error in Matrix function
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Entering edit mode
Bharti • 0
@2f4ec36f
Last seen 7 weeks ago
United Kingdom

I am getting error as

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

sessionInfo( ) R version 4.2.3 (2023-03-15 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale: [1] LC_COLLATE=English_United Kingdom.utf8 LC_CTYPE=English_United Kingdom.utf8 LC_MONETARY=English_United Kingdom.utf8 [4] LC_NUMERIC=C LC_TIME=English_United Kingdom.utf8

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

other attached packages: [1] sparseMatrixStats_1.10.0 irlba_2.3.5.1 Matrix_1.6-5 scran_1.26.2
[5] scuttle_1.8.4 SingleCellExperiment_1.20.1 SummarizedExperiment_1.28.0 Biobase_2.58.0
[9] GenomicRanges_1.50.2 GenomeInfoDb_1.34.9 IRanges_2.32.0 MatrixGenerics_1.10.0
[13] matrixStats_1.0.0 S4Vectors_0.36.2 BiocGenerics_0.44.0

loaded via a namespace (and not attached): [1] Rcpp_1.0.10 compiler_4.2.3 bluster_1.8.0 XVector_0.38.0 bitops_1.0-7
[6] BiocNeighbors_1.16.0 tools_4.2.3 DelayedMatrixStats_1.20.0 zlibbioc_1.44.0 statmod_1.5.0
[11] metapod_1.6.0 lattice_0.20-45 rlang_1.1.1 pkgconfig_2.0.3 igraph_1.5.0
[16] DelayedArray_0.24.0 cli_3.6.1 rstudioapi_0.15.0 parallel_4.2.3 GenomeInfoDbData_1.2.9
[21] cluster_2.1.4 locfit_1.5-9.7 grid_4.2.3 BiocParallel_1.32.6 limma_3.54.2
[26] edgeR_3.40.2 BiocSingular_1.14.0 magrittr_2.0.3 codetools_0.2-19 beachmat_2.14.2
[31] rsvd_1.0.5 dqrng_0.3.0 ScaledMatrix_1.6.0 RCurl_1.98-1.12

Code should be placed in three backticks as shown below


# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

sessionInfo( )
MatrixQCvis • 150 views
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@james-w-macdonald-5106
Last seen 1 hour ago
United States

See the last post here.

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