Runing
obj.atac <- obj.atac %>%
RunTFIDF() %>%
FindTopFeatures() %>%
RunSVD() %>%
RunUMAP(reduction = 'lsi', dims = 2:30, verbose = FALSE)
ERROR:
Performing TF-IDF normalization
Running SVD
Error in irlba(A = t(x = object), nv = n, work = irlba.work, tol = tol) :
function 'as_cholmod_sparse' not provided by package 'Matrix'
Here is some session information：
R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 23.10
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.11.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0
Random number generation:
RNG: L'Ecuyer-CMRG
Normal: Inversion
Sample: Rejection
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Asia/Shanghai
tzcode source: system (glibc)
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] magrittr_2.0.3 Seurat_5.2.1 SeuratObject_5.0.2 sp_2.2-0
[5] Signac_1.14.0 Matrix_1.6-5 GenomicRanges_1.52.1 GenomeInfoDb_1.38.8
[9] IRanges_2.36.0 S4Vectors_0.40.2 BiocGenerics_0.48.1
loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-3 rstudioapi_0.17.1 jsonlite_1.9.1 spatstat.utils_3.1-3
[5] farver_2.1.2 zlibbioc_1.48.2 vctrs_0.6.5 ROCR_1.0-11
[9] spatstat.explore_3.4-2 Rsamtools_2.16.0 RCurl_1.98-1.17 RcppRoll_0.3.1
[13] htmltools_0.5.8.1 sctransform_0.4.1 parallelly_1.43.0 KernSmooth_2.23-26
[17] htmlwidgets_1.6.4 ica_1.0-3 plyr_1.8.9 plotly_4.10.4
[21] zoo_1.8-13 igraph_2.1.4 mime_0.13 lifecycle_1.0.4
[25] pkgconfig_2.0.3 R6_2.6.1 fastmap_1.2.0 GenomeInfoDbData_1.2.11
[29] fitdistrplus_1.2-2 future_1.34.0 shiny_1.10.0 digest_0.6.37
[33] colorspace_2.1-1 patchwork_1.3.0 tensor_1.5 RSpectra_0.16-2
[37] irlba_2.3.5.1 labeling_0.4.3 progressr_0.15.1 spatstat.sparse_3.1-0
[41] httr_1.4.7 polyclip_1.10-7 abind_1.4-8 compiler_4.3.1
[45] withr_3.0.2 BiocParallel_1.36.0 fastDummies_1.7.5 MASS_7.3-60
[49] tools_4.3.1 lmtest_0.9-40 httpuv_1.6.15 future.apply_1.11.3
[53] goftest_1.2-3 glue_1.8.0 nlme_3.1-167 promises_1.3.2
[57] grid_4.3.1 Rtsne_0.17 cluster_2.1.8.1 reshape2_1.4.4
[61] generics_0.1.3 gtable_0.3.6 spatstat.data_3.1-6 tidyr_1.3.1
[65] data.table_1.17.0 XVector_0.42.0 spatstat.geom_3.3-6 RcppAnnoy_0.0.22
[69] ggrepel_0.9.6 RANN_2.6.2 pillar_1.10.1 stringr_1.5.1
[73] spam_2.11-1 RcppHNSW_0.6.0 later_1.4.1 splines_4.3.1
[77] dplyr_1.1.4 lattice_0.22-6 survival_3.8-3 deldir_2.0-4
[81] tidyselect_1.2.1 Biostrings_2.70.3 miniUI_0.1.1.1 pbapply_1.7-2
[85] gridExtra_2.3 scattermore_1.2 matrixStats_1.5.0 stringi_1.8.4
[89] lazyeval_0.2.2 codetools_0.2-20 tibble_3.2.1 cli_3.6.4
[93] uwot_0.2.3 xtable_1.8-4 reticulate_1.42.0 munsell_0.5.1
[97] Rcpp_1.0.14 globals_0.16.3 spatstat.random_3.3-3 png_0.1-8
[101] spatstat.univar_3.1-2 parallel_4.3.1 ggplot2_3.5.1 dotCall64_1.2
[105] bitops_1.0-9 listenv_0.9.1 viridisLite_0.4.2 scales_1.3.0
[109] ggridges_0.5.6 purrr_1.0.4 crayon_1.5.3 rlang_1.1.5
[113] cowplot_1.1.3 fastmatch_1.1-6
