-
Notifications
You must be signed in to change notification settings - Fork 17
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Error running scDblFinder #100
Comments
Please see #91 |
@chungsai please confirm whether that was the issue or not, if I don't hear from you I'll close the issue. |
Hi, I am trying this. But I can't seem to re-install irlba
Warning in install.packages : |
You're probably missing some build dependencies. Look at the rest of the output to figure out which. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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
The text was updated successfully, but these errors were encountered: