Check results for 'rEDM'

using R version 4.5.2 Patched (2026-01-31 r89382)
using platform: aarch64-apple-darwin20
R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0
running under: macOS Ventura 13.7.8
using session charset: UTF-8
checking for file ‘rEDM/DESCRIPTION’ ... OK
checking extension type ... Package
this is package ‘rEDM’ version ‘2.0.2’
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 ‘rEDM’ can be installed ... [2s/2s] OK See the install log for details.
checking installed package size ... OK
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 ... [0s/0s] 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/0s] 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 ... [2s/2s] OK
checking Rd files ... [0s/0s] 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 contents of ‘data’ directory ... OK
checking data for non-ASCII characters ... [0s/0s] OK
checking LazyData ... OK
checking data for ASCII and uncompressed saves ... OK
checking installed files from ‘inst/doc’ ... OK
checking files in ‘vignettes’ ... OK
checking examples ... [7s/2s] OK
checking for unstated dependencies in vignettes ... OK
checking package vignettes ... OK
checking re-building of vignette outputs ... [25s/22s] ERROR Error(s) in re-building vignettes: --- re-building ‘rEDM-tutorial.Rmd’ using rmarkdown 2026-11-12 00:45:00.937 R[45930:69906] XType: Using static font registry. *** caught segfault *** address 0x110, cause 'invalid permissions' *** caught segfault *** address 0x110, cause 'invalid permissions' *** caught segfault *** address 0x110, cause 'invalid permissions' *** caught segfault *** address 0x110, cause 'invalid permissions' Traceback: 1: RowCumsum(valid) 2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose) 3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend) 4: ComputeError(predictions$Observations, predictions$Predictions) 5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions) 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(values, worker, mc.cores = cores, mc.preschedule = TRUE) 17: doTryCatch(return(expr), name, parentenv, handler) 18: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 19: tryCatchList(expr, classes, parentenv, handlers) 20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL) 21: SweepApply(theta, worker, numProcess) 22: unlist(SweepApply(theta, worker, numProcess)) Traceback: 1: RowCumsum(valid) 2: 23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE) validLib = validLib, libOverlap = idx$libOverlap, backend = backend, 24: tieBreak = FALSE, verbose = verbose)eval(expr, envir) 3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, 25: eval(expr, envir) tau = tau, theta = th, exclusionRadius = exclusionRadius, 26: withVisible(eval(expr, envir)) embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { 4: watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd)ComputeError(predictions$Observations, predictions$Predictions) } if (on_message$silence) { invokeRestart("muffleMessage") 5: }}, warning = function (cnd) {SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, if (getOption("warn") >= 2 || getOption("warn") < 0) { knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, return() embedded = embedded, validLib = validLib, noTime = noTime, } ignoreNan = ignoreNan, backend = backend)$predictions) watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) 6: watcher$push(cnd)FUN(X[[i]], ...) } if (on_warning$silence) { invokeRestart("muffleWarning") 7: }}, error = function (cnd) {lapply(X = S, FUN = FUN, ...) watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) 8: watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})doTryCatch(return(expr), name, parentenv, handler) 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])28: eval(call) 29: eval(call)10: 30: tryCatchList(expr, classes, parentenv, handlers)with_handlers({ for (expr in tle$exprs) {11: tryCatch(expr, error = function(e) { ev <- withVisible(eval(expr, envir)) call <- conditionCall(e) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE if (!is.null(call)) {}, handlers) if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L31: sm <- strsplit(conditionMessage(e), "\n")[[1L]]doWithOneRestart(return(expr), restart) 32: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")withOneRestart(expr, restarts[[1L]]) if (is.na(w)) 33: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], withRestartList(expr, restarts[-nr]) type = "b") 34: if (w > LONG) doWithOneRestart(return(expr), restart) prefix <- paste0(prefix, "\n ") Traceback: 1: 35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) RowCumsum(valid)36: withRestartList(expr, restarts) 2: }37: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, else prefix <- "Error : "withRestarts(with_handlers({ validLib = validLib, libOverlap = idx$libOverlap, backend = backend, msg <- paste0(prefix, conditionMessage(e), "\n") for (expr in tle$exprs) { .Internal(seterrmessage(msg[1L])) ev <- withVisible(eval(expr, envir)) if (!silent && isTRUE(getOption("show.error.messages"))) { watcher$capture_plot_and_output() cat(msg, file = outFile) .Internal(printDeferredWarnings()) watcher$print_value(ev$value, ev$visible, envir) } } invisible(structure(msg, class = "try-error", condition = e))}) tieBreak = FALSE, verbose = verbose) TRUE 3: 12: }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, 38: tau = tau, theta = th, exclusionRadius = exclusionRadius, evaluate::evaluate(...) embedded = embedded, validLib = validLib, noTime = noTime, 39: ignoreNan = ignoreNan, backend = backend)try(lapply(X = S, FUN = FUN, ...), silent = TRUE)evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 4: keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else {ComputeError(predictions$Observations, predictions$Predictions)13: if (options$error && options$include) 0L 5: else 2L }, output_handler = knit_handlers(options$render, options)) 40: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))in_dir(input_dir(), expr) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, 14: 41: embedded = embedded, validLib = validLib, noTime = noTime, in_input_dir(evaluate(code, envir = env, new_device = FALSE, ignoreNan = ignoreNan, backend = backend)$predictions) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 6: keep_message = if (is.numeric(options$message)) TRUE else options$message, FUN(X[[i]], ...) stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 7: 0Llapply(X = S, FUN = FUN, ...) else 2LFUN(X[[i]], ...) }, output_handler = knit_handlers(options$render, options))) 8: doTryCatch(return(expr), name, parentenv, handler)15: 42: lapply(seq_len(cores), inner.do)eng_r(options) 9: 43: tryCatchOne(expr, names, parentenv, handlers[[1L]])block_exec(params) 44: 10: call_block(x)tryCatchList(expr, classes, parentenv, handlers) 16: 11: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)tryCatch(expr, error = function(e) { 45: 17: call <- conditionCall(e)process_group(group) if (!is.null(call)) {doTryCatch(return(expr), name, parentenv, handler) if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) 46: 18: dcall <- deparse(call, nlines = 1L)tryCatchOne(expr, names, parentenv, handlers[[1L]]) prefix <- paste("Error in", dcall, ": ")19: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), LONG <- 75LtryCatchList(expr, classes, parentenv, handlers) sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")20: if (is.na(w)) tryCatch(parallel::mclapply(values, worker, mc.cores = cores, error = function(e) { w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], mc.preschedule = TRUE), error = function(e) NULL) if (progress && is.function(pb$interrupt)) type = "b") pb$interrupt() if (w > LONG) if (is_R_CMD_build() || is_R_CMD_check()) prefix <- paste0(prefix, "\n ") } error <<- format(e) else prefix <- "Error : "21: msg <- paste0(prefix, conditionMessage(e), "\n") }) .Internal(seterrmessage(msg[1L]))SweepApply(theta, worker, numProcess) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile)47: .Internal(printDeferredWarnings())with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { } if (progress && is.function(pb$interrupt)) invisible(structure(msg, class = "try-error", condition = e)) }) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) 12: 22: error <<- format(e) }), list(rlang_trace_top_env = knit_global()))try(lapply(X = S, FUN = FUN, ...), silent = TRUE) unlist(SweepApply(theta, worker, numProcess))13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) 23: 14: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", FUN(X[[i]], ...) target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)15: lapply(seq_len(cores), inner.do) 48: 24: 16: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), eval(expr, envir) error = function(e) {parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)25: if (progress && is.function(pb$interrupt)) pb$interrupt()17: if (is_R_CMD_build() || is_R_CMD_check()) doTryCatch(return(expr), name, parentenv, handler)eval(expr, envir) error <<- format(e) 26: 18: