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satijalab / seurat

R toolkit for single cell genomics
http://www.satijalab.org/seurat
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Error in collect() Aug 20 Analyzing PBMC scATAC-seq tutorial #9299

Closed SaharBJ closed 1 month ago

SaharBJ commented 1 month ago
sessionInfo() R version 4.3.0 (2023-04-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) Matrix products: default BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.3.so; LAPACK version 3.8.0 locale: [1] LC_CTYPE=en_ZA.utf-8 LC_NUMERIC=C [3] LC_TIME=en_ZA.utf-8 LC_COLLATE=en_ZA.utf-8 [5] LC_MONETARY=en_ZA.utf-8 LC_MESSAGES=en_ZA.utf-8 [7] LC_PAPER=en_ZA.utf-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_ZA.utf-8 LC_IDENTIFICATION=C time zone: Africa/Johannesburg tzcode source: system (glibc) attached base packages: [1] stats4 stats graphics grDevices utils datasets methods [8] base other attached packages: [1] AnnotationHub_3.8.0 BiocFileCache_2.8.0 dbplyr_2.5.0 [4] patchwork_1.2.0 ggplot2_3.5.1 GenomicRanges_1.52.1 [7] GenomeInfoDb_1.36.4 IRanges_2.34.1 S4Vectors_0.38.2 [10] BiocGenerics_0.46.0 Seurat_5.1.0 SeuratObject_5.0.2 [13] sp_2.1-4 Signac_1.14.0 loaded via a namespace (and not attached): [1] RColorBrewer_1.1-3 jsonlite_1.8.8 [3] magrittr_2.0.3 spatstat.utils_3.1-0 [5] zlibbioc_1.46.0 vctrs_0.6.5 [7] ROCR_1.0-11 memoise_2.0.1 [9] spatstat.explore_3.3-2 Rsamtools_2.16.0 [11] RCurl_1.98-1.16 RcppRoll_0.3.1 [13] htmltools_0.5.8.1 curl_5.2.2 [15] sctransform_0.4.1 parallelly_1.38.0 [17] KernSmooth_2.23-20 htmlwidgets_1.6.4 [19] ica_1.0-3 plyr_1.8.9 [21] cachem_1.1.0 plotly_4.10.4 [23] zoo_1.8-12 igraph_2.0.3 [25] mime_0.12 lifecycle_1.0.4 [27] pkgconfig_2.0.3 Matrix_1.6-5 [29] R6_2.5.1 fastmap_1.2.0 [31] GenomeInfoDbData_1.2.10 fitdistrplus_1.2-1 [33] future_1.34.0 shiny_1.9.1 [35] digest_0.6.37 colorspace_2.1-1 [37] AnnotationDbi_1.62.2 tensor_1.5 [39] RSpectra_0.16-2 irlba_2.3.5.1 [41] RSQLite_2.3.7 filelock_1.0.3 [43] progressr_0.14.0 fansi_1.0.6 [45] spatstat.sparse_3.1-0 httr_1.4.7 [47] polyclip_1.10-7 abind_1.4-5 [49] compiler_4.3.0 bit64_4.0.5 [51] withr_3.0.1 BiocParallel_1.34.2 [53] DBI_1.2.3 fastDummies_1.7.4 [55] MASS_7.3-58.4 rappdirs_0.3.3 [57] tools_4.3.0 lmtest_0.9-40 [59] interactiveDisplayBase_1.38.0 httpuv_1.6.15 [61] future.apply_1.11.2 goftest_1.2-3 [63] glue_1.7.0 nlme_3.1-162 [65] promises_1.3.0 grid_4.3.0 [67] Rtsne_0.17 cluster_2.1.4 [69] reshape2_1.4.4 generics_0.1.3 [71] hdf5r_1.3.11 gtable_0.3.5 [73] spatstat.data_3.1-2 tidyr_1.3.1 [75] data.table_1.16.0 utf8_1.2.4 [77] XVector_0.40.0 spatstat.geom_3.3-2 [79] RcppAnnoy_0.0.22 BiocVersion_3.17.1 [81] ggrepel_0.9.6 RANN_2.6.2 [83] pillar_1.9.0 stringr_1.5.1 [85] spam_2.10-0 RcppHNSW_0.6.0 [87] later_1.3.2 splines_4.3.0 [89] dplyr_1.1.4 lattice_0.21-8 [91] bit_4.0.5 survival_3.5-5 [93] deldir_2.0-4 tidyselect_1.2.1 [95] Biostrings_2.68.1 miniUI_0.1.1.1 [97] pbapply_1.7-2 gridExtra_2.3 [99] scattermore_1.2 Biobase_2.60.0 [101] matrixStats_1.4.1 stringi_1.8.4 [103] yaml_2.3.10 lazyeval_0.2.2 [105] codetools_0.2-19 tibble_3.2.1 [107] BiocManager_1.30.25 cli_3.6.3 [109] uwot_0.2.2 xtable_1.8-4 [111] reticulate_1.39.0 munsell_0.5.1 [113] Rcpp_1.0.13 globals_0.16.3 [115] spatstat.random_3.3-1 png_0.1-8 [117] spatstat.univar_3.0-1 parallel_4.3.0 [119] blob_1.2.4 dotCall64_1.1-1 [121] bitops_1.0-8 listenv_0.9.1 [123] viridisLite_0.4.2 scales_1.3.0 [125] ggridges_0.5.6 leiden_0.4.3.1 [127] purrr_1.0.2 crayon_1.5.3 [129] rlang_1.1.4 KEGGREST_1.40.1 [131] cowplot_1.1.3 fastmatch_1.1-4 > -->
mhkowalski commented 1 month ago

Thank you for reaching out! We’re always grateful when folks take the time to make Seurat better 🙂

Unfortunately, with the details provided, we cannot reproduce your issue. To help us better understand and resolve this issue, please ensure that you provide the following information when reporting a bug:

  1. Describe your issue:

    • A clear and concise description of what the bug is — avoid just pasting in the error message.

  2. Reproducing Code Example:

    • Provide a minimal reproducible example that demonstrates the issue using one of the datasets available through SeuratData. Paste the code in a code block.
    • The code example should make use of pbmc_small or one of the datasets available through SeuratData.

  3. Error Message:

    • If any, paste the full error message (starting from line Traceback) in a code block.
    • If no error is raised, consider writing a simple test case that explicitly raises an error if the

  4. System Information:

    • Run sessionInfo() and paste the result in a code block.

We’re going to go ahead and close this issue for now, but once you’ve gathered these details, we strongly encourage you repost and we will be more than happy to help you resolve the problem.