Last updated on 2026-08-25 10:53:10 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.15.0 | 18.45 | 473.04 | 491.49 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 1.15.0 | 12.67 | 317.64 | 330.31 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 1.15.0 | 15.00 | 336.54 | 351.54 | NOTE | |
| r-devel-linux-x86_64-fedora-gcc | 1.16.0 | 15.00 | 382.73 | 397.73 | OK | |
| r-devel-windows-x86_64 | 1.15.0 | 21.00 | 454.00 | 475.00 | NOTE | |
| r-patched-linux-x86_64 | 1.15.0 | 21.33 | 455.26 | 476.59 | OK | |
| r-release-linux-x86_64 | 1.15.0 | 16.47 | 459.85 | 476.32 | OK | |
| r-release-macos-arm64 | 1.16.0 | 5.00 | 135.00 | 140.00 | OK | |
| r-release-macos-x86_64 | 1.16.0 | 16.00 | 588.00 | 604.00 | OK | |
| r-release-windows-x86_64 | 1.15.0 | 22.00 | 406.00 | 428.00 | OK | |
| r-oldrel-macos-arm64 | 1.16.0 | 4.00 | 105.00 | 109.00 | ERROR | |
| r-oldrel-macos-x86_64 | 1.15.0 | 13.00 | 539.00 | 552.00 | OK | |
| r-oldrel-windows-x86_64 | 1.15.0 | 30.00 | 602.00 | 632.00 | OK |
Version: 1.15.0
Check: R code for possible problems
Result: NOTE
Found calls to structure() using deprecated special names:
bayesplot/tests/testthat/test-ppc-errors.R (.Dim: 1, .Dimnames: 1)
'.Dim' should be changed to 'dim'.
'.Dimnames' should be changed to 'dimnames'.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-windows-x86_64
Version: 1.16.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [63s/63s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(bayesplot)
This is bayesplot version 1.16.0
- Online documentation and vignettes at mc-stan.org/bayesplot
- bayesplot theme set to bayesplot::theme_default()
* Does _not_ affect other ggplot2 plots
* See ?bayesplot_theme_set for details on theme setting
>
> Sys.unsetenv("R_TESTS")
> test_check("bayesplot")
Note: in most cases the default test statistic 'mean' is too weak to detect anything of interest.
Note: in most cases the default test statistic 'mean' is too weak to detect anything of interest.
The 'independent' method is superseded by the 'correlated' method.
`stat_bin()` using `bins = 30`. Pick better value `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value `binwidth`.
Note: `extrapolation_factor` now defaults to 1.2 (20%).
To display all posterior predictive draws, set `extrapolation_factor = Inf`.
Note: `extrapolation_factor` now defaults to 1.2 (20%).
To display all posterior predictive draws, set `extrapolation_factor = Inf`.
Note: `extrapolation_factor` now defaults to 1.2 (20%).
To display all posterior predictive draws, set `extrapolation_factor = Inf`.
Note: `extrapolation_factor` now defaults to 1.2 (20%).
To display all posterior predictive draws, set `extrapolation_factor = Inf`.
Note: `extrapolation_factor` now defaults to 1.2 (20%).
To display all posterior predictive draws, set `extrapolation_factor = Inf`.
Note: `extrapolation_factor` now defaults to 1.2 (20%).
To display all posterior predictive draws, set `extrapolation_factor = Inf`.
Note: `extrapolation_factor` now defaults to 1.2 (20%).
To display all posterior predictive draws, set `extrapolation_factor = Inf`.
i In the next major release, the default `method` will change to 'correlated'.
* To silence this message, explicitly set `method = 'independent'` or
`method = 'correlated'`.
The 'independent' method is superseded by the 'correlated' method.
i In the next major release, the default `method` will change to 'correlated'.
* To silence this message, explicitly set `method = 'independent'` or
`method = 'correlated'`.
i In the next major release, the default `method` will change to 'correlated'.
* To silence this message, explicitly set `method = 'independent'` or
`method = 'correlated'`.
The 'independent' method is superseded by the 'correlated' method.
The 'independent' method is superseded by the 'correlated' method.
The 'independent' method is superseded by the 'correlated' method.
The 'independent' method is superseded by the 'correlated' method.
`stat_bin()` using `bins = 30`. Pick better value `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value `binwidth`.
With only 1 row in 'yrep' ppc_scatter_avg is the same as ppc_scatter.
