Error during addDoubletScores

[yangshichen0713]

Hi! I was running the tutorial code on tutorial data but couldn't get past doublet scoring. I keep seeing this error. Could you help have a look? Thanks!

> ArrowFiles
[1] "ATAC-H134-1.arrow"

> doubScores <- addDoubletScores(input = ArrowFiles,
+                                k = 10, #Refers to how many cells near a "pseudo-doublet" to count.
+                                knnMethod = "UMAP", #Refers to the embedding to use for nearest neighbor search with doublet projection.
+                                LSIMethod = 1,
+                                threads = 1)
ArchR logging to : ArchRLogs/ArchR-addDoubletScores-33f37f2a7050bb-Date-2023-10-31_Time-16-39-42.log
If there is an issue, please report to github with logFile!
2023-10-31 16:39:42 : Batch Execution w/ safelapply!, 0 mins elapsed.
2023-10-31 16:39:42 : ATAC-H134-1 (1 of 1) :  Computing Doublet Statistics, 0 mins elapsed.

************************************************************
2023-10-31 16:40:20 : ERROR Found in .LSIPartialMatrix for  
LogFile = ArchRLogs/ArchR-addDoubletScores-33f37f2a7050bb-Date-2023-10-31_Time-16-39-42.log

<simpleError in validityMethod(as(object, superClass)): 找不到对象'Csparse_validate'>

************************************************************

************************************************************
2023-10-31 16:40:20 : ERROR Found in addIterativeLSI for ATAC-H134-1 (1 of 1) :  
LogFile = ArchRLogs/ArchR-addDoubletScores-33f37f2a7050bb-Date-2023-10-31_Time-16-39-42.log

<simpleError in .logError(e, fn = ".LSIPartialMatrix", info = "", errorList = errorList,     logFile = logFile): Exiting See Error Above>

************************************************************

Error in .logError(e, fn = "addIterativeLSI", info = prefix, errorList = list(ArrowFile = ArrowFile),  : 
  Exiting See Error Above

This is the log file:

           ___      .______        ______  __    __  .______      
          /   \     |   _  \      /      ||  |  |  | |   _  \     
         /  ^  \    |  |_)  |    |  ,----'|  |__|  | |  |_)  |    
        /  /_\  \   |      /     |  |     |   __   | |      /     
       /  _____  \  |  |\  \\___ |  `----.|  |  |  | |  |\  \\___.
      /__/     \__\ | _| `._____| \______||__|  |__| | _| `._____|

Logging With ArchR!

Start Time : 2023-10-31 16:39:42

------- ArchR Info

ArchRThreads = 1
ArchRGenome = Hg38

------- System Info

Computer OS = unix
Total Cores = 96

------- Session Info

R version 4.1.1 (2021-08-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 20.04.5 LTS

Matrix products: default
BLAS/LAPACK: /home/zhengyuhui/anaconda3/envs/pbmc/lib/libopenblasp-r0.3.17.so

Random number generation:
 RNG:     L'Ecuyer-CMRG 
 Normal:  Inversion 
 Sample:  Rejection 

