Running ‘testthat.R’ [16s/59s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > if(require(testthat)){
  +   suite <- Sys.getenv("TEST_SUITE")
  +   if(suite=="")suite <- NULL
  +   test_check("PeakSegJoint", filter=suite)
  + }
  Loading required package: testthat
  Loading required package: PeakSegJoint
  
   *** caught segfault ***
  address 0xfffffffffffffffd, cause 'memory not mapped'
  
  Traceback:
   1: PeakSegJointHeuristic(one.list)
   2: doTryCatch(return(expr), name, parentenv, handler)
   3: tryCatchOne(expr, names, parentenv, handlers[[1L]])
   4: tryCatchList(expr, classes, parentenv, handlers)
   5: tryCatch({    fit <- PeakSegJointHeuristic(one.list)    seg.bases <- with(fit, bin_start_end[2] - bin_start_end[1])    loss <- sapply(fit$models, "[[", "loss")/seg.bases    if (!is.finite(loss[2])) {        loss[2] <- loss[1]    }    loss}, error = function(e) {    bases.vec <- with(sample.counts, chromEnd - chromStart)    seg.bases <- sum(bases.vec)    seg.mean <- sum(sample.counts$count * bases.vec)/seg.bases    loss0 <- PoissonLoss(sample.counts$count, seg.mean, bases.vec)/seg.bases    c(loss0, loss0)})
   6: featureMatrixJoint(profile.list)
   7: eval(code, test_env)
   8: eval(code, test_env)
   9: 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)
  10: doTryCatch(return(expr), name, parentenv, handler)
  11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  12: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
  13: doTryCatch(return(expr), name, parentenv, handler)
  14: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
  15: tryCatchList(expr, classes, parentenv, handlers)
  16: 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) {    })
  17: test_code(desc, code, env = parent.frame(), default_reporter = local_interactive_reporter())
  18: test_that("feature computation works for sample with no coverage rows",     {        fmat <- featureMatrixJoint(profile.list)        expect_identical(rownames(fmat), names(profile.list))    })
  19: eval(code, test_env)
  20: eval(code, test_env)
  21: 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)
  22: doTryCatch(return(expr), name, parentenv, handler)
  23: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  24: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
  25: doTryCatch(return(expr), name, parentenv, handler)
  26: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
  27: tryCatchList(expr, classes, parentenv, handlers)
  28: 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) {    })
  29: test_code(test = NULL, code = exprs, env = env, default_reporter = StopReporter$new())
  30: source_file(path, env = env(env), desc = desc, error_call = error_call)
  31: FUN(X[[i]], ...)
  32: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
  33: doTryCatch(return(expr), name, parentenv, handler)
  34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  35: tryCatchList(expr, classes, parentenv, handlers)
  36: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
  37: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, desc = desc, error_call = error_call))
  38: 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,     desc = desc, load_package = load_package, error_call = error_call)
  39: 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,     load_package = load_package, parallel = parallel)
  40: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
  41: test_check("PeakSegJoint", filter = suite)
  An irrecoverable exception occurred. R is aborting now ...