*** caught segfault *** error when running quantile_norm function

[ProphetDarkland]

Hi, I'm doing Joint definition of cell types with your tutorial at http://htmlpreview.github.io/?https://github.com/welch-lab/liger/blob/master/vignettes/Integrating_scRNA_and_scATAC_data.html .

But when I ran this code :

pbmc.try <- quantile_norm(pbmc)

I got error messages as follows:

*** caught segfault ***
address (nil), cause 'memory not mapped'

Traceback:
 1: FUN(X[[i]], ...)
 2: lapply(object, max_factor, dims_use = use_these_factors, center_cols = do.center)
 3: quantile_norm.list(object = object@H, quantiles = quantiles,     ref_dataset = ref_dataset, min_cells = min_cells, knn_k = knn_k,     dims.use = dims.use, do.center = do.center, max_sample = max_sample,     eps = eps, refine.knn = refine.knn, rand.seed = rand.seed)
 4: quantile_norm(object = object@H, quantiles = quantiles, ref_dataset = ref_dataset,     min_cells = min_cells, knn_k = knn_k, dims.use = dims.use,     do.center = do.center, max_sample = max_sample, eps = eps,     refine.knn = refine.knn, rand.seed = rand.seed)
 5: quantile_norm.liger(pbmc)
 6: quantile_norm(pbmc)

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

My session info:

R version 4.1.0 (2021-05-18)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server 7.6 (Maipo)

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] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] Signac_1.5.0       rliger_1.0.0       patchwork_1.1.1    Matrix_1.4-0      
[5] cowplot_1.1.1      SeuratObject_4.0.4 Seurat_4.0.6  

loaded via a namespace (and not attached):
  [1] uuid_1.0-3             fastmatch_1.1-3        plyr_1.8.6            
  [4] igraph_1.2.10          repr_1.1.3             lazyeval_0.2.2        
  [7] splines_4.1.0          BiocParallel_1.28.3    listenv_0.8.0         
 [10] SnowballC_0.7.0        scattermore_0.7        GenomeInfoDb_1.30.0   
 [13] ggplot2_3.3.5          digest_0.6.29          foreach_1.5.1         
 [16] htmltools_0.5.2        fansi_1.0.0            magrittr_2.0.1        
 [19] tensor_1.5             cluster_2.1.2          doParallel_1.0.16     
 [22] ROCR_1.0-11            globals_0.14.0         Biostrings_2.62.0     
 [25] matrixStats_0.61.0     docopt_0.7.1           spatstat.sparse_2.1-0 
 [28] colorspace_2.0-2       ggrepel_0.9.1          dplyr_1.0.7           
 [31] sparsesvd_0.2          crayon_1.4.2           RCurl_1.98-1.5        
 [34] jsonlite_1.7.2         spatstat.data_2.1-2    survival_3.2-13       
 [37] zoo_1.8-9              iterators_1.0.13       glue_1.6.0            
 [40] polyclip_1.10-0        gtable_0.3.0           zlibbioc_1.40.0       
 [43] XVector_0.34.0         leiden_0.3.9           future.apply_1.8.1    
 [46] BiocGenerics_0.40.0    abind_1.4-5            scales_1.1.1          
 [49] DBI_1.1.1              miniUI_0.1.1.1         Rcpp_1.0.8            
 [52] viridisLite_0.4.0      xtable_1.8-4           riverplot_0.10        
 [55] reticulate_1.23        spatstat.core_2.3-2    bit_4.0.4             
 [58] mclust_5.4.9           stats4_4.1.0           htmlwidgets_1.5.4     
 [61] httr_1.4.2             FNN_1.1.3              RColorBrewer_1.1-2    
 [64] ellipsis_0.3.2         ica_1.0-2              farver_2.1.0          
 [67] pkgconfig_2.0.3        ggseqlogo_0.1          uwot_0.1.11           
 [70] deldir_1.0-6           utf8_1.2.2             tidyselect_1.1.1      
 [73] rlang_0.4.12           reshape2_1.4.4         later_1.3.0           
 [76] munsell_0.5.0          tools_4.1.0            generics_0.1.1        
 [79] ggridges_0.5.3         evaluate_0.14          stringr_1.4.0         
 [82] fastmap_1.1.0          goftest_1.2-3          bit64_4.0.5           
 [85] fitdistrplus_1.1-6     purrr_0.3.4            RANN_2.6.1            
 [88] pbapply_1.5-0          future_1.23.0          nlme_3.1-153          
 [91] mime_0.12              slam_0.1-49            RcppRoll_0.3.0        
 [94] hdf5r_1.3.5            compiler_4.1.0         plotly_4.10.0         
 [97] png_0.1-7              spatstat.utils_2.3-0   tibble_3.1.6          
[100] tweenr_1.0.2           stringi_1.7.6          lattice_0.20-45       
[103] IRdisplay_1.0          vctrs_0.3.8            pillar_1.6.4          
[106] lifecycle_1.0.1        spatstat.geom_2.3-1    lmtest_0.9-39         
[109] RcppAnnoy_0.0.19       data.table_1.14.2      bitops_1.0-7          
[112] irlba_2.3.5            httpuv_1.6.3           GenomicRanges_1.46.1  
[115] R6_2.5.1               promises_1.2.0.1       lsa_0.73.2            
[118] KernSmooth_2.23-20     gridExtra_2.3          IRanges_2.28.0        
[121] parallelly_1.30.0      codetools_0.2-18       MASS_7.3-54           
[124] assertthat_0.2.1       qlcMatrix_0.9.7        sctransform_0.3.3     
[127] Rsamtools_2.10.0       S4Vectors_0.32.3       GenomeInfoDbData_1.2.7
[130] mgcv_1.8-38            parallel_4.1.0         grid_4.1.0            
[133] rpart_4.1-15           IRkernel_1.2           tidyr_1.1.4           
[136] Rtsne_0.15             pbdZMQ_0.3-6           ggforce_0.3.3         
[139] shiny_1.7.1            base64enc_0.1-3       

I've searched at stackoverflow but none of the answers solve my problem, I really don't know why this error occured. So if you could help me solve this problem, I would be really appreciated.

[skpalan]

Hi, can you check if you can successfully run one of the example datasets we provided? Just to make sure if rliger is working fine.

[ProphetDarkland]

Yes, I can successfully run your example dataset in your tutorial UINMF integration of Dual-omics data.

[mvfki]

We have updated rliger quite a lot in new version 2.0. It seems that the original error message corresponds to a pretty old version so I'm closing this Issue now. Please feel free to reopen it if you try the new rliger and still encounter this error.