Nathan,
testthat is notorious for obfuscation and unhelpful output as can be clearly seen in the head of testthat.Rout.fail: > library(testthat) > library(BCEA) Attaching package: 'BCEA' The following object is masked from 'package:graphics': contour > > test_check("BCEA") *** caught segfault *** address 0x10d492ffc, cause 'memory not mapped' However this appears to be hard to debug, because it is a fall out from some memory corruption and/or allocator mistmatch: the crash happens in free() while doing GC (see below). Since it happens in the GC, many bad things happen afterwards. With some lldb magic I could trace that the crash happens during ..getNamespace(c("Matrix", "1.3-3"), "stanfit") load(test_path("data", "stanfit.RData")) but as I said that's likely too late - the memory corruption/issue likely happened before. Since BCEA itself doesn't have native code, this is likely a bug in some of the packages it depends on, but quite a serious one since it affects subsequent code in R. The list of packages loaded at the time of the crash - so one of them is the culprit: [1] "rstan" "tidyselect" "purrr" "reshape2" [5] "lattice" "V8" "colorspace" "vctrs" [9] "generics" "testthat" "stats4" "BCEA" [13] "loo" "grDevices" "R2jags" "utf8" [17] "rlang" "pkgbuild" "pillar" "glue" [21] "withr" "DBI" "matrixStats" "lifecycle" [25] "plyr" "stringr" "munsell" "gtable" [29] "coda" "codetools" "inline" "callr" [33] "ps" "parallel" "curl" "fansi" [37] "methods" "Rcpp" "scales" "desc" [41] "RcppParallel" "StanHeaders" "GrassmannOptim" "jsonlite" [45] "abind" "gridExtra" "winch" "rjags" [49] "ggplot2" "stats" "datasets" "graphics" [53] "stringi" "processx" "dplyr" "grid" [57] "rprojroot" "cli" "tools" "magrittr" [61] "tibble" "crayon" "pkgconfig" "Matrix" [65] "MASS" "ellipsis" "utils" "prettyunits" [69] "assertthat" "base" "boot" "R6" [73] "R2WinBUGS" "compiler" My guess would be that the issue could be in RcppParallel which overrides the memory allocator: * thread #1, queue = 'com.apple.main-thread', stop reason = EXC_BAD_ACCESS (code=1, address=0x11649fffc) * frame #0: 0x00000001097c517f libtbbmalloc.dylib`__TBB_malloc_safer_msize + 63 frame #1: 0x00007fff76f746fd libsystem_malloc.dylib`free + 96 frame #2: 0x00000001001c9227 libR.dylib`RunGenCollect at memory.c:1114 [opt] frame #3: 0x00000001001c9038 libR.dylib`RunGenCollect(size_needed=0) at memory.c:1896 [opt] frame #4: 0x00000001001bf769 libR.dylib`R_gc_internal(size_needed=0) at memory.c:3129 [opt] (lldb) image lookup -va 0x00000001097c517f Address: libtbbmalloc.dylib[0x000000000001117f] (libtbbmalloc.dylib.__TEXT.__text + 65375) Summary: libtbbmalloc.dylib`__TBB_malloc_safer_msize + 63 Module: file = "/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.1/RcppParallel/lib/libtbbmalloc.dylib", arch = "x86_64" Symbol: id = {0x0000060c}, range = [0x00000001097c5140-0x00000001097c5290), mangled="__TBB_malloc_safer_msize" but that's just a wild guess... (CCing Kevin just in case he can shed a light on whether TBB allocator should be involved in regular R garbage collection). Cheers, Simon > On Nov 25, 2021, at 5:37 AM, Nathan Green via R-package-devel > <r-package-devel@r-project.org> wrote: > > Hi, > I've getting an ERROR when submitting a new release of our package BCEA to > CRAN which I'm having problems understanding and reproducing. Its passing > CHECK locally and GitHub Actions standard check > (https://github.com/n8thangreen/BCEA/actions/runs/1494595896). > The message is something to do with testthat. Any help would be gratefully > received. > Thanks! > Nathan > > From https://cran.r-project.org/web/checks/check_results_BCEA.html > Here's the error message: > Check: tests, Result: ERROR > Running ‘testthat.R’ [5s/5s] > Running the tests in ‘tests/testthat.R’ failed. > Last 13 lines of output: > 33: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled > && !is.null(test)) { skip_empty() }}, expectation = > handle_expectation, skip = handle_skip, warning = handle_warning, message > = handle_message, error = handle_error), error = handle_fatal, skip = > function(e) { }) > 34: test_code(NULL, exprs, env) > 35: source_file(path, child_env(env), wrap = wrap) > 36: FUN(X[[i]], ...) > 37: lapply(test_paths, test_one_file, env = env, wrap = wrap) > 38: doTryCatch(return(expr), name, parentenv, handler) > 39: tryCatchOne(expr, names, parentenv, handlers[[1L]]) > 40: tryCatchList(expr, classes, parentenv, handlers) > 41: tryCatch(code, testthat_abort_reporter = function(cnd) { > cat(conditionMessage(cnd), "\n") NULL}) > 42: with_reporter(reporters$multi, lapply(test_paths, test_one_file, > env = env, wrap = wrap)) > 43: test_files(test_dir = test_dir, test_package = test_package, > test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, > env = env, stop_on_failure = stop_on_failure, stop_on_warning = > stop_on_warning, wrap = wrap, load_package = load_package) > 44: test_files(test_dir = path, test_paths = test_paths, test_package = > package, reporter = reporter, load_helpers = load_helpers, env = env, > stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, > wrap = wrap, load_package = load_package, parallel = parallel) > 45: test_dir("testthat", package = package, reporter = reporter, ..., > load_package = "installed") > 46: test_check("BCEA") > An irrecoverable exception occurred. R is aborting now ... > See: > <https://www.r-project.org/nosvn/R.check/r-release-macos-x86_64/BCEA-00check.html>, > > <https://www.r-project.org/nosvn/R.check/r-oldrel-macos-x86_64/BCEA-00check.html> > > Dr > Nathan Green > @: n8thangr...@yahoo.co.ukTel: 07821 318353 > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel > ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel