Error in cluster_cells(cds) function

[rachelzoeb]

I keep running into this error when running the cluster_cells() function on my monocle object. Previous steps such as creating the cds object and preprocess_cds() seem to work fine.

cds <- cluster_cells(cds) Error: as(<dsCMatrix>, "dgCMatrix") is deprecated since Matrix 1.5-0; do as(., "generalMatrix") instead

sessionInfo() R version 4.1.1 (2021-08-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Arch Linux

Matrix products: default BLAS: /software/cgeh/r/4.1.1/install/lib64/R/lib/libRblas.so LAPACK: /software/cgeh/r/4.1.1/install/lib64/R/lib/libRlapack.so

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] stats4 stats graphics grDevices utils datasets methods [8] base

other attached packages: [1] pbapply_1.5-0 dplyr_1.0.10 [3] monocle3_1.2.9 SingleCellExperiment_1.16.0 [5] SummarizedExperiment_1.24.0 GenomicRanges_1.46.1 [7] GenomeInfoDb_1.30.1 IRanges_2.28.0 [9] S4Vectors_0.32.4 MatrixGenerics_1.6.0 [11] matrixStats_0.62.0 Biobase_2.54.0 [13] BiocGenerics_0.40.0 SeuratObject_4.0.4 [15] Seurat_4.1.0

loaded via a namespace (and not attached): [1] minqa_1.2.4 Rtsne_0.16 [3] colorspace_2.0-3 deldir_1.0-6 [5] ellipsis_0.3.2 ggridges_0.5.3 [7] XVector_0.34.0 spatstat.data_2.1-4 [9] leiden_0.3.9 listenv_0.8.0 [11] ggrepel_0.9.1 fansi_1.0.3 [13] sparseMatrixStats_1.6.0 codetools_0.2-18 [15] splines_4.1.1 polyclip_1.10-0 [17] jsonlite_1.8.0 nloptr_1.2.1 [19] ica_1.0-2 cluster_2.1.2 [21] png_0.1-7 uwot_0.1.14 [23] shiny_1.7.2 sctransform_0.3.3 [25] spatstat.sparse_2.1-0 compiler_4.1.1 [27] httr_1.4.4 assertthat_0.2.1.9000 [29] Matrix_1.5-1 fastmap_1.1.0 [31] lazyeval_0.2.2 cli_3.4.0 [33] later_1.3.0 htmltools_0.5.3 [35] tools_4.1.1 igraph_1.3.4 [37] gtable_0.3.1 glue_1.6.2 [39] GenomeInfoDbData_1.2.7 RANN_2.6.1 [41] reshape2_1.4.4 Rcpp_1.0.9 [43] scattermore_0.8 vctrs_0.4.1 [45] nlme_3.1-152 DelayedMatrixStats_1.16.0 [47] lmtest_0.9-40 spatstat.random_2.2-0 [49] stringr_1.4.1 globals_0.16.1 [51] lme4_1.1-31 mime_0.12 [53] miniUI_0.1.1.1 lifecycle_1.0.2 [55] irlba_2.3.5 goftest_1.2-3 [57] terra_1.6-17 future_1.28.0 [59] MASS_7.3-54 zlibbioc_1.40.0 [61] zoo_1.8-10 scales_1.2.1 [63] spatstat.core_2.4-2 promises_1.2.0.1 [65] spatstat.utils_2.3-0 parallel_4.1.1 [67] RColorBrewer_1.1-3 leidenbase_0.1.11 [69] reticulate_1.24 gridExtra_2.3 [71] ggplot2_3.3.6 rpart_4.1-15 [73] stringi_1.7.8 boot_1.3-28 [75] rlang_1.0.5 pkgconfig_2.0.3 [77] bitops_1.0-7 lattice_0.20-44 [79] ROCR_1.0-11 purrr_0.3.4 [81] tensor_1.5 patchwork_1.1.1 [83] htmlwidgets_1.5.4 cowplot_1.1.1 [85] tidyselect_1.1.2 parallelly_1.32.1 [87] RcppAnnoy_0.0.19 plyr_1.8.7 [89] magrittr_2.0.3 R6_2.5.1 [91] generics_0.1.3 DelayedArray_0.20.0 [93] pillar_1.8.1 mgcv_1.8-36 [95] fitdistrplus_1.1-8 survival_3.2-11 [97] abind_1.4-5 RCurl_1.98-1.8 [99] tibble_3.1.8 future.apply_1.8.1 [101] KernSmooth_2.23-20 utf8_1.2.2 [103] spatstat.geom_2.4-0 plotly_4.10.0 [105] grid_4.1.1 data.table_1.14.2 [107] digest_0.6.29 xtable_1.8-4 [109] tidyr_1.2.1 httpuv_1.6.6 [111] munsell_0.5.0 viridisLite_0.4.1