locale:
 [1] LC_CTYPE=zh_CN.UTF-8       LC_NUMERIC=C               LC_TIME=zh_CN.UTF-8        LC_COLLATE=zh_CN.UTF-8     LC_MONETARY=zh_CN.UTF-8   
 [6] LC_MESSAGES=zh_CN.UTF-8    LC_PAPER=zh_CN.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] BSgenome.Hsapiens.UCSC.hg38_1.4.4 BiocManager_1.30.18               doRNG_1.8.6                      
 [4] rngtools_1.5.2                    foreach_1.5.2                     GSEABase_1.56.0                  
 [7] graph_1.72.0                      annotate_1.72.0                   XML_3.99-0.8                     
[10] AUCell_1.16.0                     rsvd_1.0.5                        scMetabolism_0.2.1               
[13] ggrepel_0.9.4                     ggpubr_0.6.0                      harmony_0.1.0                    
[16] reshape2_1.4.4                    RColorBrewer_1.1-3                cowplot_1.1.1                    
[19] BSgenome_1.62.0                   rtracklayer_1.54.0                forcats_0.5.2                    
[22] dplyr_1.1.3                       purrr_1.0.2                       readr_2.1.3                      
[25] tidyr_1.3.0                       tibble_3.2.1                      tidyverse_1.3.2                  
[28] Rsamtools_2.10.0                  Biostrings_2.62.0                 XVector_0.34.0                   
[31] pryr_0.1.5                        rhdf5_2.38.1                      SummarizedExperiment_1.24.0      
[34] MatrixGenerics_1.6.0              Rcpp_1.0.11                       Matrix_1.6-1.1                   
[37] matrixStats_0.63.0                data.table_1.14.8                 stringr_1.5.0                    
[40] plyr_1.8.9                        magrittr_2.0.3                    gtable_0.3.4                     
[43] gtools_3.9.3                      gridExtra_2.3                     ArchR_1.0.2                      
[46] EnsDb.Hsapiens.v86_2.99.0         ensembldb_2.18.4                  AnnotationFilter_1.18.0          
[49] GenomicFeatures_1.46.5            AnnotationDbi_1.56.2              Biobase_2.54.0                   
[52] GenomicRanges_1.46.1              GenomeInfoDb_1.35.15              IRanges_2.28.0                   
[55] S4Vectors_0.32.4                  BiocGenerics_0.40.0               patchwork_1.1.3                  
[58] ggplot2_3.4.4                     SeuratObject_4.1.3                Seurat_4.3.0.1                   
[61] Signac_1.7.0                     

loaded via a namespace (and not attached):
  [1] rappdirs_0.3.3           scattermore_0.8          R.methodsS3_1.8.2        bit64_4.0.5              irlba_2.3.5             
  [6] DelayedArray_0.20.0      R.utils_2.12.0           doParallel_1.0.17        KEGGREST_1.34.0          RCurl_1.98-1.8          
 [11] generics_0.1.3           RSQLite_2.2.17           RANN_2.6.1               future_1.28.0            bit_4.0.4               
 [16] tzdb_0.4.0               spatstat.data_3.0-0      xml2_1.3.3               lubridate_1.9.0          httpuv_1.6.6            
 [21] assertthat_0.2.1         gargle_1.2.1             hms_1.1.2                promises_1.2.0.1         fansi_1.0.5             
 [26] restfulr_0.0.15          progress_1.2.2           dbplyr_2.2.1             readxl_1.4.1             igraph_1.3.4            
 [31] DBI_1.1.3                htmlwidgets_1.6.2        spatstat.geom_3.0-3      googledrive_2.0.0        ellipsis_0.3.2          
 [36] backports_1.4.1          biomaRt_2.50.3           deldir_1.0-6             vctrs_0.6.4              Cairo_1.5-12.2          
 [41] ROCR_1.0-11              abind_1.4-5              cachem_1.0.8             withr_2.5.1              progressr_0.11.0        
 [46] sctransform_0.3.5        GenomicAlignments_1.30.0 prettyunits_1.2.0        goftest_1.2-3            cluster_2.1.4           
 [51] lazyeval_0.2.2           crayon_1.5.2             spatstat.explore_3.0-5   labeling_0.4.3           pkgconfig_2.0.3         
 [56] nlme_3.1-155             ProtGenerics_1.26.0      rlang_1.1.1              globals_0.16.1           lifecycle_1.0.3         
 [61] miniUI_0.1.1.1           filelock_1.0.2           BiocFileCache_2.2.1      modelr_0.1.10            cellranger_1.1.0        
 [66] polyclip_1.10-0          lmtest_0.9-40            carData_3.0-5            Rhdf5lib_1.16.0          zoo_1.8-11              
 [71] reprex_2.0.2             GlobalOptions_0.1.2      ggridges_0.5.3           googlesheets4_1.0.1      png_0.1-7               
 [76] viridisLite_0.4.2        rjson_0.2.21             bitops_1.0-7             R.oo_1.25.0              KernSmooth_2.23-20      
 [81] rhdf5filters_1.6.0       blob_1.2.3               shape_1.4.6              parallelly_1.32.1        spatstat.random_3.0-1   
 [86] rstatix_0.7.2            ggsignif_0.6.4           scales_1.2.1             memoise_2.0.1            ica_1.0-3               
 [91] zlibbioc_1.40.0          compiler_4.1.1           BiocIO_1.4.0             clue_0.3-61              fitdistrplus_1.1-8      
 [96] cli_3.6.1                listenv_0.8.0            pbapply_1.7-2            MASS_7.3-58.1            tidyselect_1.2.0        
[101] stringi_1.7.6            yaml_2.3.5               fastmatch_1.1-3          tools_4.1.1              timechange_0.1.1        
[106] future.apply_1.9.1       circlize_0.4.15          rstudioapi_0.15.0        farver_2.1.1             Rtsne_0.16              
[111] digest_0.6.33            rgeos_0.5-9              shiny_1.7.2              car_3.1-2                broom_1.0.5             
[116] later_1.3.0              RcppAnnoy_0.0.19         httr_1.4.4               ComplexHeatmap_2.10.0    colorspace_2.1-0        
[121] rvest_1.0.3              fs_1.6.3                 tensor_1.5               reticulate_1.26          splines_4.1.1           
[126] uwot_0.1.14              RcppRoll_0.3.0           spatstat.utils_3.0-1     sp_1.5-0                 plotly_4.10.0           
[131] xtable_1.8-4             jsonlite_1.8.7           R6_2.5.1                 pillar_1.9.0             htmltools_0.5.6         
[136] mime_0.12                glue_1.6.2               fastmap_1.1.1            BiocParallel_1.28.3      codetools_0.2-18        
[141] utf8_1.2.4               lattice_0.20-45          spatstat.sparse_3.0-0    curl_4.3.2               leiden_0.4.3            
[146] survival_3.4-0           munsell_0.5.0            GetoptLong_1.0.5         GenomeInfoDbData_1.2.7   iterators_1.0.14        
[151] haven_2.5.1             

