Last updated on 2026-02-12 12:51:09 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.7 | NOTE | ||||
| r-devel-linux-x86_64-debian-gcc | 0.1.7 | 10.33 | 107.05 | 117.38 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 0.1.7 | 25.00 | 254.76 | 279.76 | NOTE | |
| r-devel-linux-x86_64-fedora-gcc | 0.1.7 | 23.00 | 246.43 | 269.43 | NOTE | |
| r-devel-macos-arm64 | 0.1.7 | 4.00 | 35.00 | 39.00 | ERROR | |
| r-devel-windows-x86_64 | 0.1.7 | 16.00 | 149.00 | 165.00 | NOTE | |
| r-patched-linux-x86_64 | 0.1.7 | 13.03 | 147.57 | 160.60 | NOTE | |
| r-release-linux-x86_64 | 0.1.7 | 13.32 | 147.54 | 160.86 | NOTE | |
| r-release-macos-arm64 | 0.1.7 | NOTE | ||||
| r-release-macos-x86_64 | 0.1.7 | 8.00 | 127.00 | 135.00 | NOTE | |
| r-release-windows-x86_64 | 0.1.7 | 16.00 | 148.00 | 164.00 | NOTE | |
| r-oldrel-macos-arm64 | 0.1.7 | NOTE | ||||
| r-oldrel-macos-x86_64 | 0.1.7 | 8.00 | 96.00 | 104.00 | NOTE | |
| r-oldrel-windows-x86_64 | 0.1.7 | 22.00 | 198.00 | 220.00 | NOTE |
Version: 0.1.7
Check: CRAN incoming feasibility
Result: NOTE
Maintainer: ‘Manuel Pfeuffer <manuel.pfeuffer@hu-berlin.de>’
The Description field contains
<doi:10.1111/biom.13706>. See Stöcker et. al. (2022) <arXiv:2203.10522>
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 0.1.7
Check: Rd files
Result: NOTE
checkRd: (-1) fit_mean.Rd:54: Lost braces
54 | \code{t_optims}{optimal parametrizations}
| ^
checkRd: (-1) fit_mean.Rd:55: Lost braces
55 | \code{G_optims}{optimal rotations}
| ^
checkRd: (-1) fit_mean.Rd:56: Lost braces
56 | \code{b_optims}{optimal scalings}
| ^
checkRd: (-1) fit_mean.Rd:57: Lost braces
57 | \code{n_optims}{optimal re-normalization}
| ^
checkRd: (-1) fit_mean.Rd:58: Lost braces
58 | \code{n_iter}{number of iterations until convergence}
| ^
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-macos-arm64, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 0.1.7
Check: examples
Result: ERROR
Running examples in ‘elastes-Ex.R’ failed
The error most likely occurred in:
> ### Name: compute_elastic_shape_mean
> ### Title: Compute an elastic full Procrustes mean for a collection of
> ### curves
> ### Aliases: compute_elastic_shape_mean
>
> ### ** Examples
>
> curve <- function(t){
+ rbind(t*cos(13*t), t*sin(13*t))
+ }
> set.seed(18)
> data_curves <- lapply(1:4, function(i){
+ m <- sample(10:15, 1)
+ delta <- abs(rnorm(m, mean = 1, sd = 0.05))
+ t <- cumsum(delta)/sum(delta)
+ data.frame(t(curve(t)) + 0.07*t*matrix(cumsum(rnorm(2*length(delta))),
+ ncol = 2))
+ })
>
> #randomly rotate and scale curves
> rand_scale <- function(curve){ ( 0.5 + runif(1) ) * curve }
> rand_rotate <- function(curve){
+ names <- colnames(curve)
+ theta <- 2*pi*runif(1)
+ mat <- matrix(c(cos(theta), sin(theta), -sin(theta), cos(theta)), nrow = 2, ncol = 2)
+ curve.rot <- as.matrix(curve) %*% t(mat)
+ curve.rot <- as.data.frame(curve.rot)
+ colnames(curve.rot) <- names
+ return(curve.rot)
+ }
> data_curves <- lapply(data_curves, rand_scale)
> data_curves <- lapply(data_curves, rand_rotate)
>
> #compute smooth procrustes mean with 2 order penalty
> knots <- seq(0,1, length = 11)
> elastic_shape_mean <- compute_elastic_shape_mean(
+ data_curves,
+ knots = knots,
+ type = "smooth",
+ penalty = 2
+ )
*** caught segfault ***
address 0x1, cause 'invalid permissions'
Traceback:
1: eigen(t(L.inv) %*% beta.mat %*% L.inv)
2: fit_mean(srv_data_curves = srv_data_curves, knots = knots, type = type, penalty = penalty, var_type = var_type, pfit_method = pfit_method, max_iter = max_iter, eps = eps, verbose = verbose, cluster = cluster, smooth_warp = smooth_warp)
3: compute_elastic_shape_mean(data_curves, knots = knots, type = "smooth", penalty = 2)
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-macos-arm64
Version: 0.1.7
Check: tests
Result: ERROR
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(elastes)
>
> test_check("elastes")
*** caught segfault ***
address 0x1, cause 'invalid permissions'
Traceback:
1: eigen(t(L.inv) %*% beta.mat %*% L.inv)
2: fit_mean(srv_data_curves = srv_data_curves, knots = knots, type = type, penalty = penalty, var_type = var_type, pfit_method = pfit_method, max_iter = max_iter, eps = eps, verbose = verbose, cluster = cluster, smooth_warp = smooth_warp)
3: compute_elastic_shape_mean(data_curves)
4: eval(code, test_env)
5: eval(code, test_env)
6: 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)
