I just updated a few packages, and Matrix is one of them (now version 1.6-2).
After that, runUMAP stopped to work producing this error:
Error: processing vignette 'cell_type_annotation.Rmd' failed with diagnostics: function 'as_cholmod_sparse' not provided by package 'Matrix'
library(MouseGastrulationData)
library(scater)
sce <- WTChimeraData(samples = 5, type = "processed")
sce <- logNormCounts(sce)
sce <- runPCA(sce)
sce <- runUMAP(sce, dimred = "PCA")
My sessionInfo( )
> sessionInfo()
R version 4.3.0 (2023-04-21)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.6.1
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-x86_64/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: Europe/Rome
tzcode source: internal
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] scater_1.30.0 ggplot2_3.4.4 scuttle_1.12.0
[4] MouseGastrulationData_1.16.0 SpatialExperiment_1.12.0 SingleCellExperiment_1.24.0
[7] SummarizedExperiment_1.32.0 Biobase_2.62.0 GenomicRanges_1.54.1
[10] GenomeInfoDb_1.38.1 IRanges_2.36.0 S4Vectors_0.40.1
[13] BiocGenerics_0.48.1 MatrixGenerics_1.14.0 matrixStats_1.1.0
loaded via a namespace (and not attached):
[1] DBI_1.1.3 bitops_1.0-7
[3] gridExtra_2.3 rlang_1.1.2
[5] magrittr_2.0.3 compiler_4.3.0
[7] RSQLite_2.3.3 DelayedMatrixStats_1.24.0
[9] png_0.1-8 vctrs_0.6.4
[11] pkgconfig_2.0.3 crayon_1.5.2
[13] fastmap_1.1.1 dbplyr_2.4.0
[15] magick_2.8.1 XVector_0.42.0
[17] ellipsis_0.3.2 utf8_1.2.4
[19] promises_1.2.1 ggbeeswarm_0.7.2
[21] purrr_1.0.2 bit_4.0.5
[23] xfun_0.41 zlibbioc_1.48.0
[25] cachem_1.0.8 beachmat_2.18.0
[27] blob_1.2.4 later_1.3.1
[29] DelayedArray_0.28.0 BiocParallel_1.36.0
[31] interactiveDisplayBase_1.40.0 irlba_2.3.5.1
[33] parallel_4.3.0 R6_2.5.1
[35] Rcpp_1.0.11 knitr_1.45
[37] FNN_1.1.3.2 httpuv_1.6.12
[39] Matrix_1.6-2 tidyselect_1.2.0
[41] viridis_0.6.4 rstudioapi_0.15.0
[43] abind_1.4-5 yaml_2.3.7
[45] codetools_0.2-19 curl_5.1.0
[47] lattice_0.22-5 tibble_3.2.1
[49] shiny_1.7.5.1 withr_2.5.2
[51] KEGGREST_1.42.0 BumpyMatrix_1.10.0
[53] BiocFileCache_2.10.1 ExperimentHub_2.10.0
[55] Biostrings_2.70.1 pillar_1.9.0
[57] BiocManager_1.30.22 filelock_1.0.2
[59] generics_0.1.3 RCurl_1.98-1.13
[61] BiocVersion_3.18.0 sparseMatrixStats_1.14.0
[63] munsell_0.5.0 scales_1.2.1
[65] xtable_1.8-4 glue_1.6.2
[67] tools_4.3.0 AnnotationHub_3.10.0
[69] BiocNeighbors_1.20.0 ScaledMatrix_1.10.0
[71] grid_4.3.0 AnnotationDbi_1.64.1
[73] colorspace_2.1-0 GenomeInfoDbData_1.2.11
[75] beeswarm_0.4.0 BiocSingular_1.18.0
[77] vipor_0.4.5 rsvd_1.0.5
[79] cli_3.6.1 rappdirs_0.3.3
[81] fansi_1.0.5 viridisLite_0.4.2
[83] S4Arrays_1.2.0 dplyr_1.1.3
[85] uwot_0.1.16 gtable_0.3.4
[87] digest_0.6.33 ggrepel_0.9.4
[89] SparseArray_1.2.2 rjson_0.2.21
[91] memoise_2.0.1 htmltools_0.5.7
[93] lifecycle_1.0.4 httr_1.4.7
[95] mime_0.12 bit64_4.0.5
Thanks
https://stackoverflow.com/questions/77442906/runumap-code-error-after-merged-spatial-transcriptomic-objects