Last updated on 2024-10-02 15:49:37 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2024.6.27 | 8.31 | 61.69 | 70.00 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2024.6.27 | 5.70 | 44.97 | 50.67 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2024.10.1 | 117.96 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2024.10.1 | 110.99 | ERROR | |||
| r-devel-windows-x86_64 | 2024.6.27 | 15.00 | 99.00 | 114.00 | OK | |
| r-patched-linux-x86_64 | 2024.6.27 | 8.28 | 58.73 | 67.01 | OK | |
| r-release-linux-x86_64 | 2024.6.27 | 7.11 | 58.68 | 65.79 | OK | |
| r-release-macos-arm64 | 2024.6.27 | 39.00 | OK | |||
| r-release-macos-x86_64 | 2024.10.1 | 60.00 | OK | |||
| r-release-windows-x86_64 | 2024.6.27 | 14.00 | 99.00 | 113.00 | OK | |
| r-oldrel-macos-arm64 | 2024.6.27 | 47.00 | OK | |||
| r-oldrel-macos-x86_64 | 2024.10.1 | 62.00 | OK | |||
| r-oldrel-windows-x86_64 | 2024.6.27 | 16.00 | 102.00 | 118.00 | OK |
Version: 2024.10.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [16s/57s]
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