[R-pkg-devel] CRAN submission error when running tests in testthat
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:
,
Dr
Nathan Green
@: n8thangr...@yahoo.co.ukTel: 07821 318353
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Re: [R-pkg-devel] rstan issue [Was: CRAN submission error when running tests in testthat]
t;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: 0x0001097c517f libtbbmalloc.dylib`__TBB_malloc_safer_msize +
>63
> frame #1: 0x7fff76f746fd libsystem_malloc.dylib`free + 96
> frame #2: 0x0001001c9227 libR.dylib`RunGenCollect at memory.c:1114
>[opt]
> frame #3: 0x0001001c9038 libR.dylib`RunGenCollect(size_needed=0) at
>memory.c:1896 [opt]
> frame #4: 0x0001001bf769 libR.dylib`R_gc_internal(size_needed=0) at
>memory.c:3129 [opt]
>
> (lldb) image lookup -va 0x0001097c517f
> Address: libtbbmalloc.dylib[0x0001117f]
>(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 = {0x060c}, range =
>[0x0001097c5140-0x0001097c5290), 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
> > 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)
> >
