Last updated on 2024-10-16 22:49:58 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.5.6 | 15.22 | 176.76 | 191.98 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.5.6 | 10.82 | 158.48 | 169.30 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.5.6 | 293.95 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.5.6 | 221.35 | ERROR | |||
| r-devel-windows-x86_64 | 1.5.6 | 21.00 | 223.00 | 244.00 | OK | |
| r-patched-linux-x86_64 | 1.5.6 | OK | ||||
| r-release-linux-x86_64 | 1.5.6 | 14.10 | 172.42 | 186.52 | OK | |
| r-release-macos-arm64 | 1.5.6 | 117.00 | OK | |||
| r-release-macos-x86_64 | 1.5.6 | 227.00 | OK | |||
| r-release-windows-x86_64 | 1.5.6 | 21.00 | 225.00 | 246.00 | OK | |
| r-oldrel-macos-arm64 | 1.5.6 | 121.00 | OK | |||
| r-oldrel-macos-x86_64 | 1.5.6 | 204.00 | OK | |||
| r-oldrel-windows-x86_64 | 1.5.6 | 24.00 | 269.00 | 293.00 | OK |
Version: 1.5.6
Check: examples
Result: ERROR
Running examples in ‘seriation-Ex.R’ failed
The error most likely occurred in:
> ### Name: uniscale
> ### Title: Fit an Unidimensional Scaling for a Seriation Order
> ### Aliases: uniscale MDS_stress get_config plot_config
> ### Keywords: optimize
>
> ### ** Examples
>
> data(SupremeCourt)
> d <- as.dist(SupremeCourt)
> d
Breyer Ginsburg Kennedy OConnor Rehnquist Scalia Souter Stevens
Ginsburg 0.11966
Kennedy 0.25000 0.26709
OConnor 0.20940 0.25214 0.15598
Rehnquist 0.29915 0.30769 0.12179 0.16239
Scalia 0.35256 0.36966 0.18803 0.20726 0.14316
Souter 0.11752 0.09615 0.24790 0.22009 0.29274 0.33761
Stevens 0.16239 0.14530 0.32692 0.32906 0.40171 0.43803 0.16880
Thomas 0.35897 0.36752 0.17735 0.20513 0.13675 0.06624 0.33120 0.43590
>
> # embedding-based methods return "configuration" attribute
> # plot_config visualizes the configuration
> o <- seriate(d, method = "sammon")
> get_order(o)
Stevens Ginsburg Breyer Souter OConnor Kennedy Rehnquist Thomas
8 2 1 7 4 3 5 9
Scalia
6
> plot_config(o)
>
> # the configuration (Note: objects are in the original order in d)
> get_config(o)
Breyer Ginsburg Kennedy OConnor Rehnquist Scalia
-0.14684960 -0.19296338 0.08295734 0.02409031 0.14664466 0.25573113
Souter Stevens Thomas
-0.10664165 -0.28273566 0.21976686
>
> # angle methods return a 2D configuration
> o <- seriate(d, method = "MDS_angle")
> get_order(o)
Stevens Souter Ginsburg Breyer OConnor Rehnquist Kennedy Scalia
8 7 2 1 4 5 3 6
Thomas
9
> get_config(o)
[,1] [,2]
Breyer -0.14049676 5.127010e-02
Ginsburg -0.15882157 -9.597189e-05
Kennedy 0.07540714 -1.955142e-03
OConnor 0.05058155 8.506621e-02
Rehnquist 0.14235840 3.586661e-02
Scalia 0.19613081 -4.444093e-02
Souter -0.12683772 -6.267484e-03
Stevens -0.23446211 -6.798782e-02
Thomas 0.19614026 -5.145556e-02
> plot_config(o, )
>
>
> # calculate a configuration for a seriation method that does not
> # create a configuration
> o <- seriate(d, method = "ARSA")
*** caught segfault ***
address 0x1, cause 'memory not mapped'
Traceback:
1: method$fun(x, control = control)
2: system.time(order <- method$fun(x, control = control))
3: seriate.dist(d, method = "ARSA")
4: seriate(d, method = "ARSA")
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.5.6
Check: tests
Result: ERROR
Running ‘testthat.R’ [9s/25s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library("testthat")
>
> library("seriation")
> test_check("seriation")
dist
-> testing ARSA ...