------- Log Info

2023-10-31 16:39:42 : addDoubletScores Input-Parameters, Class = list

addDoubletScores Input-Parameters$input: length = 1
[1] "ATAC-H134-1.arrow"

addDoubletScores Input-Parameters$useMatrix: length = 1
[1] "TileMatrix"

addDoubletScores Input-Parameters$k: length = 1
[1] 10

addDoubletScores Input-Parameters$nTrials: length = 1
[1] 5

addDoubletScores Input-Parameters$dimsToUse: length = 30
[1] 1 2 3 4 5 6

addDoubletScores Input-Parameters$LSIMethod: length = 1
[1] 1

addDoubletScores Input-Parameters$scaleDims: length = 1
[1] FALSE

addDoubletScores Input-Parameters$corCutOff: length = 1
[1] 0.75

addDoubletScores Input-Parameters$knnMethod: length = 1
[1] "UMAP"

addDoubletScores Input-Parameters$outDir: length = 1
[1] "QualityControl"

addDoubletScores Input-Parameters$threads: length = 1
[1] 1

addDoubletScores Input-Parameters$force: length = 1
[1] FALSE

addDoubletScores Input-Parameters$parallelParam: length = 0
NULL

addDoubletScores Input-Parameters$verbose: length = 1
[1] TRUE

addDoubletScores Input-Parameters$logFile: length = 1
[1] "ArchRLogs/ArchR-addDoubletScores-33f37f2a7050bb-Date-2023-10-31_Time-16-39-42.log"

2023-10-31 16:39:42 : Batch Execution w/ safelapply!, 0 mins elapsed.
2023-10-31 16:39:42 : ATAC-H134-1 (1 of 1) :  Computing Doublet Statistics, 0 mins elapsed.
2023-10-31 16:39:43 : Running IterativeLSI, 0.018 mins elapsed.