Runing
obj.atac <- obj.atac %>%
RunTFIDF() %>%
FindTopFeatures() %>%
RunSVD() %>%
RunUMAP(reduction = 'lsi', dims = 2:30, verbose = FALSE)
ERROR:
Performing TF-IDF normalization
Running SVD
Error in irlba(A = t(x = object), nv = n, work = irlba.work, tol = tol) :
function 'as_cholmod_sparse' not provided by package 'Matrix'
Here is some session information：
R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 23.10
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.11.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0
Random number generation:
RNG: L'Ecuyer-CMRG
Normal: Inversion
Sample: Rejection
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Asia/Shanghai
tzcode source: system (glibc)
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] magrittr_2.0.3 Seurat_5.2.1 SeuratObject_5.0.2 sp_2.2-0
[5] Signac_1.14.0 Matrix_1.6-5 GenomicRanges_1.52.1 GenomeInfoDb_1.38.8
[9] IRanges_2.36.0 S4Vectors_0.40.2 BiocGenerics_0.48.1
loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-3 rstudioapi_0.17.1 jsonlite_1.9.1 spatstat.utils_3.1-3
[5] farver_2.1.2 zlibbioc_1.48.2 vctrs_0.6.5 ROCR_1.0-11
[9] spatstat.explore_3.4-2 Rsamtools_2.16.0 RCurl_1.98-1.17 RcppRoll_0.3.1
[13] htmltools_0.5.8.1 sctransform_0.4.1 parallelly_1.43.0 KernSmooth_2.23-26
[17] htmlwidgets_1.6.4 ica_1.0-3 plyr_1.8.9 plotly_4.10.4
[21] zoo_1.8-13 igraph_2.1.4 mime_0.13 lifecycle_1.0.4
[25] pkgconfig_2.0.3 R6_2.6.1 fastmap_1.2.0 GenomeInfoDbData_1.2.11
[29] fitdistrplus_1.2-2 future_1.34.0 shiny_1.10.0 digest_0.6.37
[33] colorspace_2.1-1 patchwork_1.3.0 tensor_1.5 RSpectra_0.16-2
[37] irlba_2.3.5.1 labeling_0.4.3 progressr_0.15.1 spatstat.sparse_3.1-0
[41] httr_1.4.7 polyclip_1.10-7 abind_1.4-8 compiler_4.3.1
[45] withr_3.0.2 BiocParallel_1.36.0 fastDummies_1.7.5 MASS_7.3-60
[49] tools_4.3.1 lmtest_0.9-40 httpuv_1.6.15 future.apply_1.11.3
[53] goftest_1.2-3 glue_1.8.0 nlme_3.1-167 promises_1.3.2
[57] grid_4.3.1 Rtsne_0.17 cluster_2.1.8.1 reshape2_1.4.4
[61] generics_0.1.3 gtable_0.3.6 spatstat.data_3.1-6 tidyr_1.3.1
[65] data.table_1.17.0 XVector_0.42.0 spatstat.geom_3.3-6 RcppAnnoy_0.0.22
[69] ggrepel_0.9.6 RANN_2.6.2 pillar_1.10.1 stringr_1.5.1
[73] spam_2.11-1 RcppHNSW_0.6.0 later_1.4.1 splines_4.3.1
[77] dplyr_1.1.4 lattice_0.22-6 survival_3.8-3 deldir_2.0-4
[81] tidyselect_1.2.1 Biostrings_2.70.3 miniUI_0.1.1.1 pbapply_1.7-2
[85] gridExtra_2.3 scattermore_1.2 matrixStats_1.5.0 stringi_1.8.4
[89] lazyeval_0.2.2 codetools_0.2-20 tibble_3.2.1 cli_3.6.4
[93] uwot_0.2.3 xtable_1.8-4 reticulate_1.42.0 munsell_0.5.1
[97] Rcpp_1.0.14 globals_0.16.3 spatstat.random_3.3-3 png_0.1-8
[101] spatstat.univar_3.1-2 parallel_4.3.1 ggplot2_3.5.1 dotCall64_1.2
[105] bitops_1.0-9 listenv_0.9.1 viridisLite_0.4.2 scales_1.3.0
[109] ggridges_0.5.6 purrr_1.0.4 crayon_1.5.3 rlang_1.1.5
[113] cowplot_1.1.3 fastmatch_1.1-6