstat.utils_3.0-4          XVector_0.42.0               
[105] htmltools_0.5.7               pkgconfig_2.0.3              
[107] sparseMatrixStats_1.14.0      ensembldb_2.26.0             
[109] dbplyr_2.4.0                  fastmap_1.1.1                
[111] rlang_1.1.3                   htmlwidgets_1.6.4            
[113] shiny_1.8.0                   DelayedMatrixStats_1.24.0    
[115] zoo_1.8-12                    jsonlite_1.8.8               
[117] BiocParallel_1.36.0           BiocSingular_1.18.0          
[119] RCurl_1.98-1.14               magrittr_2.0.3               
[121] GenomeInfoDbData_1.2.11       dotCall64_1.1-1              
[123] munsell_0.5.0                 Rcpp_1.0.12                  
[125] babelgene_22.9                viridis_0.6.5                
[127] reticulate_1.35.0             stringi_1.8.3                
[129] zlibbioc_1.48.0               MASS_7.3-60.0.1              
[131] AnnotationHub_3.10.0          plyr_1.8.9                   
[133] parallel_4.3.2                listenv_0.9.1                
[135] ggrepel_0.9.5                 deldir_2.0-2                 
[137] Biostrings_2.70.2             splines_4.3.2                
[139] tensor_1.5                    hms_1.1.3                    
[141] locfit_1.5-9.8                spatstat.geom_3.2-7          
[143] reshape2_1.4.4                biomaRt_2.58.2               
[145] ScaledMatrix_1.10.0           BiocVersion_3.18.1           
[147] XML_3.99-0.16.1               BiocManager_1.30.22          
[149] httpuv_1.6.14                 RANN_2.6.1                   
[151] tidyr_1.3.1                   purrr_1.0.2                  
[153] polyclip_1.10-6               future_1.33.0                
[155] scattermore_1.2               rsvd_1.0.5                   
[157] xtable_1.8-4                  AnnotationFilter_1.26.0      
[159] restfulr_0.0.15               later_1.3.2                  
[161] viridisLite_0.4.2             tibble_3.2.1                 
[163] GenomicAlignments_1.38.2      memoise_2.0.1                
[165] beeswarm_0.4.0                AnnotationDbi_1.64.1         
[167] cluster_2.1.6                 globals_0.16.2