nhenry50
commented
7 months ago Hi,
Thanks a lot for this great package!
I have the same issue when I run the example from the help of ancombc2. The ancombc2 function returns me this:
Obtaining initial estimates ...
ML iteration = 1, epsilon = 3.9
Estimating sample-specific biases ...
Le chargement a nécessité le package : foreach
Le chargement a nécessité le package : rngtools
Sensitivity analysis for pseudo-count addition to 0s: ...
ANCOM-BC2 primary results ...
ANCOM-BC2 global test ...
ANCOM-BC2 multiple pairwise comparisons ...
ANCOM-BC2 multiple pairwise comparisons against the reference group ...
ANCOM-BC2 pattern analysis ...
*** caught segfault ***
address 0x1, cause 'memory not mapped'
Traceback:
1: t(X_coeff)
2: t(X_coeff)
3: matrix(t(X_coeff), nrow = nrow(coeffs[[1]]), byrow = TRUE)
4: reduction_format_constr(object, problem, cons, exp_cone_order)
5: reduction_format_constr(object, problem, cons, exp_cone_order)
6: group_coeff_offset(object, problem, neq_constr, ECOS()@exp_cone_order)
7: group_coeff_offset(object, problem, neq_constr, ECOS()@exp_cone_order)
8: perform(r, problem)
9: perform(r, problem)
10: perform(object@.solving_chain, object@.intermediate_problem)
11: perform(object@.solving_chain, object@.intermediate_problem)
12: psolve(a, ...)
13: psolve(a, ...)
14: CVXR::solve(problem, solver = solver)
15: CVXR::solve(problem, solver = solver)
16: doTryCatch(return(expr), name, parentenv, handler)
17: tryCatchOne(expr, names, parentenv, handlers[[1L]])
18: tryCatchList(expr, classes, parentenv, handlers)
19: 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, nlines = 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))})
20: try(CVXR::solve(problem, solver = solver), silent = TRUE)
21: withCallingHandlers(expr, message = function(c) if (inherits(c, classes)) tryInvokeRestart("muffleMessage"))
22: suppressMessages(result <- try(CVXR::solve(problem, solver = solver), silent = TRUE))
23: FUN(X[[i]], ...)
24: lapply(X = contrast, FUN = fun_list[[1]], beta_hat = beta_hat_sub[i, ], vcov_hat = vcov_hat_sub[[i]], solver = solver)
25: unlist(lapply(X = contrast, FUN = fun_list[[1]], beta_hat = beta_hat_sub[i, ], vcov_hat = vcov_hat_sub[[i]], solver = solver))
26: eval(xpr, envir = envir)
27: eval(xpr, envir = envir)
28: doTryCatch(return(expr), name, parentenv, handler)
29: tryCatchOne(expr, names, parentenv, handlers[[1L]])
30: tryCatchList(expr, classes, parentenv, handlers)
31: tryCatch(eval(xpr, envir = envir), error = function(e) e)
32: doTryCatch(return(expr), name, parentenv, handler)
33: tryCatchOne(expr, names, parentenv, handlers[[1L]])
34: tryCatchList(expr, classes, parentenv, handlers)
35: tryCatch({ repeat { args <- nextElem(it) if (obj$verbose) { cat(sprintf("evaluation # %d:\n", i)) print(args) } for (a in names(args)) assign(a, args[[a]], pos = envir, inherits = FALSE) r <- tryCatch(eval(xpr, envir = envir), error = function(e) e) if (obj$verbose) { cat("result of evaluating expression:\n") print(r) } tryCatch(accumulator(list(r), i), error = function(e) { cat("error calling combine function:\n") print(e) NULL }) i <- i + 1 }}, error = function(e) { if (!identical(conditionMessage(e), "StopIteration")) stop(simpleError(conditionMessage(e), expr))})