tryCatchOne(expr, names, parentenv, handlers[[1L]])withVisible(eval(expr, envir)) 19: 27: tryCatchList(expr, classes, parentenv, handlers)withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) 20: {tryCatch(parallel::mclapply(values, worker, mc.cores = cores, watcher$capture_plot_and_output() mc.preschedule = TRUE), error = function(e) NULL) if (on_message$capture) { watcher$push(cnd)21: SweepApply(theta, worker, numProcess) }), list(rlang_trace_top_env = knit_global())), function(loc) { } 22: setwd(wd)unlist(SweepApply(theta, worker, numProcess)) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) if (on_message$silence) { paste0("\n", rule(), error, "\n", rule())) invokeRestart("muffleMessage")}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) } }, warning = function (cnd) 49: 23: {process_file(text, output) if (getOption("warn") >= 2 || getOption("warn") < 0) {PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", 50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 51: return()rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), E = E, showPlot = TRUE) output_dir = getwd(), ...) 24: eval(expr, envir)52: vweave_rmarkdown(...) }25: watcher$capture_plot_and_output() if (on_warning$capture) {53: engine$weave(file, quiet = quiet, encoding = enc)eval(expr, envir) cnd <- sanitize_call(cnd)54: watcher$push(cnd)doTryCatch(return(expr), name, parentenv, handler) } if (on_warning$silence) { invokeRestart("muffleWarning")26: 55: withVisible(eval(expr, envir))tryCatchOne(expr, names, parentenv, handlers[[1L]]) 27: 56: }}, error = function (cnd) tryCatchList(expr, classes, parentenv, handlers){ watcher$capture_plot_and_output()57: cnd <- sanitize_call(cnd)tryCatch({ watcher$push(cnd) engine$weave(file, quiet = quiet, encoding = enc) switch(on_error, continue = invokeRestart("eval_continue"), withCallingHandlers(code, error = function (e) stop = invokeRestart("eval_stop"), error = NULL) setwd(startdir)})rlang::entrace(e), message = function (cnd) output <- find_vignette_product(name, by = "weave", engine = engine){ if (!have.makefile && vignette_is_tex(output)) {28: watcher$capture_plot_and_output() texi2pdf(file = output, clean = FALSE, quiet = quiet) if (on_message$capture) { output <- find_vignette_product(name, by = "texi2pdf", watcher$push(cnd) engine = engine)eval(call) 29: } outputs <- c(outputs, output)eval(call) }}, error = function(e) { if (on_message$silence) { 30: thisOK <<- FALSE invokeRestart("muffleMessage") fails <<- c(fails, file) } message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", }, warning = function (cnd) file, conditionMessage(e)))}){ 58: if (getOption("warn") >= 2 || getOption("warn") < 0) {tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", return()with_handlers({ } for (expr in tle$exprs) { watcher$capture_plot_and_output() ev <- withVisible(eval(expr, envir)) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpUd2XsP/file93027e8fdc2b.rds") watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd)An irrecoverable exception occurred. R is aborting now ... watcher$print_value(ev$value, ev$visible, envir) } TRUE watcher$push(cnd)}, handlers) } if (on_warning$silence) {31: invokeRestart("muffleWarning")doWithOneRestart(return(expr), restart) }}, error = function (cnd) {32: watcher$capture_plot_and_output()withOneRestart(expr, restarts[[1L]]) 33: withRestartList(expr, restarts[-nr]) 34: doWithOneRestart(return(expr), restart) cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)35: })withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 36: 28: eval(call) withRestartList(expr, restarts)29: eval(call) 30: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir)37: }withRestarts(with_handlers({ TRUE for (expr in tle$exprs) {}, handlers) ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output()31: watcher$print_value(ev$value, ev$visible, envir)doWithOneRestart(return(expr), restart) 32: }withOneRestart(expr, restarts[[1L]]) TRUE 33: }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) withRestartList(expr, restarts[-nr]) 38: 34: evaluate::evaluate(...)doWithOneRestart(return(expr), restart) 39: 35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 36: withRestartList(expr, restarts) 37: withRestarts(with_handlers({evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, for (expr in tle$exprs) { keep_message = if (is.numeric(options$message)) TRUE else options$message, ev <- withVisible(eval(expr, envir)) stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) watcher$capture_plot_and_output() 0L