`Segmentation fault (core dumped)`

[bschilder]

This seems to be happening on Linux (and maybe Windows?) but not Mac on GHA VMs. Unclear why, but it might have something to do with system dependencies, though not sure for which R packages. Perhaps data.table or XML?

• https://github.com/Rdatatable/data.table/issues/3369
• https://support.bioconductor.org/p/75920/

https://github.com/RajLabMSSM/echogithub/actions/runs/3657949232/jobs/6182121292#step:5:2121

Traceback:
 1: `[.data.table`(dt, , `:=`((cols), lapply(.SD, unlist)), .SDcols = cols)
 2: dt[, `:=`((cols), lapply(.SD, unlist)), .SDcols = cols]
 3: unlist_dt(dt = dt, exclude = "size", verbose = FALSE)
 4: github_files(owner = owner, repo = repo, query = query, branch = branch,     token = token, verbose = verbose)
 5: github_pages_files(owner = "RajLabMSSM", repo = "Fine_Mapping",     branch = "master")
 6: eval(code, test_env)
 7: eval(code, test_env)
 8: 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)
 9: doTryCatch(return(expr), name, parentenv, handler)
10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
11: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
12: doTryCatch(return(expr), name, parentenv, handler)
13: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
14: tryCatchList(expr, classes, parentenv, handlers)
15: 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) {    })
16: test_code(desc, code, env = parent.frame(), reporter = reporter)
17: test_that("github_pages_files works", {    dt <- github_pages_files(owner = "RajLabMSSM", repo = "echolocatoR")    testthat::expect_gte(nrow(dt), 20)    links_df <- github_pages_files(owner = "RajLabMSSM", repo = "Fine_Mapping",         branch = "master")    testthat::expect_gte(nrow(links_df), 220)})
18: eval(code, test_env)
19: eval(code, test_env)
20: 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)
21: doTryCatch(return(expr), name, parentenv, handler)
22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
23: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
24: doTryCatch(return(expr), name, parentenv, handler)
25: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
26: tryCatchList(expr, classes, parentenv, handlers)
27: 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) {    })
28: test_code(NULL, exprs, env)
29: source_file(path, child_env(env), wrap = wrap)
30: FUN(X[[i]], ...)
31: lapply(test_paths, test_one_file, env = env, wrap = wrap)
32: doTryCatch(return(expr), name, parentenv, handler)
33: tryCatchOne(expr, names, parentenv, handlers[[1L]])
34: tryCatchList(expr, classes, parentenv, handlers)
35: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
36: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, wrap = wrap))
37: test_files_serial(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)
38: 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)
39: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
40: test_check(pkg)
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)

[bschilder]

By chance, is this something you've come across before, @lcolladotor ?

[lcolladotor]

I have not seen this before.

Hmm, this is likely unrelated. But maybe setting the number of threads (I think it's setDTthreads() ) to 1 will help. data.table has a tendency to use all the cores it detects.

[bschilder]

I have not seen this before.

Hmm, this is likely unrelated. But maybe setting the number of threads (I think it's setDTthreads() ) to 1 will help. data.table has a tendency to use all the cores it detects.

Cool, I'll give that a try, thanks!

[bschilder]

Just a note, adding data.table::setDTthreads(threads = 1) to the zzz.R file didn't seem to help in this situation. https://github.com/RajLabMSSM/echogithub/blob/c21ab7343973828bd9c4d398e18c8182d7ad1733/R/zzz.R So I think the source of the issue might be something else.