7: doTryCatch(return(expr), name, parentenv, handler)
8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
9: tryCatchList(expr, classes, parentenv, handlers)
10: 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)
11: doWithOneRestart(return(expr), restart)
12: withOneRestart(expr, restarts[[1L]])
13: 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() { })
14: test_code(code, parent.frame())
15: test_that("Test computed variance and distances in [0,1]", { mean <- compute_elastic_shape_mean(data_curves) expect_gt(mean$variance, 0) expect_lte(mean$variance, 1) for (d in mean$distances) { expect_gte(d, 0) expect_lte(d, 1) }})
16: eval(code, test_env)
17: eval(code, test_env)
18: withCallingHandlers({ eval(code, test_env) new_expectations <- the$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$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
19: doTryCatch(return(expr), name, parentenv, handler)
20: tryCatchOne(expr, names, parentenv, handlers[[1L]])
21: tryCatchList(expr, classes, parentenv, handlers)
22: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$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$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
23: doWithOneRestart(return(expr), restart)
24: withOneRestart(expr, restarts[[1L]])
25: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$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$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
26: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
27: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
28: FUN(X[[i]], ...)
29: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
30: doTryCatch(return(expr), name, parentenv, handler)
31: tryCatchOne(expr, names, parentenv, handlers[[1L]])
32: tryCatchList(expr, classes, parentenv, handlers)
33: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
34: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
35: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call)
36: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle)
37: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
38: test_check("elastes")
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-macos-arm64
Version: 0.1.7
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘elastes.Rmd’ using rmarkdown
*** caught segfault ***
address 0x1, cause 'invalid permissions'
Traceback:
1: eigen(t(L.inv) %*% beta.mat %*% L.inv)
2: fit_mean(srv_data_curves = srv_data_curves, knots = knots, type = type, penalty = penalty, var_type = var_type, pfit_method = pfit_method, max_iter = max_iter, eps = eps, verbose = verbose, cluster = cluster, smooth_warp = smooth_warp)
3: compute_elastic_shape_mean(digit3, knots = seq(0, 1, length = 11), type = "smooth")
4: eval(expr, envir)
5: eval(expr, envir)
6: withVisible(eval(expr, envir))
7: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
8: eval(call)
9: eval(call)
10: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
11: doWithOneRestart(return(expr), restart)
12: withOneRestart(expr, restarts[[1L]])
13: withRestartList(expr, restarts[-nr])
14: doWithOneRestart(return(expr), restart)
15: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
16: withRestartList(expr, restarts)
17: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
18: evaluate::evaluate(...)
19: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
20: in_dir(input_dir(), expr)
21: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
22: eng_r(options)
23: block_exec(params)
24: call_block(x)
25: process_group(group)
26: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
27: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
28: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
29: process_file(text, output)
30: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
31: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
32: vweave_rmarkdown(...)
33: engine$weave(file, quiet = quiet, encoding = enc)
34: doTryCatch(return(expr), name, parentenv, handler)
35: tryCatchOne(expr, names, parentenv, handlers[[1L]])
36: tryCatchList(expr, classes, parentenv, handlers)
37: 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)))})
38: tools::buildVignettes(dir = "/Volumes/Builds/packages/sonoma-arm64/results/4.6/elastes.Rcheck/vign_test/elastes", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp5xBZzb/filea712289d0c9a.rds")
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-macos-arm64