[R-pkg-devel] CRAN submission error when running tests in testthat
Simon Urbanek
@|mon@urb@nek @end|ng |rom R-project@org
Thu Nov 25 21:54:21 CET 2021
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 using 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
> @: n8thangreen using yahoo.co.ukTel: 07821 318353
>
>
> [[alternative HTML version deleted]]
>
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