36: e$fun(obj, substitute(ex), parent.frame(), e$data)
37: (function (obj, ex) { e <- getDoPar() e$fun(obj, substitute(ex), parent.frame(), e$data)})(list(args = seq_len(n_tax)(.doRNG.stream = list(c(10407L, 2065493122L, -89260517L, -1856578912L, -1505283551L, -156249746L, 1239108375L), c(10407L, 1134170993L, -366534976L, -1952316947L, -1544256773L, -493282195L, 550079468L), c(10407L, 1568093054L, 772568389L, -54726601L, 1966827634L, -723992270L, -701559637L), c(10407L, 1097329108L, 25352133L, 1122433235L, 37457753L, -763252219L, 241246645L), c(10407L, -321322163L, -573957246L, -1772300094L, -1968781714L, -2058900039L, -1593125685L), c(10407L, 491526067L, 468994105L, -1157175011L, -765375177L, -1622626902L, -1049214349L))), argnames = c("i", ".doRNG.stream"), evalenv = <environment>, specified = character(0), combineInfo = list(fun = function (..., deparse.level = 1) .Internal(rbind(deparse.level, ...)), in.order = TRUE, has.init = FALSE, init = NULL, final = NULL, multi.combine = TRUE, max.combine = 100), errorHandling = "stop", packages = "doRNG", export = NULL, noexport = NULL, options = list(), verbose = FALSE), { { rngtools::RNGseed(.doRNG.stream) } { beta_hat_opt = unlist(lapply(X = contrast, FUN = fun_list[[1]], beta_hat = beta_hat_sub[i, ], vcov_hat = vcov_hat_sub[[i]], solver = solver)) }})
38: do.call(`%dopar%`, list(obj, ex), envir = parent.frame())
39: foreach(i = seq_len(n_tax), .combine = rbind) %dorng% { beta_hat_opt = unlist(lapply(X = contrast, FUN = fun_list[[1]], beta_hat = beta_hat_sub[i, ], vcov_hat = vcov_hat_sub[[i]], solver = solver))}
40: .ancombc_trend(x = x, group = group, beta_hat = beta_hat, var_hat = var_hat, vcov_hat = vcov_hat, p_adj_method = p_adj_method, alpha = alpha, trend_control = trend_control)
41: ancombc2(data = tse, assay_name = "counts", tax_level = "Phylum", fix_formula = "nationality + timepoint + bmi_group", rand_formula = NULL, p_adj_method = "holm", pseudo_sens = TRUE, prv_cut = 0.1, lib_cut = 1000, s0_perc = 0.05, group = "bmi_group", struc_zero = TRUE, neg_lb = TRUE, alpha = 0.05, n_cl = 1, verbose = TRUE, global = TRUE, pairwise = TRUE, dunnet = TRUE, trend = TRUE, iter_control = list(tol = 0.01, max_iter = 1, verbose = TRUE), em_control = list(tol = 1e-05, max_iter = 1), lme_control = lme4::lmerControl(), mdfdr_control = list(fwer_ctrl_method = "holm", B = 1), trend_control = list(contrast = list(matrix(c(1, 0, -1, 1), nrow = 2, byrow = TRUE)), node = list(2), solver = "ECOS", B = 1))I am using ANCOMBC 2.2.2:
> sessionInfo()
R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.3 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
locale:
[1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C LC_TIME=fr_FR.UTF-8
[4] LC_COLLATE=fr_FR.UTF-8 LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=fr_FR.UTF-8
