Error running scDblFinder

[chungsai]

Hello,

I'm trying to use this function on my seurat object.

After combining a list of seurat objects, and SCTransform them in layers in seurat 5.

Ran clusters, then UMAP.

I did counts = LayerData(merged_samples, assay = "SCT", layer = "counts")

counts = scDblFinder(counts, samples=merged_samples$sample_name)

However,

I always get this following error even with differen sample sets. I also did a complete clean restore/reinstall of my MacOS and it changed from a blank slate from Ventura to Sonoma. Yet, re-running the script, I get the same error. I also tried joining layers and running the normal scale, normalize, etc.. pipeline. No difference was made.

Error: BiocParallel errors " 4 remote errors, element index: 1, 2, 3, 4 0 unevaluated and other errors first remote error: Error in value[3L]: An error occured while processing sample 'Dark01': 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) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Sonoma 14.3.1

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Toronto tzcode source: internal

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

other attached packages: [1] scDblFinder_1.17.1 BiocParallel_1.36.0 UCell_2.6.2
[4] DDRTree_0.1.5 irlba_2.3.5.1 VGAM_1.1-9
[7] pheatmap_1.0.12 SoupX_1.6.2 harmony_1.2.0
[10] gprofiler2_0.2.3 multtest_2.58.0 DelayedMatrixStats_1.24.0
[13] DelayedArray_0.28.0 SparseArray_1.2.4 S4Arrays_1.2.0
[16] abind_1.4-5 limma_3.58.1 fgsea_1.28.0
[19] GSVA_1.50.0 GSEABase_1.64.0 graph_1.80.0
[22] annotate_1.80.0 XML_3.99-0.16.1 AUCell_1.24.0
[25] devtools_2.4.5 usethis_2.2.3 Matrix_1.6-5
[28] scran_1.30.2 scuttle_1.12.0 SingleCellExperiment_1.24.0 [31] SummarizedExperiment_1.32.0 GenomicRanges_1.54.1 GenomeInfoDb_1.38.6
[34] MatrixGenerics_1.14.0 matrixStats_1.2.0 presto_1.0.0
[37] data.table_1.15.0 Rcpp_1.0.12 org.Hs.eg.db_3.18.0
[40] ggplot2_3.5.0 biomaRt_2.58.2 stringr_1.5.1
[43] org.Rn.eg.db_3.18.0 AnnotationDbi_1.64.1 IRanges_2.36.0
[46] S4Vectors_0.40.2 Biobase_2.62.0 BiocGenerics_0.48.1
[49] viridis_0.6.5 viridisLite_0.4.2 BiocManager_1.30.22
[52] Seurat_5.0.1 SeuratObject_5.0.1 sp_2.1-3

