CRAN Package Check Results for Package PeakSegJoint

Last updated on 2024-10-10 23:50:59 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2024.10.1 8.39 61.37 69.76 OK
r-devel-linux-x86_64-debian-gcc 2024.10.1 5.82 44.43 50.25 OK
r-devel-linux-x86_64-fedora-clang 2024.10.1 117.96 OK
r-devel-linux-x86_64-fedora-gcc 2024.10.1 104.97 ERROR
r-devel-windows-x86_64 2024.10.1 14.00 100.00 114.00 OK
r-patched-linux-x86_64 2024.10.1 7.63 58.12 65.75 OK
r-release-linux-x86_64 2024.10.1 7.97 58.14 66.11 OK
r-release-macos-arm64 2024.10.1 38.00 OK
r-release-macos-x86_64 2024.10.1 60.00 OK
r-release-windows-x86_64 2024.10.1 14.00 98.00 112.00 OK
r-oldrel-macos-arm64 2024.10.1 41.00 OK
r-oldrel-macos-x86_64 2024.10.1 62.00 OK
r-oldrel-windows-x86_64 2024.10.1 16.00 103.00 119.00 OK

Check Details

Version: 2024.10.1
Check: tests
Result: ERROR Running ‘testthat.R’ [15s/20s] 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 ... Flavor: r-devel-linux-x86_64-fedora-gcc