*** caught segfault ***
address 0x1, cause 'memory not mapped'
Traceback:
1: method$fun(x, control = control)
2: system.time(order <- method$fun(x, control = control))
3: seriate.dist(d, method = m)
4: seriate(d, method = m)
5: system.time(o <- seriate(d, method = m))
6: FUN(X[[i]], ...)
7: lapply(X = X, FUN = FUN, ...)
8: sapply(methods, function(m) { cat(" -> testing", format(m, width = 13), "... ") tm <- system.time(o <- seriate(d, method = m)) cat("took", formatC(tm[3], digits = 4), "s.\n") o})
9: eval(code, test_env)
10: eval(code, test_env)
11: 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)
12: doTryCatch(return(expr), name, parentenv, handler)
13: tryCatchOne(expr, names, parentenv, handlers[[1L]])
14: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
15: doTryCatch(return(expr), name, parentenv, handler)
16: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
17: tryCatchList(expr, classes, parentenv, handlers)
18: 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) { })
19: test_code(desc, code, env = parent.frame(), default_reporter = local_interactive_reporter())
20: test_that("test if seriate.dist returns expected results", { cat("\n dist\n") methods <- list_seriation_methods(kind = "dist") methods <- setdiff(methods, "metaMDS") os <- sapply(methods, function(m) { cat(" -> testing", format(m, width = 13), "... ") tm <- system.time(o <- seriate(d, method = m)) cat("took", formatC(tm[3], digits = 4), "s.\n") o }) expect_true(all(sapply(os, length) == nrow(x))) hclusts <- os[sapply(os, function(x) inherits(x, "hclust"))] expect_setequal(object = names(hclusts), expected = c("GW", "GW_average", "GW_complete", "GW_single", "GW_ward", "HC", "HC_average", "HC_complete", "HC_single", "HC_ward", "OLO", "OLO_average", "OLO_complete", "OLO_single", "OLO_ward", extra_hclust)) integers <- os[sapply(os, is.integer)] expect_setequal(object = names(integers), expected = c("ARSA", "Enumerate", "BBURCG", "BBWRCG", "Identity", "MDS", "MDS_angle", "monoMDS", "isomap", "isoMDS", "Sammon_mapping", "QAP_2SUM", "QAP_BAR", "QAP_Inertia", "QAP_LS", "R2E", "Random", "Reverse", "GSA", "SGD", "Spectral", "Spectral_norm", "SPIN_NH", "SPIN_STS", "TSP", "VAT", extra_integer)) expect_setequal(c(names(hclusts), names(integers)), expected = names(os)) ORDERS <- sapply(X = os, FUN = get_order, dim = 1, simplify = FALSE) for (o in ORDERS) { expect_type(o, "integer") expect_mapequal(o, expected = c(a = 1, b = 2, c = 3, d = 4)) expect_type(names(o), "character") } for (n in names(hclusts)) { expect_equal(hclusts[[n]][["labels"]], expected = letters[1:4]) } for (n in names(hclusts)) { expect_equal(object = names(ORDERS[[n]]), expected = hclusts[[n]][["labels"]][hclusts[[n]][["order"]]]) } deterMethods <- c("BBURCG", "BBWRCG", "GW", "GW_average", "GW_complete", "GW_single", "GW_ward", "HC", "HC_average", "HC_complete", "HC_single", "HC_ward", "Identity", "MDS", "isoMDS", "Sammon_mapping", "MDS_angle", "Spectral", "Spectral_norm", "VAT") correct <- list(BBURCG = c(a = 1L, b = 2L, d = 4L, c = 3L), BBWRCG = c(a = 1L, b = 2L, d = 4L, c = 3L), GW = c(a = 1L, b = 2L, d = 4L, c = 3L), GW_average = c(a = 1L, b = 2L, d = 4L, c = 3L), GW_complete = c(a = 1L, b = 2L, d = 4L, c = 3L), GW_single = c(a = 1L, b = 2L, d = 4L, c = 3L), GW_ward = c(a = 1L, b = 2L, d = 4L, c = 3L), HC = structure(1:4, names = c("a", "b", "c", "d")), HC_average = structure(1:4, names = c("a", "b", "c", "d")), HC_complete = structure(1:4, names = c("a", "b", "c", "d")), HC_single = structure(1:4, names = c("a", "b", "c", "d")), HC_ward = structure(1:4, names = c("a", "b", "c", "d")), Identity = structure(1:4, names = c("a", "b", "c", "d")), MDS = c(a = 1L, b = 2L, d = 4L, c = 3L), isoMDS = c(a = 1L, b = 2L, d = 4L, c = 3L), Sammon_mapping = c(a = 1L, b = 2L, d = 4L, c = 3L), MDS_angle = c(a = 1L, b = 2L, d = 4L, c = 3L), R2E = c(c = 3L, d = 4L, b = 2L, a = 1L), Spectral = c(c = 3L, d = 4L, b = 2L, a = 1L), Spectral_norm = c(c = 3L, d = 4L, b = 2L, a = 1L), VAT = c(c = 3L, d = 4L, b = 2L, a = 1L)) for (m in deterMethods) expect_true(identical(correct[[m]], get_order(os[[m]])) || identical(correct[[m]], rev(get_order(os[[m]]))), label = paste("Seriation method", m, "does not return the correct order!\n"))})
21: eval(code, test_env)
22: eval(code, test_env)
23: 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)
24: doTryCatch(return(expr), name, parentenv, handler)
25: tryCatchOne(expr, names, parentenv, handlers[[1L]])
26: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
27: doTryCatch(return(expr), name, parentenv, handler)
28: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
29: tryCatchList(expr, classes, parentenv, handlers)
30: 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) { })
31: test_code(test = NULL, code = exprs, env = env, default_reporter = StopReporter$new())
32: source_file(path, env = env(env), desc = desc, error_call = error_call)
33: FUN(X[[i]], ...)
34: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
35: doTryCatch(return(expr), name, parentenv, handler)
36: tryCatchOne(expr, names, parentenv, handlers[[1L]])
37: tryCatchList(expr, classes, parentenv, handlers)
38: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
39: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call))
40: 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)
41: 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)
42: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
43: test_check("seriation")
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.5.6
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘seriation.Rnw’ using Sweave
*** caught segfault ***
address 0x1, cause 'memory not mapped'
Traceback:
1: method$fun(x, control = control)
2: system.time(order <- method$fun(x, control = control))
3: seriate.dist(d, m)
4: seriate(d, m)
5: FUN(X[[i]], ...)
6: lapply(X = X, FUN = FUN, ...)
7: sapply(methods, FUN = function(m) seriate(d, m))
8: eval(expr, .GlobalEnv)
9: eval(expr, .GlobalEnv)
10: withVisible(eval(expr, .GlobalEnv))
11: doTryCatch(return(expr), name, parentenv, handler)
12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
13: tryCatchList(expr, classes, parentenv, handlers)
14: 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))})
15: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
16: evalFunc(ce, options)
17: tryCatchList(expr, classes, parentenv, handlers)
18: tryCatch(evalFunc(ce, options), finally = { cat("\n") sink()})
19: driver$runcode(drobj, chunk, chunkopts)
20: utils::Sweave(...)
21: engine$weave(file, quiet = quiet, encoding = enc)
22: doTryCatch(return(expr), name, parentenv, handler)
23: tryCatchOne(expr, names, parentenv, handlers[[1L]])
24: tryCatchList(expr, classes, parentenv, handlers)
25: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
26: tools::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-devel/seriation.Rcheck/vign_test/seriation", skip = TRUE, ser_elibs = "/tmp/RtmpT9jyjx/file305c6e2d4601a4.rds")
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-linux-x86_64-fedora-gcc