CRAN Package Check Results for Maintainer ‘Manuel Pfeuffer <manuel.pfeuffer at hu-berlin.de>’

Last updated on 2026-02-15 07:51:14 CET.

Package	ERROR	NOTE
elastes	1	13

Package elastes

Current CRAN status: ERROR: 1, NOTE: 13

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/1s] 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/RtmpsL5q2S/file1405733ccfd64.rds") An irrecoverable exception occurred. R is aborting now ... Flavor: r-devel-macos-arm64