[7] LC_PAPER=fr_FR.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C
time zone: Europe/Ljubljana
tzcode source: system (glibc)
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] mia_1.8.0 MultiAssayExperiment_1.26.0 TreeSummarizedExperiment_2.8.0
[4] Biostrings_2.68.1 XVector_0.40.0 SingleCellExperiment_1.22.0
[7] SummarizedExperiment_1.30.2 Biobase_2.60.0 GenomicRanges_1.52.0
[10] GenomeInfoDb_1.36.1 IRanges_2.34.1 S4Vectors_0.38.1
[13] BiocGenerics_0.46.0 MatrixGenerics_1.12.3 matrixStats_1.0.0
[16] ANCOMBC_2.2.2
loaded via a namespace (and not attached):
[1] rstudioapi_0.15.0 jsonlite_1.8.7 magrittr_2.0.3
[4] TH.data_1.1-2 ggbeeswarm_0.7.2 nloptr_2.0.3
[7] rmarkdown_2.23 zlibbioc_1.46.0 vctrs_0.6.3
[10] memoise_2.0.1 minqa_1.2.5 DelayedMatrixStats_1.22.1
[13] RCurl_1.98-1.12 base64enc_0.1-3 htmltools_0.5.5
[16] S4Arrays_1.0.5 energy_1.7-11 BiocNeighbors_1.18.0
[19] cellranger_1.1.0 Formula_1.2-5 htmlwidgets_1.6.2
[22] sandwich_3.0-2 plyr_1.8.8 DECIPHER_2.28.0
[25] zoo_1.8-12 cachem_1.0.8 rootSolve_1.8.2.3
[28] lifecycle_1.0.3 iterators_1.0.14 pkgconfig_2.0.3
[31] rsvd_1.0.5 Matrix_1.6-3 R6_2.5.1
[34] fastmap_1.1.1 GenomeInfoDbData_1.2.10 rbibutils_2.2.14
[37] digest_0.6.33 Exact_3.2 numDeriv_2016.8-1.1
[40] colorspace_2.1-0 scater_1.28.0 irlba_2.3.5.1
[43] RSQLite_2.3.1 Hmisc_5.1-0 vegan_2.6-4
[46] beachmat_2.16.0 fansi_1.0.4 mgcv_1.9-1
[49] httr_1.4.6 abind_1.4-5 compiler_4.3.2
[52] rngtools_1.5.2 proxy_0.4-27 bit64_4.0.5
[55] withr_2.5.0 doParallel_1.0.17 gsl_2.1-8
[58] htmlTable_2.4.1 backports_1.4.1 BiocParallel_1.34.2
[61] DBI_1.1.3 viridis_0.6.4 MASS_7.3-60
[64] DelayedArray_0.26.7 permute_0.9-7 gtools_3.9.4
[67] CVXR_1.0-11 gld_2.6.6 tools_4.3.2
[70] vipor_0.4.5 foreign_0.8-86 beeswarm_0.4.0
[73] ape_5.7-1 nnet_7.3-19 glue_1.6.2
[76] nlme_3.1-163 grid_4.3.2 checkmate_2.2.0
[79] reshape2_1.4.4 cluster_2.1.6 generics_0.1.3
[82] gtable_0.3.3 class_7.3-22 tidyr_1.3.0
[85] data.table_1.14.8 lmom_2.9 BiocSingular_1.16.0
[88] ScaledMatrix_1.8.1 utf8_1.2.3 ggrepel_0.9.3
[91] foreach_1.5.2 pillar_1.9.0 stringr_1.5.0
[94] yulab.utils_0.0.6 splines_4.3.2 dplyr_1.1.2
[97] treeio_1.24.3 lattice_0.22-5 survival_3.5-7
[100] gmp_0.7-2 bit_4.0.5 DirichletMultinomial_1.42.0
[103] tidyselect_1.2.0 scuttle_1.10.2 knitr_1.43
[106] gridExtra_2.3 xfun_0.39 expm_0.999-7
[109] stringi_1.7.12 lazyeval_0.2.2 boot_1.3-28
[112] evaluate_0.21 codetools_0.2-19 tibble_3.2.1
[115] cli_3.6.1 rpart_4.1.23 DescTools_0.99.49
[118] Rdpack_2.4 munsell_0.5.0 Rcpp_1.0.11
[121] readxl_1.4.3 parallel_4.3.2 blob_1.2.4
[124] ggplot2_3.4.2 doRNG_1.8.6 sparseMatrixStats_1.12.2
[127] bitops_1.0-7 lme4_1.1-35.1 Rmpfr_0.9-2
[130] decontam_1.20.0 viridisLite_0.4.2 mvtnorm_1.2-2
[133] tidytree_0.4.4 lmerTest_3.1-3 scales_1.2.1
[136] e1071_1.7-13 purrr_1.0.1 crayon_1.5.2
[139] rlang_1.1.1 multcomp_1.4-25
Any clue about what could cause this error?
Thanks!
Nico
Maggie8888
Hi, I attempted to run the ancombc2 function using the example provided in ?ancombc, but it resulted in an aborted R session. Could you please help me with fixing this issue?
Thanks, Dana.