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: outer(X, Y)
2: -theta %o% x
3: posterior::gpdfit(exp(x) - exp_cutoff, sort_x = FALSE)
4: psis_smooth_tail(lw_tail, cutoff)
5: is_fun(log_ratios_i = log_ratios[, i], tail_len_i = tail_len[i])
6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)
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(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)
16: parallel::mclapply(X = seq_len(N), mc.cores = cores, FUN = function(i) is_fun(log_ratios_i = log_ratios[, i], tail_len_i = tail_len[i]))
17: do_importance_sampling(log_ratios, r_eff = r_eff, cores = cores, method = method)
18: importance_sampling.matrix(log_ratios, ..., r_eff = r_eff, cores = cores, method = "psis")
19: psis.matrix(-log_lik(fit), cores = 2)
20: psis(-log_lik(fit), cores = 2)
21: withCallingHandlers(expr, warning = function(w) if (inherits(w, classes)) tryInvokeRestart("muffleWarning"))
22: suppressWarnings(psis1 <- psis(-log_lik(fit), cores = 2))
23: eval(code, test_env)
24: eval(code, test_env)
25: 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)
26: doTryCatch(return(expr), name, parentenv, handler)
27: tryCatchOne(expr, names, parentenv, handlers[[1L]])
28: tryCatchList(expr, classes, parentenv, handlers)
29: 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)
30: doWithOneRestart(return(expr), restart)
31: withOneRestart(expr, restarts[[1L]])
32: 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() { })
33: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
34: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
35: FUN(X[[i]], ...)
36: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
37: doTryCatch(return(expr), name, parentenv, handler)
38: tryCatchOne(expr, names, parentenv, handlers[[1L]])
39: tryCatchList(expr, classes, parentenv, handlers)
40: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
41: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
42: 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)
43: 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)
44: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
45: test_check("bayesplot")
An irrecoverable exception occurred. R is aborting now ...
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: outer(X, Y)
2: -theta %o% x
3: posterior::gpdfit(exp(x) - exp_cutoff, sort_x = FALSE)
4: psis_smooth_tail(lw_tail, cutoff)
5: is_fun(log_ratios_i = log_ratios[, i], tail_len_i = tail_len[i])
6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)
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(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)
16: parallel::mclapply(X = seq_len(N), mc.cores = cores, FUN = function(i) is_fun(log_ratios_i = log_ratios[, i], tail_len_i = tail_len[i]))
17: do_importance_sampling(log_ratios, r_eff = r_eff, cores = cores, method = method)
18: importance_sampling.matrix(log_ratios, ..., r_eff = r_eff, cores = cores, method = "psis")
19: psis.matrix(-log_lik(fit), cores = 2)
20: psis(-log_lik(fit), cores = 2)
21: withCallingHandlers(expr, warning = function(w) if (inherits(w, classes)) tryInvokeRestart("muffleWarning"))
22: suppressWarnings(psis1 <- psis(-log_lik(fit), cores = 2))
23: eval(code, test_env)
24: eval(code, test_env)
25: 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)
26: doTryCatch(return(expr), name, parentenv, handler)
27: tryCatchOne(expr, names, parentenv, handlers[[1L]])
28: tryCatchList(expr, classes, parentenv, handlers)
29: 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)
30: doWithOneRestart(return(expr), restart)
31: withOneRestart(expr, restarts[[1L]])
32: 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() { })
33: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
34: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
35: FUN(X[[i]], ...)
36: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
37: doTryCatch(return(expr), name, parentenv, handler)
38: tryCatchOne(expr, names, parentenv, handlers[[1L]])
39: tryCatchList(expr, classes, parentenv, handlers)
40: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
41: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
42: 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)
43: 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)
44: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
45: test_check("bayesplot")
An irrecoverable exception occurred. R is aborting now ...
Saving _problems/test-ppc-loo-16.R
With only 1 row in 'yrep' ppc_scatter_avg is the same as ppc_scatter.
Note: in most cases the default test statistic 'mean' is too weak to detect anything of interest.
Note: in most cases the default test statistic 'mean' is too weak to detect anything of interest.
Note: in most cases the default test statistic 'mean' is too weak to detect anything of interest.
Note: in most cases the default test statistic 'mean' is too weak to detect anything of interest.
Note: in most cases the default test statistic 'mean' is too weak to detect anything of interest.
Note: in most cases the default test statistic 'mean' is too weak to detect anything of interest.
Note: in most cases the default test statistic 'mean' is too weak to detect anything of interest.
