ScRNAseq analysis scran :: quickcluster Error
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Last seen 3 months ago

Hello! I am having an error while doing normalization for my scRNAseq data, I would appreciate the help of anyone who countered the same problem the error is during quickcluster command as follow:

clust <- quickCluster(sce) 
Error in (function (A, nv = 5, nu = nv, maxit = 1000, work = nv + 7, reorth = TRUE,  : 
  function 'as_cholmod_sparse' not provided by package 'Matrix

R version 4.3.2 (2023-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22621)

Matrix products: default

[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8    LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                           LC_TIME=English_United States.utf8    

time zone: Europe/Berlin
tzcode source: internal

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

other attached packages:
 [1] RSpectra_0.16-1             patchwork_1.1.3             BiocParallel_1.34.2         lubridate_1.9.3            
 [5] forcats_1.0.0               stringr_1.5.1               dplyr_1.1.4                 purrr_1.0.2                
 [9] readr_2.1.4                 tidyr_1.3.0                 tibble_3.2.1                tidyverse_2.0.0.9000       
[13] scater_1.28.0               ggplot2_3.4.4               scran_1.28.2                scuttle_1.10.2             
[17] future_1.33.0               sctransform_0.4.1           Matrix_1.6-3                SingleCellExperiment_1.22.0
[21] SummarizedExperiment_1.30.2 Biobase_2.60.0              GenomicRanges_1.52.0        GenomeInfoDb_1.36.1        
[25] IRanges_2.34.1              S4Vectors_0.38.1            MatrixGenerics_1.12.3       matrixStats_1.1.0          
[29] AnnotationHub_3.8.0         BiocFileCache_2.8.0         dbplyr_2.3.4                BiocGenerics_0.46.0        

loaded via a namespace (and not attached):
  [1] rstudioapi_0.15.0             magrittr_2.0.3                ggbeeswarm_0.7.2              GenomicFeatures_1.52.2       
  [5] BiocIO_1.10.0                 zlibbioc_1.46.0               vctrs_0.6.4                   memoise_2.0.1                
  [9] Rsamtools_2.16.0              DelayedMatrixStats_1.22.6     RCurl_1.98-1.13               htmltools_0.5.7              
 [13] S4Arrays_1.0.5                progress_1.2.2                curl_5.1.0                    BiocNeighbors_1.18.0         
 [17] parallelly_1.36.0             htmlwidgets_1.6.4             plyr_1.8.9                    cachem_1.0.8                 
 [21] GenomicAlignments_1.36.0      igraph_1.5.1                  mime_0.12                     lifecycle_1.0.4              
 [25] pkgconfig_2.0.3               rsvd_1.0.5                    R6_2.5.1                      fastmap_1.1.1                
 [29] GenomeInfoDbData_1.2.10       shiny_1.8.0                   digest_0.6.33                 colorspace_2.1-0             
 [33] AnnotationDbi_1.62.2          dqrng_0.3.2                   irlba_2.3.5.1                 RSQLite_2.3.3                
 [37] beachmat_2.16.0               filelock_1.0.2                fansi_1.0.5                   timechange_0.2.0             
 [41] httr_1.4.7                    abind_1.4-5                   compiler_4.3.2                withr_2.5.2                  
 [45] bit64_4.0.5                   viridis_0.6.4                 DBI_1.1.3                     biomaRt_2.56.1               
 [49] MASS_7.3-60                   rappdirs_0.3.3                DelayedArray_0.26.7           rjson_0.2.21                 
 [53] bluster_1.10.0                tools_4.3.2                   vipor_0.4.5                   beeswarm_0.4.0               
 [57] interactiveDisplayBase_1.38.0 httpuv_1.6.12                 future.apply_1.11.0           glue_1.6.2                   
 [61] restfulr_0.0.15               promises_1.2.1                grid_4.3.2                    cluster_2.1.4                
 [65] reshape2_1.4.4                generics_0.1.3                gtable_0.3.4                  tzdb_0.4.0                   
 [69] ensembldb_2.24.1              hms_1.1.3                     metapod_1.8.0                 BiocSingular_1.16.0          
 [73] ScaledMatrix_1.8.1            xml2_1.3.5                    utf8_1.2.4                    XVector_0.40.0               
 [77] ggrepel_0.9.4                 BiocVersion_3.17.1            pillar_1.9.0                  limma_3.56.2                 
 [81] later_1.3.1                   lattice_0.21-9                rtracklayer_1.60.1            bit_4.0.5                    
 [85] tidyselect_1.2.0              locfit_1.5-9.8                Biostrings_2.68.1             gridExtra_2.3                
 [89] ProtGenerics_1.32.0           edgeR_3.42.4                  statmod_1.5.0                 DT_0.30                      
 [93] stringi_1.8.2                 lazyeval_0.2.2                yaml_2.3.7                    codetools_0.2-19             
 [97] BiocManager_1.30.22           cli_3.6.1                     xtable_1.8-4                  munsell_0.5.0                
[101] Rcpp_1.0.11                   globals_0.16.2                png_0.1-8                     XML_3.99-0.16                
[105] parallel_4.3.2                ellipsis_0.3.2                blob_1.2.4                    prettyunits_1.2.0            
[109] AnnotationFilter_1.24.0       sparseMatrixStats_1.12.2      bitops_1.0-7                  listenv_0.9.0                
[113] viridisLite_0.4.2             scales_1.3.0                  crayon_1.5.2                  rlang_1.1.2                  
[117] KEGGREST_1.40.1              

thank you in advance!


scRNAseq quickcluster scRNA scran • 756 views
Entering edit mode
ATpoint ★ 4.0k
Last seen 2 days ago

Please google errors, this has been asked recently. Same error, different Bioc package, same root cause: scater runUMAP fails with error "function 'as_cholmod_sparse' not provided by package 'Matrix'"

Entering edit mode

I googled the error but didn't counter this one! it worked perfectly thank you for your help!


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