Open zhenzuo2 opened 3 years ago
R version 4.1.0 (2021-05-18) Platform: x86_64-conda-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux Server 7.3 (Maipo)
Matrix products: default BLAS/LAPACK: /storage/chen/home/zz4/miniconda3/lib/libopenblasp-r0.3.15.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] parallel stats4 stats graphics grDevices utils datasets [8] methods base
other attached packages:
[1] SingleCellExperiment_1.14.1 SummarizedExperiment_1.22.0
[3] Biobase_2.52.0 GenomicRanges_1.44.0
[5] GenomeInfoDb_1.28.0 IRanges_2.26.0
[7] S4Vectors_0.30.0 BiocGenerics_0.38.0
[9] MatrixGenerics_1.4.0 matrixStats_0.59.0
[11] metacell_0.3.6
loaded via a namespace (and not attached):
[1] Rcpp_1.0.6 lattice_0.20-44 tidyr_1.1.3
[4] png_0.1-7 zoo_1.8-9 assertthat_0.2.1
[7] digest_0.6.27 utf8_1.2.1 RSpectra_0.16-0
[10] IRdisplay_1.0 R6_2.5.0 repr_1.1.3
[13] evaluate_0.14 ggplot2_3.3.3 pillar_1.6.1
[16] zlibbioc_1.38.0 rlang_0.4.11 uuid_0.1-4
[19] Rgraphviz_2.36.0 Matrix_1.3-3 pdist_1.2
[22] reticulate_1.20 RCurl_1.98-1.3 igraph_1.2.6
[25] tgstat_2.3.16 munsell_0.5.0 umap_0.2.7.0
[28] DelayedArray_0.18.0 compiler_4.1.0 pkgconfig_2.0.3
[31] askpass_1.1 base64enc_0.1-3 htmltools_0.5.1.1
[34] openssl_1.4.4 tidyselect_1.1.1 GenomeInfoDbData_1.2.6
[37] tibble_3.1.2 tgconfig_0.1.2 fansi_0.5.0
[40] crayon_1.4.1 dplyr_1.0.6 bitops_1.0-7
[43] grid_4.1.0 tgutil_0.1.6 jsonlite_1.7.2
[46] gtable_0.3.0 lifecycle_1.0.0 DBI_1.1.1
[49] magrittr_2.0.1 scales_1.1.1 graph_1.70.0
[52] XVector_0.32.0 dbscan_1.1-8 ellipsis_0.3.2
[55] generics_0.1.0 vctrs_0.3.8 IRkernel_1.2
[58] lpSolveAPI_5.5.2.0-17.7 tools_4.1.0 glue_1.4.2
[61] purrr_0.3.4 yaml_2.2.1 colorspace_2.0-1
[64] cluster_2.1.2 pbdZMQ_0.3-5
I got this dead kernel when running mcell_mc_from_coclust_balanced(). It also shows
filtered NA left with NA based on co-cluster imbalance
Another issue is mcell_coclust_filt_by_k_deg(). I have to rename cell labels to "1", "2", .... or as.numeric(names(thresh_Kr)) will not work.
as.numeric(names(thresh_Kr)) should work with parsable strings, not just "1". However, this issue appears to happen to multiple users lately, possibly related to the R version 4.1.0. I haven't reproduced this issue yet, will write back quickly when we find a workaround. In the meantime, you can try to downgrade R.
That is correct. I have no issue with R4.0.5
Thanks for the info, will update
This issue should be solved now for 4.1.0 as well, please let us know if you encounter any other problems with the current R versions.
caught segfault address 0x558cbaa2fc00, cause 'memory not mapped'
Traceback: 1: tgs_graph_cover(edges, min_mc_size, cooling = tgs_clust_cool, burn_in = tgs_clust_burn) 2: mcell_mc_from_coclust_balanced(coc_id = "retina_coc500", mat_id = "retina", mc_id = "retina_mc", K = 30, min_mc_size = 30, alpha = 2) 3: eval(expr, envir, enclos) 4: eval(expr, envir, enclos) 5: withVisible(eval(expr, envir, enclos)) 6: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler) 7: doTryCatch(return(expr), name, parentenv, handler) 8: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 9: tryCatchList(expr, classes, parentenv, handlers) 10: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))}) 11: try(f, silent = TRUE) 12: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)) 13: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))) 14: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing) 15: evaluate(request$content$code, envir = .GlobalEnv, output_handler = oh, stop_on_error = 1L) 16: doTryCatch(return(expr), name, parentenv, handler) 17: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 18: tryCatchList(expr, names[-nh], parentenv, handlers[-nh]) 19: doTryCatch(return(expr), name, parentenv, handler) 20: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]]) 21: tryCatchList(expr, classes, parentenv, handlers) 22: tryCatch(evaluate(request$content$code, envir = .GlobalEnv, output_handler = oh, stop_on_error = 1L), interrupt = function(cond) { log_debug("Interrupt during execution") interrupted <<- TRUE}, error = .self$handle_error) 23: executor$execute(msg) 24: handle_shell() 25: kernel$run() 26: IRkernel::main() An irrecoverable exception occurred. R is aborting now ...