loaded via a namespace (and not attached): [1] fs_1.6.3 spatstat.sparse_3.0-3 bitops_1.0-7 httr_1.4.7
[5] RColorBrewer_1.1-3 profvis_0.3.8 tools_4.3.2 sctransform_0.4.1
[9] utf8_1.2.4 R6_2.5.1 HDF5Array_1.30.1 lazyeval_0.2.2
[13] uwot_0.1.16 rhdf5filters_1.14.1 urlchecker_1.0.1 withr_3.0.0
[17] prettyunits_1.2.0 gridExtra_2.3 progressr_0.14.0 textshaping_0.3.7
[21] cli_3.6.2 spatstat.explore_3.2-6 fastDummies_1.7.3 labeling_0.4.3
[25] slam_0.1-50 spatstat.data_3.0-4 ggridges_0.5.6 pbapply_1.7-2
[29] Rsamtools_2.18.0 systemfonts_1.0.5 R.utils_2.12.3 scater_1.30.1
[33] parallelly_1.37.0 sessioninfo_1.2.2 rstudioapi_0.15.0 RSQLite_2.3.5
[37] BiocIO_1.12.0 generics_0.1.3 combinat_0.0-8 ica_1.0-3
[41] spatstat.random_3.2-2 dplyr_1.1.4 ggbeeswarm_0.7.2 fansi_1.0.6
[45] R.methodsS3_1.8.2 lifecycle_1.0.4 yaml_2.3.8 edgeR_4.0.16
[49] glmGamPoi_1.14.3 rhdf5_2.46.1 BiocFileCache_2.10.1 Rtsne_0.17
[53] grid_4.3.2 blob_1.2.4 promises_1.2.1 dqrng_0.3.2
[57] crayon_1.5.2 miniUI_0.1.1.1 lattice_0.22-5 beachmat_2.18.1
[61] cowplot_1.1.3 KEGGREST_1.42.0 knitr_1.45 pillar_1.9.0
[65] metapod_1.10.1 rjson_0.2.21 xgboost_1.7.7.1 future.apply_1.11.1
[69] codetools_0.2-19 fastmatch_1.1-4 leiden_0.4.3.1 glue_1.7.0
[73] leidenbase_0.1.27 remotes_2.4.2.1 vctrs_0.6.5 png_0.1-8
[77] spam_2.10-0 gtable_0.3.4 cachem_1.0.8 xfun_0.42
[81] mime_0.12 HSMMSingleCell_1.22.0 survival_3.5-8 fastICA_1.2-4
[85] statmod_1.5.0 bluster_1.12.0 ellipsis_0.3.2 fitdistrplus_1.1-11
[89] ROCR_1.0-11 nlme_3.1-164 bit64_4.0.5 progress_1.2.3
[93] filelock_1.0.3 RcppAnnoy_0.0.22 vipor_0.4.7 KernSmooth_2.23-22
[97] colorspace_2.1-0 DBI_1.2.2 processx_3.8.3 tidyselect_1.2.0
[101] bit_4.0.5 compiler_4.3.2 curl_5.2.0 BiocNeighbors_1.20.2
[105] hdf5r_1.3.9 xml2_1.3.6 desc_1.4.3 plotly_4.10.4
[109] rtracklayer_1.62.0 scales_1.3.0 lmtest_0.9-40 callr_3.7.5
[113] rappdirs_0.3.3 digest_0.6.34 goftest_1.2-3 spatstat.utils_3.0-4
[117] rmarkdown_2.25 XVector_0.42.0 htmltools_0.5.7 pkgconfig_2.0.3
[121] sparseMatrixStats_1.14.0 dbplyr_2.4.0 fastmap_1.1.1 rlang_1.1.3
[125] htmlwidgets_1.6.4 shiny_1.8.0 farver_2.1.1 zoo_1.8-12
[129] jsonlite_1.8.8 R.oo_1.26.0 BiocSingular_1.18.0 RCurl_1.98-1.14
[133] magrittr_2.0.3 GenomeInfoDbData_1.2.11 dotCall64_1.1-1 patchwork_1.2.0
[137] Rhdf5lib_1.24.2 munsell_0.5.0 reticulate_1.35.0 stringi_1.8.3
[141] zlibbioc_1.48.0 MASS_7.3-60.0.1 plyr_1.8.9 pkgbuild_1.4.3
[145] parallel_4.3.2 listenv_0.9.1 ggrepel_0.9.5 deldir_2.0-2
[149] Biostrings_2.70.2 tensor_1.5 hms_1.1.3 locfit_1.5-9.8
[153] ps_1.7.6 igraph_2.0.2 spatstat.geom_3.2-8 RcppHNSW_0.6.0
[157] reshape2_1.4.4 ScaledMatrix_1.10.0 pkgload_1.3.4 evaluate_0.23
[161] httpuv_1.6.14 RANN_2.6.1 tidyr_1.3.1 purrr_1.0.2
[165] polyclip_1.10-6 future_1.33.1 scattermore_1.2 rsvd_1.0.5
[169] xtable_1.8-4 restfulr_0.0.15 RSpectra_0.16-1 later_1.3.2
[173] ragg_1.2.7 tibble_3.2.1 beeswarm_0.4.0 GenomicAlignments_1.38.2 [177] memoise_2.0.1 cluster_2.1.6 globals_0.16.2

[plger]

Please see #91

[plger]

@chungsai please confirm whether that was the issue or not, if I don't hear from you I'll close the issue.

[chungsai]

Hi, I am trying this. But I can't seem to re-install irlba

install.packages("irlba", type = "source")

Warning in install.packages : installation of package ‘irlba’ had non-zero exit status

[plger]

You're probably missing some build dependencies. Look at the rest of the output to figure out which.