Check results for 'SeaSondeR'

using R Under development (unstable) (2026-02-12 r89409)
using platform: aarch64-apple-darwin23
R was compiled by Apple clang version 17.0.0 (clang-1700.3.19.1) GNU Fortran (GCC) 14.2.0
running under: macOS Sequoia 15.7.1
using session charset: UTF-8 * current time: 2026-02-13 02:24:08 UTC
checking for file ‘SeaSondeR/DESCRIPTION’ ... OK
this is package ‘SeaSondeR’ version ‘0.2.8’
package encoding: UTF-8
checking package namespace information ... OK
checking package dependencies ... OK
checking if this is a source package ... OK
checking if there is a namespace ... OK
checking for executable files ... OK
checking for hidden files and directories ... OK
checking for portable file names ... OK
checking for sufficient/correct file permissions ... OK
checking whether package ‘SeaSondeR’ can be installed ... [4s/4s] OK See the install log for details.
checking installed package size ... INFO installed size is 10.1Mb sub-directories of 1Mb or more: css_data 8.7Mb
checking package directory ... OK
checking ‘build’ directory ... OK
checking DESCRIPTION meta-information ... OK
checking top-level files ... OK
checking for left-over files ... OK
checking index information ... OK
checking package subdirectories ... OK
checking code files for non-ASCII characters ... OK
checking R files for syntax errors ... OK
checking whether the package can be loaded ... [1s/1s] OK
checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
checking whether the package can be unloaded cleanly ... [0s/0s] OK
checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
checking whether the namespace can be unloaded cleanly ... [0s/1s] OK
checking loading without being on the library search path ... [0s/0s] OK
checking dependencies in R code ... OK
checking S3 generic/method consistency ... OK
checking replacement functions ... OK
checking foreign function calls ... OK
checking R code for possible problems ... [3s/3s] OK
checking Rd files ... [1s/1s] OK
checking Rd metadata ... OK
checking Rd cross-references ... OK
checking for missing documentation entries ... OK
checking for code/documentation mismatches ... OK
checking Rd \usage sections ... OK
checking Rd contents ... OK
checking for unstated dependencies in examples ... OK
checking installed files from ‘inst/doc’ ... OK
checking files in ‘vignettes’ ... OK
checking examples ... [1s/1s] ERROR Running examples in ‘SeaSondeR-Ex.R’ failed The error most likely occurred in: > ### Name: seasonder_MUSICLonLat > ### Title: Map MUSIC Bearings to Geographic Coordinates > ### Aliases: seasonder_MUSICLonLat seasonder_MUSIC_LonLat > > ### ** Examples > > # Create a SeaSondeRCS object for MUSIC example > cs_file <- system.file("css_data/CSS_TORA_24_04_04_0700.cs", package = "SeaSondeR") > apm_file <- system.file("css_data/MeasPattern.txt", package = "SeaSondeR") > apm_obj <- seasonder_readSeaSondeRAPMFile(apm_file) seasonder_createSeaSondeRAPM: APM object created successfully. > cs_obj <- seasonder_createSeaSondeRCS(cs_file, seasonder_apm_object = apm_obj) new_SeaSondeRCS: SeaSondeRCS object created successfully. > cs_obj <- seasonder_initMUSICData( + cs_obj, + range_cells = c(rep(5,11), rep(4,11)), + doppler_bins = c(c(669:679),c(674:684)) + ) > cs_obj <- seasonder_runMUSIC(cs_obj) seasonder_runMUSIC: MUSIC algorithm started. *** caught segfault *** address 0x1, cause 'invalid permissions' Traceback: 1: eigen(C, symmetric = TRUE) 2: .f(.x[[i]], ...) 