2023-10-31 16:39:43 : IterativeLSI Input-Parameters, Class = list

IterativeLSI Input-Parameters$ArchRProj: length = 1

IterativeLSI Input-Parameters$useMatrix: length = 1
[1] "TileMatrix"

IterativeLSI Input-Parameters$name: length = 1
[1] "IterativeLSI"

IterativeLSI Input-Parameters$iterations: length = 1
[1] 2

IterativeLSI Input-Parameters$firstSelection: length = 1
[1] "top"

IterativeLSI Input-Parameters$depthCol: length = 1
[1] "nFrags"

IterativeLSI Input-Parameters$varFeatures: length = 1
[1] 25000

IterativeLSI Input-Parameters$dimsToUse: length = 30
[1] 1 2 3 4 5 6

IterativeLSI Input-Parameters$LSIMethod: length = 1
[1] 1

IterativeLSI Input-Parameters$scaleDims: length = 1
[1] FALSE

IterativeLSI Input-Parameters$corCutOff: length = 1
[1] 0.75

IterativeLSI Input-Parameters$binarize: length = 1
[1] TRUE

IterativeLSI Input-Parameters$outlierQuantiles: length = 0
NULL

IterativeLSI Input-Parameters$filterBias: length = 1
[1] FALSE

IterativeLSI Input-Parameters$sampleCellsPre: length = 1
[1] 10000

IterativeLSI Input-Parameters$projectCellsPre: length = 1
[1] FALSE

IterativeLSI Input-Parameters$sampleCellsFinal: length = 0
NULL

IterativeLSI Input-Parameters$selectionMethod: length = 1
[1] "var"

IterativeLSI Input-Parameters$scaleTo: length = 1
[1] 10000

IterativeLSI Input-Parameters$totalFeatures: length = 1
[1] 5e+05

IterativeLSI Input-Parameters$filterQuantile: length = 1
[1] 0.995

IterativeLSI Input-Parameters$excludeChr: length = 0
NULL

IterativeLSI Input-Parameters$saveIterations: length = 1
[1] FALSE

IterativeLSI Input-Parameters$nPlot: length = 1
[1] 10000

IterativeLSI Input-Parameters$outDir: length = 1
[1] "/media/AnalysisTempDisk2/Yangshichen/0_HIV/HIV-ATAC-HDs/tmp/tmp-33f37f5e50a608-Date-2023-10-31_Time-16-39-42"

IterativeLSI Input-Parameters$threads: length = 1
[1] 1

IterativeLSI Input-Parameters$seed: length = 1
[1] 1

IterativeLSI Input-Parameters$verbose: length = 1
[1] FALSE

IterativeLSI Input-Parameters$force: length = 1
[1] TRUE

IterativeLSI Input-Parameters$logFile: length = 1
[1] "ArchRLogs/ArchR-addDoubletScores-33f37f2a7050bb-Date-2023-10-31_Time-16-39-42.log"

2023-10-31 16:39:43 : Computing Total Across All Features, 0.002 mins elapsed.
2023-10-31 16:39:46 : Computing Top Features, 0.05 mins elapsed.
###########
2023-10-31 16:39:49 : Running LSI (1 of 2) on Top Features, 0.107 mins elapsed.
###########
2023-10-31 16:39:49 : Creating Partial Matrix, 0.107 mins elapsed.
2023-10-31 16:40:19 : Computing LSI, 0.607 mins elapsed.

2023-10-31 16:40:19 : LSI Parameters, Class = list

LSI Parameters$: length = 1

1 function (name)      
2 .Internal(args(name))

LSI Parameters$mat: nRows = 25000, nCols = 5105
LSI Parameters$mat: NonZeroEntries = 11344310, EntryRange = [ 1 , 1 ]
5 x 5 sparse Matrix of class "dgCMatrix"

************************************************************
2023-10-31 16:40:20 : ERROR Found in .LSIPartialMatrix for  
LogFile = ArchRLogs/ArchR-addDoubletScores-33f37f2a7050bb-Date-2023-10-31_Time-16-39-42.log

