Skip to content
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

Closed
chungsai opened this issue Mar 1, 2024 · 4 comments
Closed

Error running scDblFinder #100

chungsai opened this issue Mar 1, 2024 · 4 comments

Comments

@chungsai
Copy link

chungsai commented Mar 1, 2024

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

@plger
Copy link
Owner

plger commented Mar 1, 2024

Please see #91

@plger
Copy link
Owner

plger commented Mar 8, 2024

@chungsai please confirm whether that was the issue or not, if I don't hear from you I'll close the issue.

@chungsai
Copy link
Author

chungsai commented Mar 9, 2024

Hi, I am trying this. But I can't seem to re-install irlba

install.packages("irlba", type = "source")

Warning in install.packages :
installation of package ‘irlba’ had non-zero exit status

@plger
Copy link
Owner

plger commented Mar 12, 2024

You're probably missing some build dependencies. Look at the rest of the output to figure out which.

@plger plger closed this as completed Mar 29, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants