silksmoothie
commented
2 months ago Wow I'm sorry Tatyana I didn't see this until now. I will check on this and get back to you. If this is still an issue for you, I would suspect that setting log.file = F as a parameter might be a temporary fix.
Hey Kai,
BigSur is not running for me because the log_warning function appears to be missing. How can I correct this?
I tried with correlations = T and correlations = F, and the error is the same both ways.
Thanks!
epi_bigsur <- BigSur(epi, variable.feature=T, correlations=T)
[1] "Pipeline started execution." Error in log_warning() : could not find function "log_warning" [1] "Error in log_warning() : could not find function \"log_warning\"\n" [1] "Traceback:" [1] "10: doWithOneRestart(return(expr), restart)"
[2] "9: withOneRestart(expr, restarts[[1L]])"
[3] "8: withRestarts({"
[4] " .Internal(.signalCondition(simpleWarning(msg, call), msg, "
[5] " call))"
[6] " .Internal(.dfltWarn(msg, call))"
[7] " }, muffleWarning = function() NULL)"
[8] "7: .signalSimpleWarning(\"sparse->dense coercion: allocating vector of size 7.0 GiB\", " [9] " base::quote(asMethod(object)))"
[10] "6: asMethod(object)"
[11] "5: as(x, \"matrix\")"
[12] "4: as.matrix.Matrix(GetAssayData(object = seuratob, slot = counts.slot))"
[13] "3: as.matrix(GetAssayData(object = seuratob, slot = counts.slot))"
[14] "2: get.residuals(seurat.obj, assay, counts.slot, c, depthlist)"
[15] "1: BigSur(epi, variable.feature = T, correlations = T)"
sessionInfo() R version 4.2.2 (2022-10-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Rocky Linux 8.8 (Green Obsidian)
Matrix products: default BLAS/LAPACK: /opt/apps/OpenBLAS/0.3.21/lib/libopenblas_zenp-r0.3.21.so
locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] BigSur_1.0.1 Seurat_5.0.3 SeuratObject_5.0.1 sp_2.1-3
loaded via a namespace (and not attached): [1] Rtsne_0.17 colorspace_2.1-0 deldir_2.0-4
[4] ellipsis_0.3.2 ggridges_0.5.6 RcppHNSW_0.6.0
[7] spatstat.data_3.0-4 leiden_0.4.3.1 listenv_0.9.1
[10] ggrepel_0.9.5 RSpectra_0.16-1 fansi_1.0.6
[13] codetools_0.2-18 splines_4.2.2 rootSolve_1.8.2.4
[16] polyclip_1.10-6 spam_2.10-0 jsonlite_1.8.8
[19] common_1.1.2 ica_1.0-3 cluster_2.1.4
[22] png_0.1-8 uwot_0.1.16 shiny_1.8.0
[25] sctransform_0.4.1 spatstat.sparse_3.0-3 compiler_4.2.2
[28] httr_1.4.7 Matrix_1.6-5 fastmap_1.1.1
[31] lazyeval_0.2.2 cli_3.6.2 later_1.3.2
[34] htmltools_0.5.7 tools_4.2.2 igraph_2.0.3
[37] dotCall64_1.1-1 gtable_0.3.4 glue_1.7.0
[40] RANN_2.6.1 reshape2_1.4.4 dplyr_1.1.4
[43] Rcpp_1.0.12 scattermore_1.2 vctrs_0.6.5
[46] spatstat.explore_3.2-7 nlme_3.1-160 progressr_0.14.0
[49] lmtest_0.9-40 spatstat.random_3.2-3 stringr_1.5.1
[52] globals_0.16.3 mime_0.12 miniUI_0.1.1.1
[55] lifecycle_1.0.4 irlba_2.3.5.1 goftest_1.2-3
[58] future_1.33.1 MASS_7.3-58.1 zoo_1.8-12
[61] scales_1.3.0 promises_1.2.1 spatstat.utils_3.0-4
[64] parallel_4.2.2 RColorBrewer_1.1-3 reticulate_1.35.0
[67] pbapply_1.7-2 gridExtra_2.3 ggplot2_3.5.0
[70] stringi_1.8.3 fastDummies_1.7.3 logr_1.3.6
[73] rlang_1.1.3 pkgconfig_2.0.3 moments_0.14.1
[76] matrixStats_1.2.0 pracma_2.4.4 lattice_0.20-45
[79] ROCR_1.0-11 purrr_1.0.2 tensor_1.5
[82] patchwork_1.2.0 htmlwidgets_1.6.4 cowplot_1.1.3
[85] tidyselect_1.2.1 parallelly_1.37.1 RcppAnnoy_0.0.22
[88] plyr_1.8.9 magrittr_2.0.3 R6_2.5.1
[91] generics_0.1.3 withr_3.0.0 pillar_1.9.0
[94] fitdistrplus_1.1-11 survival_3.4-0 abind_1.4-5
[97] tibble_3.2.1 future.apply_1.11.1 KernSmooth_2.23-20
[100] utf8_1.2.4 spatstat.geom_3.2-9 plotly_4.10.4
[103] grid_4.2.2 data.table_1.15.2 digest_0.6.35
[106] xtable_1.8-4 tidyr_1.3.1 httpuv_1.6.14
[109] munsell_0.5.0 viridisLite_0.4.2