<simpleError in validityMethod(as(object, superClass)): 找不到对象'Csparse_validate'>

2023-10-31 16:40:20 : errorList, Class = list

errorList$: length = 1

1 function (name)      
2 .Internal(args(name))

errorList$ArrowFiles: length = 1
[1] "ATAC-H134-1.arrow"

errorList$useMatrix: length = 1
[1] "TileMatrix"

errorList$cellNames: length = 5105
[1] "ATAC-H134-1#ATAC-H134-1_BC01716_N14" "ATAC-H134-1#ATAC-H134-1_BC01673_N13" "ATAC-H134-1#ATAC-H134-1_BC03254_N14"
[4] "ATAC-H134-1#ATAC-H134-1_BC00150_N05" "ATAC-H134-1#ATAC-H134-1_BC00414_N18" "ATAC-H134-1#ATAC-H134-1_BC00065_N08"

errorList$cellDepth: length = 5105
ATAC-H134-1#ATAC-H134-1_BC01716_N14 ATAC-H134-1#ATAC-H134-1_BC01673_N13 ATAC-H134-1#ATAC-H134-1_BC03254_N14 
                           4.999913                            4.999300                            4.988563 
ATAC-H134-1#ATAC-H134-1_BC00150_N05 ATAC-H134-1#ATAC-H134-1_BC00414_N18 ATAC-H134-1#ATAC-H134-1_BC00065_N08 
                           4.983103                            4.982389                            4.975073 

errorList$sampleNames: length = 5105
[1] "ATAC-H134-1" "ATAC-H134-1" "ATAC-H134-1" "ATAC-H134-1" "ATAC-H134-1" "ATAC-H134-1"

errorList$dimsToUse: length = 30
[1] 1 2 3 4 5 6

errorList$binarize: length = 1
[1] TRUE

errorList$outlierQuantiles: length = 0
NULL

errorList$LSIMethod: length = 1
[1] 1

errorList$scaleTo: length = 1
[1] 10000

errorList$sampleCells: length = 0
NULL

errorList$projectAll: length = 0
logical(0)

errorList$threads: length = 1
[1] 1

errorList$seed: length = 1
[1] 1

errorList$useIndex: length = 1
[1] FALSE

errorList$tstart: length = 1
[1] "2023-10-31 16:39:43 CST"

errorList$verbose: length = 1
[1] FALSE

errorList$logFile: length = 1
[1] "ArchRLogs/ArchR-addDoubletScores-33f37f2a7050bb-Date-2023-10-31_Time-16-39-42.log"

errorList$outLSI: length = 1
[1] "Error with outLSI!"

errorList$matSVD: length = 1
[1] "Error with matSVD!"

************************************************************

************************************************************
2023-10-31 16:40:20 : ERROR Found in addIterativeLSI for ATAC-H134-1 (1 of 1) :  
LogFile = ArchRLogs/ArchR-addDoubletScores-33f37f2a7050bb-Date-2023-10-31_Time-16-39-42.log

<simpleError in .logError(e, fn = ".LSIPartialMatrix", info = "", errorList = errorList,     logFile = logFile): Exiting See Error Above>

2023-10-31 16:40:20 : errorList, Class = list

errorList$ArrowFile: length = 1
[1] "ATAC-H134-1.arrow"

************************************************************

[rcorces]

Hi @yangshichen0713! Thanks for using ArchR! Please make sure that your post belongs in the Issues section. Only bugs and error reports belong in the Issues section. Usage questions and feature requests should be posted in the Discussions section, not in Issues.
It is worth noting that there are very few actual bugs in ArchR. If you are getting an error, it is probably something specific to your dataset, usage, or computational environment, all of which are extremely challenging to troubleshoot. As such, we require reproducible examples (preferably using the tutorial dataset) from users who want assistance. If you cannot reproduce your error, we will not be able to help. Before going through the work of making a reproducible example, search the previous Issues, Discussions, function definitions, or the ArchR manual and you will likely find the answers you are looking for. If your post does not contain a reproducible example, it is unlikely to receive a response.
In addition to a reproducible example, you must do the following things before we help you, unless your original post already contained this information: 1. If you've encountered an error, have you already searched previous Issues to make sure that this hasn't already been solved? 2. Did you post your log file? If not, add it now. 3.__ Remove any screenshots that contain text and instead copy and paste the text using markdown's codeblock syntax (three consecutive backticks). You can do this by editing your original post.

[maxbond233]

I solved this problem by re-installing irlba using install.package('irlba').