Coverageplot freezes R

[AnaisJulien]

Hi,

I'm using Signac regularly but since last week as soon as I want to use the coverageplot function, R freezes and I have to quit Rstudio and restart it.

I tried to reinstall all the packages, R and Rstudio but nothing works.

Here my session: R version 4.4.1 (2024-06-14) Platform: x86_64-apple-darwin20 Running under: macOS Ventura 13.6.9

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0

Random number generation: RNG: L'Ecuyer-CMRG Normal: Inversion Sample: Rejection

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: Europe/Stockholm tzcode source: internal

attached base packages: [1] grid stats4 stats graphics grDevices utils datasets methods base

other attached packages: [1] Seurat_5.1.0 SeuratObject_5.0.2 sp_2.1-4 Signac_1.14.0 rhdf5_2.48.0 Rcpp_1.0.13
[7] Matrix_1.7-0 data.table_1.16.0 stringr_1.5.1 plyr_1.8.9 magrittr_2.0.3 ggplot2_3.5.1
[13] gtable_0.3.5 gtools_3.9.5 gridExtra_2.3 ArchR_1.0.2 monocle3_1.4.17 SingleCellExperiment_1.26.0 [19] SummarizedExperiment_1.34.0 GenomicRanges_1.56.0 GenomeInfoDb_1.40.0 IRanges_2.38.0 S4Vectors_0.42.0 MatrixGenerics_1.16.0
[25] matrixStats_1.4.1 Biobase_2.64.0 BiocGenerics_0.50.0

loaded via a namespace (and not attached): [1] RcppAnnoy_0.0.22 splines_4.4.1 later_1.3.2 bitops_1.0-8 tibble_3.2.1 polyclip_1.10-7 fastDummies_1.7.4
[8] lifecycle_1.0.4 globals_0.16.3 lattice_0.22-6 MASS_7.3-60.2 plotly_4.10.4 httpuv_1.6.15 sctransform_0.4.1
[15] spam_2.10-0 spatstat.sparse_3.1-0 reticulate_1.39.0 cowplot_1.1.3 pbapply_1.7-2 DBI_1.2.3 minqa_1.2.8
[22] RColorBrewer_1.1-3 abind_1.4-5 zlibbioc_1.50.0 Rtsne_0.17 purrr_1.0.2 presto_1.0.0 yulab.utils_0.1.7
[29] GenomeInfoDbData_1.2.12 ggrepel_0.9.6 irlba_2.3.5.1 listenv_0.9.1 spatstat.utils_3.1-0 pheatmap_1.0.12 goftest_1.2-3
[36] RSpectra_0.16-2 spatstat.random_3.3-1 fitdistrplus_1.2-1 parallelly_1.38.0 leiden_0.4.3.1 codetools_0.2-20 DelayedArray_0.30.1
[43] RcppRoll_0.3.1 tidyselect_1.2.1 UCSC.utils_1.0.0 lme4_1.1-35.5 spatstat.explore_3.3-2 jsonlite_1.8.8 progressr_0.14.0
[50] ggridges_0.5.6 survival_3.6-4 tools_4.4.1 ica_1.0-3 glue_1.7.0 SparseArray_1.4.3 dplyr_1.1.4
[57] withr_3.0.1 fastmap_1.2.0 boot_1.3-30 rhdf5filters_1.16.0 fansi_1.0.6 digest_0.6.37 R6_2.5.1
[64] mime_0.12 colorspace_2.1-1 scattermore_1.2 GO.db_3.19.1 Cairo_1.6-2 tensor_1.5 spatstat.data_3.1-2
[71] RSQLite_2.3.7 utf8_1.2.4 tidyr_1.3.1 generics_0.1.3 httr_1.4.7 htmlwidgets_1.6.4 S4Arrays_1.4.0
[78] uwot_0.2.2 pkgconfig_2.0.3 blob_1.2.4 lmtest_0.9-40 XVector_0.44.0 htmltools_0.5.8.1 dotCall64_1.1-1
[85] scales_1.3.0 png_0.1-8 spatstat.univar_3.0-1 rstudioapi_0.16.0 reshape2_1.4.4 nlme_3.1-164 nloptr_2.1.1
[92] cachem_1.1.0 zoo_1.8-12 KernSmooth_2.23-24 parallel_4.4.1 miniUI_0.1.1.1 AnnotationDbi_1.66.0 pillar_1.9.0
[99] vctrs_0.6.5 RANN_2.6.2 promises_1.3.0 xtable_1.8-4 cluster_2.1.6 cli_3.6.3 compiler_4.4.1
[106] Rsamtools_2.20.0 rlang_1.1.4 crayon_1.5.3 future.apply_1.11.2 fs_1.6.4 stringi_1.8.4 viridisLite_0.4.2
[113] deldir_2.0-4 BiocParallel_1.38.0 munsell_0.5.1 Biostrings_2.72.0 lazyeval_0.2.2 spatstat.geom_3.3-2 GOSemSim_2.30.0
[120] RcppHNSW_0.6.0 patchwork_1.2.0 bit64_4.0.5 future_1.34.0 Rhdf5lib_1.26.0 KEGGREST_1.44.0 shiny_1.9.1
[127] ROCR_1.0-11 igraph_2.0.3 memoise_2.0.1 fastmatch_1.1-4 bit_4.0.5

Do you have any idea how to solve the problem ?

Thank you,

Anais

[timoast]

I haven't seen this problem, how many cells do you have and what is the size of the region that you're plotting? Can you show the code you're running?

[timoast]

Closing this as I haven't heard back. Please reopen if you're still having problems and can provide the information requested above