3: .Primitive(".Call")(list(name = "map_impl", address = <pointer: 0x600001e929a0>, dll = list(name = "purrr", path = "/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/purrr/libs/purrr.so", dynamicLookup = FALSE, handle = <pointer: 0x76373080>, info = <pointer: 0x600003a90cc0>, forceSymbols = FALSE), numParameters = 6L), <environment>, "list", FALSE, 14L, NULL, 1L) 4: call_with_cleanup(map_impl, environment(), .type, .progress, n, names, i) 5: withCallingHandlers(expr, error = function(cnd) { if (i == 0L) { } else { message <- c(i = "In index: {i}.") if (!is.null(names) && !is.na(names[[i]]) && names[[i]] != "") { name <- names[[i]] message <- c(message, i = "With name: {name}.") } else { name <- NULL } cli::cli_abort(message, location = i, name = name, parent = cnd, call = error_call, class = "purrr_error_indexed") }}) 6: with_indexed_errors(i = i, names = names, error_call = .purrr_error_call, call_with_cleanup(map_impl, environment(), .type, .progress, n, names, i)) 7: map_("list", .x, .f, ..., .progress = .progress) 8: purrr::map(cov, seasonder_eigen_decomp_C) 9: .Call(dplyr_mask_eval_all_mutate, quo, private) 10: eval() 11: mask$eval_all_mutate(quo) 12: mutate_col(dots[[i]], data, mask, new_columns) 13: withCallingHandlers(for (i in seq_along(dots)) { poke_error_context(dots, i, mask = mask) context_poke("column", old_current_column) new_columns <- mutate_col(dots[[i]], data, mask, new_columns)}, error = dplyr_error_handler(dots = dots, mask = mask, bullets = mutate_bullets, error_call = error_call, error_class = "dplyr:::mutate_error"), warning = dplyr_warning_handler(state = warnings_state, mask = mask, error_call = error_call)) 14: mutate_cols(.data, dplyr_quosures(...), by) 15: mutate.data.frame(., eigen = purrr::map(cov, seasonder_eigen_decomp_C)) 16: dplyr::mutate(., eigen = purrr::map(cov, seasonder_eigen_decomp_C)) 17: MUSIC %<>% dplyr::mutate(eigen = purrr::map(cov, seasonder_eigen_decomp_C)) 18: seasonder_MUSICCovDecomposition(.) 19: out %<>% seasonder_MUSICCovDecomposition() 20: seasonder_runMUSIC(cs_obj) An irrecoverable exception occurred. R is aborting now ...
checking for unstated dependencies in ‘tests’ ... OK
checking tests ... [3s/3s] ERROR Running ‘testthat.R’ [3s/3s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(SeaSondeR) > > test_check("SeaSondeR") Attaching package: 'magrittr' The following objects are masked from 'package:testthat': equals, is_less_than, not *** caught segfault *** address 0x1, cause 'invalid permissions' Traceback: 1: eigen(C, symmetric = TRUE) 2: .f(.x[[i]], ...) 3: .Primitive(".Call")(list(name = "map_impl", address = <pointer: 0x6000025fc700>, dll = list(name = "purrr", path = "/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/purrr/libs/purrr.so", dynamicLookup = FALSE, handle = <pointer: 0x76384250>, info = <pointer: 0x6000001fc180>, forceSymbols = FALSE), numParameters = 6L), <environment>, "list", FALSE, 4608L, NULL, 1L) 4: call_with_cleanup(map_impl, environment(), .type, .progress, n, names, i) 5: withCallingHandlers(expr, error = function(cnd) { if (i == 0L) { } else { message <- c(i = "In index: {i}.") if (!is.null(names) && !is.na(names[[i]]) && names[[i]] != "") { name <- names[[i]] message <- c(message, i = "With name: {name}.") } else { name <- NULL } cli::cli_abort(message, location = i, name = name, parent = cnd, call = error_call, class = "purrr_error_indexed") }}) 6: with_indexed_errors(i = i, names = names, error_call = .purrr_error_call, call_with_cleanup(map_impl, environment(), .type, .progress, n, names, i)) 7: map_("list", .x, .f, ..., .progress = .progress) 8: purrr::map(cov, seasonder_eigen_decomp_C) 9: .Call(dplyr_mask_eval_all_mutate, quo, private) 10: eval() 11: mask$eval_all_mutate(quo) 12: mutate_col(dots[[i]], data, mask, new_columns) 13: withCallingHandlers(for (i in seq_along(dots)) { poke_error_context(dots, i, mask = mask) context_poke("column", old_current_column) new_columns <- mutate_col(dots[[i]], data, mask, new_columns)}, error = dplyr_error_handler(dots = dots, mask = mask, bullets = mutate_bullets, error_call = error_call, error_class = "dplyr:::mutate_error"), warning = dplyr_warning_handler(state = warnings_state, mask = mask, error_call = error_call)) 14: mutate_cols(.data, dplyr_quosures(...), by) 15: mutate.data.frame(., eigen = purrr::map(cov, seasonder_eigen_decomp_C)) 16: dplyr::mutate(., eigen = purrr::map(cov, seasonder_eigen_decomp_C)) 17: MUSIC %<>% dplyr::mutate(eigen = purrr::map(cov, seasonder_eigen_decomp_C)) 18: seasonder_MUSICCovDecomposition(.) 19: out %<>% seasonder_MUSICCovDecomposition() 20: seasonder_runMUSIC(.) 21: out %<>% seasonder_runMUSIC() 22: seasonder_runMUSICInFOR(seasonder_cs_obj) 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, parent.frame()) 34: test_that("El fichero exportado coincide con el fichero de referencia", { CS_file_path <- system.file("css_data/CSS_TORA_24_04_04_0700.cs", package = "SeaSondeR") APM_path <- system.file("css_data/MeasPattern.txt", package = "SeaSondeR") seasonder_disableMessages() seasonder_apm_obj <- seasonder_readSeaSondeRAPMFile(APM_path) seasonder_cs_obj <- seasonder_createSeaSondeRCS(CS_file_path, seasonder_apm_object = seasonder_apm_obj) first_order_settings <- list(nsm = 2, fdown = 10^(10/10), flim = 10^(20/10), noisefact = 10^(6/10), currmax = 2, reject_distant_bragg = TRUE, reject_noise_ionospheric = FALSE, reject_noise_ionospheric_threshold = 0) seasonder_cs_obj <- seasonder_computeFORs(seasonder_cs_obj, FOR_control = first_order_settings) MUSIC_options <- list(doppler_interpolation = 2, smoothNoiseLevel = TRUE, PPMIN = 5, PWMAX = 50) seasonder_cs_obj <- seasonder_setMUSICOptions(seasonder_cs_obj, MUSIC_options) seasonder_cs_obj <- seasonder_runMUSICInFOR(seasonder_cs_obj) lluv_temp_path <- tempfile(pattern = "CSS_TORA_24_04_04_0700", fileext = ".ruv") AngSeg <- purrr::list_c(lapply(45:61, function(i) list(c(i, 313, 360), c(i, 0, 31)))) seasonder_exportLLUVRadialMetrics(seasonder_cs_obj, LLUV_path = lluv_temp_path, AngSeg = AngSeg) expected_metrics_text <- readLines(system.file("css_data/CSS_TORA_24_04_04_0700.ruv", package = "SeaSondeR")) radial_metrics_text <- readLines(lluv_temp_path) filter_text <- function(txt) { txt[!grepl("^%ProcessedTimeStamp", txt)] } expected_metrics_text <- filter_text(expected_metrics_text) radial_metrics_text <- filter_text(radial_metrics_text) expect_equal(radial_metrics_text, expected_metrics_text) }) 35: eval(code, test_env) 36: eval(code, test_env) 37: 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) 38: doTryCatch(return(expr), name, parentenv, handler) 39: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 40: tryCatchList(expr, classes, parentenv, handlers) 41: 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) 42: doWithOneRestart(return(expr), restart) 43: withOneRestart(expr, restarts[[1L]]) 44: 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() { }) 45: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new()) 46: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call) 47: FUN(X[[i]], ...) 48: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call) 49: doTryCatch(return(expr), name, parentenv, handler) 50: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 51: tryCatchList(expr, classes, parentenv, handlers) 52: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL}) 53: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)) 54: 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) 55: 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) 56: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed") 57: test_check("SeaSondeR") An irrecoverable exception occurred. R is aborting now ...
