SeuratでUMAPが使えない問題
去年の11月ぐらいからSeuratでRunUMAPしたら
function 'as_cholmod_sparse' not provided by package 'Matrix'
というエラーが出てUMAPが出来なかった
Matrixというパッケージを再インストールするなり
Seuratのバージョンを古いやつに戻してみたり
色々試してみたがうんともすんとも
そこからSeuratを使うことを諦めてbulkのデータばっかり使っていたが
３か月ぶりにSeuratを使ったら同じ症状が出たのでGoogle先生に聞いてみたら
Matrixパッケージの再インストール以外に
irlbaパッケージを再インストールしたら良いとのことが書いてあったので
やってみた
remove.packages('irlba')
install.packages('irlba')
そしたらなんか直ってしまったので
メモとしてここに投稿
sessionInfo()
R version 4.2.3 (2023-03-15 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22621)
Matrix products: default
locale:
[1] LC_COLLATE=Japanese_Japan.utf8 LC_CTYPE=Japanese_Japan.utf8 LC_MONETARY=Japanese_Japan.utf8
[4] LC_NUMERIC=C LC_TIME=Japanese_Japan.utf8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] data.table_1.14.10 patchwork_1.1.3 SeuratObject_5.0.1 Seurat_4.3.0.1 dplyr_1.1.4
loaded via a namespace (and not attached):
[1] spam_2.10-0 AnnotationHub_3.6.0 BiocFileCache_2.6.1
[4] plyr_1.8.9 igraph_1.6.0 lazyeval_0.2.2
[7] sp_2.1-2 splines_4.2.3 listenv_0.9.0
[10] scattermore_1.2 GenomeInfoDb_1.34.9 ggplot2_3.4.4
[13] digest_0.6.33 htmltools_0.5.7 fansi_1.0.5
[16] celldex_1.8.0 magrittr_2.0.3 memoise_2.0.1
[19] tensor_1.5 cluster_2.1.4 ROCR_1.0-11
[22] globals_0.16.2 Biostrings_2.66.0 matrixStats_1.2.0
[25] spatstat.sparse_3.0-3 colorspace_2.1-0 blob_1.2.4
[28] rappdirs_0.3.3 ggrepel_0.9.4 crayon_1.5.2
[31] RCurl_1.98-1.13 jsonlite_1.8.8 progressr_0.14.0
[34] spatstat.data_3.0-3 survival_3.5-7 zoo_1.8-12
[37] glue_1.6.2 polyclip_1.10-6 gtable_0.3.4
[40] zlibbioc_1.44.0 XVector_0.38.0 leiden_0.4.3.1
[43] DelayedArray_0.24.0 future.apply_1.11.1 BiocGenerics_0.44.0
[46] abind_1.4-5 scales_1.3.0 DBI_1.2.0
[49] spatstat.random_3.2-2 miniUI_0.1.1.1 Rcpp_1.0.11
[52] viridisLite_0.4.2 xtable_1.8-4 reticulate_1.34.0
[55] bit_4.0.5 dotCall64_1.1-1 stats4_4.2.3
[58] htmlwidgets_1.6.4 httr_1.4.7 RColorBrewer_1.1-3
[61] ellipsis_0.3.2 ica_1.0-3 farver_2.1.1
[64] pkgconfig_2.0.3 uwot_0.1.16 deldir_2.0-2
[67] dbplyr_2.4.0 utf8_1.2.4 labeling_0.4.3
[70] tidyselect_1.2.0 rlang_1.1.2 reshape2_1.4.4
[73] later_1.3.2 AnnotationDbi_1.60.2 munsell_0.5.0
[76] BiocVersion_3.16.0 tools_4.2.3 cachem_1.0.8
[79] cli_3.6.1 generics_0.1.3 RSQLite_2.3.4
[82] ExperimentHub_2.6.0 ggridges_0.5.5 stringr_1.5.1
[85] fastmap_1.1.1 goftest_1.2-3 yaml_2.3.8
[88] bit64_4.0.5 fitdistrplus_1.1-11 purrr_1.0.2
[91] RANN_2.6.1 KEGGREST_1.38.0 nlme_3.1-162
[94] pbapply_1.7-2 future_1.33.1 sparseMatrixStats_1.10.0
[97] mime_0.12 ggrastr_1.0.2 compiler_4.2.3
[100] rstudioapi_0.15.0 beeswarm_0.4.0 plotly_4.10.3
[103] filelock_1.0.3 curl_5.2.0 png_0.1-8
[106] interactiveDisplayBase_1.36.0 spatstat.utils_3.0-4 tibble_3.2.1
[109] stringi_1.8.3 lattice_0.20-45 Matrix_1.6-3
[112] vctrs_0.6.4 pillar_1.9.0 lifecycle_1.0.4
[115] BiocManager_1.30.22 spatstat.geom_3.2-7 lmtest_0.9-40
[118] RcppAnnoy_0.0.21 cowplot_1.1.2 bitops_1.0-7
[121] irlba_2.3.5.1 httpuv_1.6.13 GenomicRanges_1.50.2
[124] R6_2.5.1 promises_1.2.1 KernSmooth_2.23-20
[127] gridExtra_2.3 vipor_0.4.7 IRanges_2.32.0
[130] parallelly_1.36.0 codetools_0.2-19 MASS_7.3-58.2
[133] SummarizedExperiment_1.28.0 withr_2.5.2 sctransform_0.4.1
[136] S4Vectors_0.36.2 GenomeInfoDbData_1.2.9 parallel_4.2.3
[139] grid_4.2.3 tidyr_1.3.0 DelayedMatrixStats_1.20.0
[142] MatrixGenerics_1.10.0 Rtsne_0.17 spatstat.explore_3.2-5
[145] Biobase_2.58.0 shiny_1.8.0 ggbeeswarm_0.7.2
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