[ FAIL 1 | WARN 18 | SKIP 89 | PASS 1496 ]
══ Skipped tests (89) ══════════════════════════════════════════════════════════
• On CRAN (89): 'test-aesthetics.R:229:3', 'test-extractors.R:132:3',
'test-mcmc-diagnostics.R:115:3', 'test-mcmc-diagnostics.R:129:3',
'test-mcmc-diagnostics.R:144:3', 'test-mcmc-diagnostics.R:155:3',
'test-mcmc-diagnostics.R:166:3', 'test-mcmc-diagnostics.R:180:3',
'test-mcmc-diagnostics.R:192:3', 'test-mcmc-distributions.R:224:3',
'test-mcmc-distributions.R:239:3', 'test-mcmc-distributions.R:254:3',
'test-mcmc-distributions.R:266:3', 'test-mcmc-distributions.R:275:3',
'test-mcmc-distributions.R:284:3', 'test-mcmc-distributions.R:293:3',
'test-mcmc-distributions.R:302:3', 'test-mcmc-intervals.R:196:3',
'test-mcmc-intervals.R:224:3', 'test-mcmc-intervals.R:258:3',
'test-mcmc-nuts.R:95:3', 'test-mcmc-nuts.R:107:3', 'test-mcmc-nuts.R:119:3',
'test-mcmc-nuts.R:131:3', 'test-mcmc-nuts.R:143:3',
'test-mcmc-recover.R:104:3', 'test-mcmc-recover.R:113:3',
'test-mcmc-recover.R:125:3', 'test-mcmc-scatter-and-parcoord.R:468:3',
'test-mcmc-scatter-and-parcoord.R:498:3',
'test-mcmc-scatter-and-parcoord.R:515:3',
'test-mcmc-scatter-and-parcoord.R:532:3', 'test-mcmc-traces.R:165:3',
'test-mcmc-traces.R:189:3', 'test-mcmc-traces.R:215:3',
'test-mcmc-traces.R:251:3', 'test-mcmc-traces.R:284:3',
'test-mcmc-traces.R:313:3', 'test-mcmc-traces.R:342:3',
'test-ppc-calibration.R:329:3', 'test-ppc-calibration.R:346:3',
'test-ppc-calibration.R:364:3', 'test-ppc-calibration.R:397:3',
'test-ppc-calibration.R:433:3', 'test-ppc-calibration.R:451:3',
'test-ppc-calibration.R:499:3', 'test-ppc-censoring.R:80:3',
'test-ppc-censoring.R:127:3', 'test-ppc-discrete.R:139:3',
'test-ppc-discrete.R:173:3', 'test-ppc-discrete.R:195:3',
'test-ppc-discrete.R:241:3', 'test-ppc-distributions.R:350:3',
'test-ppc-distributions.R:369:3', 'test-ppc-distributions.R:401:3',
'test-ppc-distributions.R:414:3', 'test-ppc-distributions.R:439:3',
'test-ppc-distributions.R:474:3', 'test-ppc-distributions.R:495:3',
'test-ppc-distributions.R:517:3', 'test-ppc-distributions.R:526:3',
'test-ppc-distributions.R:539:3', 'test-ppc-distributions.R:564:3',
'test-ppc-distributions.R:586:3', 'test-ppc-distributions.R:630:3',
'test-ppc-distributions.R:667:1', 'test-ppc-distributions.R:692:1',
'test-ppc-distributions.R:720:1', 'test-ppc-distributions.R:752:3',
'test-ppc-errors.R:101:3', 'test-ppc-errors.R:110:3',
'test-ppc-errors.R:119:3', 'test-ppc-errors.R:128:3',
'test-ppc-errors.R:140:3', 'test-ppc-errors.R:149:3',
'test-ppc-errors.R:163:3', 'test-ppc-intervals.R:119:3',
'test-ppc-intervals.R:144:3', 'test-ppc-intervals.R:170:3',
'test-ppc-intervals.R:204:3', 'test-ppc-scatterplots.R:65:3',
'test-ppc-scatterplots.R:85:3', 'test-ppc-scatterplots.R:105:3',
'test-ppc-test-statistics.R:147:3', 'test-ppc-test-statistics.R:200:3',
'test-ppc-test-statistics.R:234:3', 'test-ppc-test-statistics.R:291:3',
'test-ppd-marginal.R:22:3', 'test-ppd-marginal.R:56:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-ppc-loo.R:14:3'): (code run outside of `test_that()`) ──────────
Error in `vapply(x, FUN = match.arg(fun), FUN.VALUE = fun_val, item)`: values must be length 1500,
but FUN(X[[1]]) result is length 0
Backtrace:
▆
1. ├─base::suppressWarnings(psis1 <- psis(-log_lik(fit), cores = 2)) at test-ppc-loo.R:14:3
2. │ └─base::withCallingHandlers(...)
3. ├─loo::psis(-log_lik(fit), cores = 2)
4. └─loo:::psis.matrix(-log_lik(fit), cores = 2)
5. └─loo:::importance_sampling.matrix(...)
6. └─loo:::do_importance_sampling(...)
7. └─loo:::psis_apply(lw_list, "log_weights", fun_val = numeric(S))
8. └─base::vapply(x, FUN = match.arg(fun), FUN.VALUE = fun_val, item)
[ FAIL 1 | WARN 18 | SKIP 89 | PASS 1496 ]
Error:
! Test failures.
Execution halted
Flavor: r-oldrel-macos-arm64