checking for unstated dependencies in vignettes ... OK
checking package vignettes ... OK
checking re-building of vignette outputs ... [7s/7s] ERROR Error(s) in re-building vignettes: sh: line 1: 24231 Segmentation fault: 11 '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo > '/Volumes/Temp/tmp/RtmpjMSuNr/file5e7d117501a9' 2>&1 < '/Volumes/Temp/tmp/RtmpjMSuNr/file5e7d18c00733' --- re-building ‘RadialMetricsExport.Rmd’ using rmarkdown *** caught segfault *** address 0x1, cause 'invalid permissions' Traceback: 1: eigen(C, symmetric = TRUE) 2: .f(.x[[i]], ...) 3: .Primitive(".Call")(list(name = "map_impl", address = <pointer: 0x600000eda040>, dll = list(name = "purrr", path = "/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/purrr/libs/purrr.so", dynamicLookup = FALSE, handle = <pointer: 0x76374660>, info = <pointer: 0x600002ad4a20>, forceSymbols = FALSE), numParameters = 6L), <environment>, "list", FALSE, 2318L, NULL, 1L) 4: call_with_cleanup(map_impl, environment(), .type, .progress, n, names, i) 5: withCallingHandlers(expr, error = function(cnd) { if (i == 0L) { } else { message <- c(i = "In index: {i}.") if (!is.null(names) && !is.na(names[[i]]) && names[[i]] != "") { name <- names[[i]] message <- c(message, i = "With name: {name}.") } else { name <- NULL } cli::cli_abort(message, location = i, name = name, parent = cnd, call = error_call, class = "purrr_error_indexed") }}) 6: with_indexed_errors(i = i, names = names, error_call = .purrr_error_call, call_with_cleanup(map_impl, environment(), .type, .progress, n, names, i)) 7: map_("list", .x, .f, ..., .progress = .progress) 8: purrr::map(cov, seasonder_eigen_decomp_C) 9: .Call(dplyr_mask_eval_all_mutate, quo, private) 10: eval() 11: mask$eval_all_mutate(quo) 12: mutate_col(dots[[i]], data, mask, new_columns) 13: withCallingHandlers(for (i in seq_along(dots)) { poke_error_context(dots, i, mask = mask) context_poke("column", old_current_column) new_columns <- mutate_col(dots[[i]], data, mask, new_columns)}, error = dplyr_error_handler(dots = dots, mask = mask, bullets = mutate_bullets, error_call = error_call, error_class = "dplyr:::mutate_error"), warning = dplyr_warning_handler(state = warnings_state, mask = mask, error_call = error_call)) 14: mutate_cols(.data, dplyr_quosures(...), by) 15: mutate.data.frame(., eigen = purrr::map(cov, seasonder_eigen_decomp_C)) 16: dplyr::mutate(., eigen = purrr::map(cov, seasonder_eigen_decomp_C)) 17: MUSIC %<>% dplyr::mutate(eigen = purrr::map(cov, seasonder_eigen_decomp_C)) 18: seasonder_MUSICCovDecomposition(.) 19: out %<>% seasonder_MUSICCovDecomposition() 20: seasonder_runMUSIC(.) 21: out %<>% seasonder_runMUSIC() 22: seasonder_runMUSICInFOR(cs_obj) 23: eval(expr, envir) 24: eval(expr, envir) 25: withVisible(eval(expr, envir)) 26: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$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$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)}) 27: eval(call) 28: eval(call) 29: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers) 30: doWithOneRestart(return(expr), restart) 31: withOneRestart(expr, restarts[[1L]]) 32: withRestartList(expr, restarts[-nr]) 33: doWithOneRestart(return(expr), restart) 34: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 35: withRestartList(expr, restarts) 36: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) 37: evaluate::evaluate(...) 38: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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)) 39: in_dir(input_dir(), expr) 40: 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$render, options))) 41: eng_r(options) 42: block_exec(params) 43: call_block(x) 44: process_group(group) 45: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }) 46: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())) 47: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) 48: process_file(text, output) 49: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 50: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) 51: vweave_rmarkdown(...) 52: engine$weave(file, quiet = quiet, encoding = enc) 53: doTryCatch(return(expr), name, parentenv, handler) 54: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 55: tryCatchList(expr, classes, parentenv, handlers) 56: 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) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))}) 57: tools:::.buildOneVignette("RadialMetricsExport.Rmd", "/Volumes/Builds/packages/sonoma-arm64/results/4.6/SeaSondeR.Rcheck/vign_test/SeaSondeR", TRUE, FALSE, "RadialMetricsExport", "UTF-8", "/Volumes/Temp/tmp/RtmpjMSuNr/file5e7d5996295a.rds") An irrecoverable exception occurred. R is aborting now ... --- re-building ‘SeaSondeAPM.Rmd’ using rmarkdown --- finished re-building ‘SeaSondeAPM.Rmd’ --- re-building ‘SeaSondeCS.Rmd’ using rmarkdown --- finished re-building ‘SeaSondeCS.Rmd’ --- re-building ‘intro.Rmd’ using rmarkdown --- finished re-building ‘intro.Rmd’ SUMMARY: processing the following file failed: ‘RadialMetricsExport.Rmd’ Error: Vignette re-building failed. Execution halted
checking PDF version of manual ... [6s/6s] OK
DONE Status: 3 ERRORs
using check arguments '--no-clean-on-error '