Last updated on 2026-02-15 07:51:13 CET.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| ampir | 1 | 2 | 11 |
Current CRAN status: ERROR: 1, NOTE: 2, OK: 11
Version: 1.1.0
Check: dependencies in R code
Result: NOTE
Namespace in Imports field not imported from: ‘kernlab’
All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(ampir)
>
> test_check("ampir")
Could not run prediction for 1 proteins because they were either too short or contained invalid amino acids
Could not run prediction for 2 proteins because they were either too short or contained invalid amino acids
Could not run prediction for 1 proteins because they were either too short or contained invalid amino acids
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: kernelMult(kernelf(object), newdata, xmatrix(object)[[p]], coef(object)[[p]])
2: kernelMult(kernelf(object), newdata, xmatrix(object)[[p]], coef(object)[[p]])
3: as.vector(kernelMult(kernelf(object), newdata, xmatrix(object)[[p]], coef(object)[[p]]) - b(object)[p])
4: .SigmoidPredict(as.vector(kernelMult(kernelf(object), newdata, xmatrix(object)[[p]], coef(object)[[p]]) - b(object)[p]), prob.model(object)[[p]]$A, prob.model(object)[[p]]$B)
5: .local(object, ...)
6: kernlab::predict(modelFit, newdata, type = "probabilities")
7: kernlab::predict(modelFit, newdata, type = "probabilities")
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
12: try(kernlab::predict(modelFit, newdata, type = "probabilities"), silent = TRUE)
13: method$prob(modelFit = modelFit, newdata = newdata, submodels = param)
14: probFunction(method = object$modelInfo, modelFit = object$finalModel, newdata = newdata, preProc = object$preProcess)
15: predict.train(model, df_features[, predictors], type = "prob")
16: FUN(X[[i]], ...)
17: lapply(X = S, FUN = FUN, ...)
18: doTryCatch(return(expr), name, parentenv, handler)
19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
20: tryCatchList(expr, classes, parentenv, handlers)
21: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
22: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
23: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
24: FUN(X[[i]], ...)
25: lapply(seq_len(cores), inner.do)
26: mclapply(chunks, predict_amps_core, df, model, min_len, mc.cores = n_cores)
27: predict_amps(test_df, n_cores = 2)
28: eval(code, test_env)
29: eval(code, test_env)
30: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
31: doTryCatch(return(expr), name, parentenv, handler)
32: tryCatchOne(expr, names, parentenv, handlers[[1L]])
33: tryCatchList(expr, classes, parentenv, handlers)
34: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
35: doWithOneRestart(return(expr), restart)
36: withOneRestart(expr, restarts[[1L]])
37: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
38: test_code(code, parent.frame())
39: test_that("predict_amps works with multiple cores", { skip_on_os("windows") test_df <- readRDS("../testdata/xbench.rds") result_1core <- predict_amps(test_df, n_cores = 1) expect_equal(dim(result_1core), c(16, 3)) result_2core <- predict_amps(test_df, n_cores = 2) expect_equal(result_1core, result_2core)})
40: eval(code, test_env)
41: eval(code, test_env)
42: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
43: doTryCatch(return(expr), name, parentenv, handler)
44: tryCatchOne(expr, names, parentenv, handlers[[1L]])
45: tryCatchList(expr, classes, parentenv, handlers)
46: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
47: doWithOneRestart(return(expr), restart)
48: withOneRestart(expr, restarts[[1L]])
49: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
50: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
51: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
52: FUN(X[[i]], ...)
53: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
54: doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
58: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
59: 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, shuffle = shuffle, error_call = error_call)
60: 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, shuffle = shuffle)
61: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
62: test_check("ampir")
An irrecoverable exception occurred. R is aborting now ...
Traceback:
1: kernelMult(kernelf(object), newdata, xmatrix(object)[[p]], coef(object)[[p]])
2: kernelMult(kernelf(object), newdata, xmatrix(object)[[p]], coef(object)[[p]])
3: as.vector(kernelMult(kernelf(object), newdata, xmatrix(object)[[p]], coef(object)[[p]]) - b(object)[p])
4: .SigmoidPredict(as.vector(kernelMult(kernelf(object), newdata, xmatrix(object)[[p]], coef(object)[[p]]) - b(object)[p]), prob.model(object)[[p]]$A, prob.model(object)[[p]]$B)
5: .local(object, ...)
6: kernlab::predict(modelFit, newdata, type = "probabilities")
7: kernlab::predict(modelFit, newdata, type = "probabilities")
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
12: try(kernlab::predict(modelFit, newdata, type = "probabilities"), silent = TRUE)
13: method$prob(modelFit = modelFit, newdata = newdata, submodels = param)
14: probFunction(method = object$modelInfo, modelFit = object$finalModel, newdata = newdata, preProc = object$preProcess)
15: predict.train(model, df_features[, predictors], type = "prob")
16: FUN(X[[i]], ...)
17: lapply(X = S, FUN = FUN, ...)
18: doTryCatch(return(expr), name, parentenv, handler)
19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
20: tryCatchList(expr, classes, parentenv, handlers)
21: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
22: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
23: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
24: FUN(X[[i]], ...)
25: lapply(seq_len(cores), inner.do)
26: mclapply(chunks, predict_amps_core, df, model, min_len, mc.cores = n_cores)
27: predict_amps(test_df, n_cores = 2)
28: eval(code, test_env)
29: eval(code, test_env)
30: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
31: doTryCatch(return(expr), name, parentenv, handler)
32: tryCatchOne(expr, names, parentenv, handlers[[1L]])
33: tryCatchList(expr, classes, parentenv, handlers)
34: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
35: doWithOneRestart(return(expr), restart)
36: withOneRestart(expr, restarts[[1L]])
37: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
38: test_code(code, parent.frame())
39: test_that("predict_amps works with multiple cores", { skip_on_os("windows") test_df <- readRDS("../testdata/xbench.rds") result_1core <- predict_amps(test_df, n_cores = 1) expect_equal(dim(result_1core), c(16, 3)) result_2core <- predict_amps(test_df, n_cores = 2) expect_equal(result_1core, result_2core)})
40: eval(code, test_env)
41: eval(code, test_env)
42: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
43: doTryCatch(return(expr), name, parentenv, handler)
44: tryCatchOne(expr, names, parentenv, handlers[[1L]])
45: tryCatchList(expr, classes, parentenv, handlers)
46: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
47: doWithOneRestart(return(expr), restart)
48: withOneRestart(expr, restarts[[1L]])
49: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
50: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
51: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
52: FUN(X[[i]], ...)
53: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
54: doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
58: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
59: 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, shuffle = shuffle, error_call = error_call)
60: 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, shuffle = shuffle)
61: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
62: test_check("ampir")
An irrecoverable exception occurred. R is aborting now ...
Saving _problems/test-predict-amps-199.R
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 82 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-predict-amps.R:197:3'): predict_amps works with multiple cores ──
Expected `result_1core` to equal `result_2core`.
Differences:
`actual` is length 3
`expected` is length 2
`names(actual)`: "seq_name" "seq_aa" "prob_AMP"
`names(expected)`: "seq_name" "seq_aa"
`actual$prob_AMP` is a double vector (0.0237263013580434, 0.0302258304066241, 0.0433991662785352, 0.0393783553576832, 0.618460240944596, ...)
`expected$prob_AMP` is absent
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 82 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-macos-arm64
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