watcher$print_value(ev$value, ev$visible, envir) else 2L } }, output_handler = knit_handlers(options$render, options)) TRUE40: }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)in_dir(input_dir(), expr) 38: 41: evaluate::evaluate(...)in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 39: keep_message = if (is.numeric(options$message)) TRUE else options$message, evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, stop_on_error = if (is.numeric(options$error)) options$error else { keep_message = if (is.numeric(options$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)) 40: in_dir(input_dir(), expr) 41: 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$render, options))) 42: eng_r(options) 43: block_exec(params) 44: call_block(x) 45: if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))) 42: eng_r(options) 43: block_exec(params) process_group(group)44: call_block(x)46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { Traceback: 1: if (progress && is.function(pb$interrupt)) RowCumsum(valid) pb$interrupt()45: if (is_R_CMD_build() || is_R_CMD_check()) process_group(group) 2: error <<- format(e)FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, 46: }) validLib = validLib, libOverlap = idx$libOverlap, backend = backend, 47: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { tieBreak = FALSE, verbose = verbose) if (progress && is.function(pb$interrupt)) if (progress && is.function(pb$interrupt)) pb$interrupt() 3: pb$interrupt()SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, if (is_R_CMD_build() || is_R_CMD_check()) tau = tau, theta = th, exclusionRadius = exclusionRadius, error <<- format(e) embedded = embedded, validLib = validLib, noTime = noTime, if (is_R_CMD_build() || is_R_CMD_check()) }), list(rlang_trace_top_env = knit_global())) error <<- format(e) ignoreNan = ignoreNan, backend = backend) }) 47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 4: error = function(e) {48: ComputeError(predictions$Observations, predictions$Predictions)xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), if (progress && is.function(pb$interrupt)) error = function(e) { pb$interrupt() if (progress && is.function(pb$interrupt)) if (is_R_CMD_build() || is_R_CMD_check()) 5: error <<- format(e)SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, pb$interrupt() }), list(rlang_trace_top_env = knit_global())) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, if (is_R_CMD_build() || is_R_CMD_check()) 48: ignoreNan = ignoreNan, backend = backend)$predictions)xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error <<- format(e) error = function(e) { }), list(rlang_trace_top_env = knit_global())), function(loc) { 6: setwd(wd) if (progress && is.function(pb$interrupt)) FUN(X[[i]], ...) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) 7: error <<- format(e) paste0("\n", rule(), error, "\n", rule())) }), list(rlang_trace_top_env = knit_global())), function(loc) {lapply(X = S, FUN = FUN, ...) setwd(wd) write_utf8(res, output %n% stdout())}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) 8: doTryCatch(return(expr), name, parentenv, handler)49: 9: paste0("\nQuitting from ", loc, if (!is.null(error)) process_file(text, output)tryCatchOne(expr, names, parentenv, handlers[[1L]]) paste0("\n", rule(), error, "\n", rule())) 10: }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)tryCatchList(expr, classes, parentenv, handlers)50: 11: tryCatch(expr, error = function(e) {49: call <- conditionCall(e)process_file(text, output) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L)knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ")50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) LONG <- 75L 51: sm <- strsplit(conditionMessage(e), "\n")[[1L]]rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], output_dir = getwd(), ...) type = "b")51: if (w > LONG) prefix <- paste0(prefix, "\n ")52: }rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), vweave_rmarkdown(...) 53: engine$weave(file, quiet = quiet, encoding = enc) output_dir = getwd(), ...) 52: 54: doTryCatch(return(expr), name, parentenv, handler) else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n")55: tryCatchOne(expr, names, parentenv, handlers[[1L]]) .Internal(seterrmessage(msg[1L]))vweave_rmarkdown(...) if (!silent && isTRUE(getOption("show.error.messages"))) { 53: 56: engine$weave(file, quiet = quiet, encoding = enc) cat(msg, file = outFile) .Internal(printDeferredWarnings()) 54: }doTryCatch(return(expr), name, parentenv, handler) invisible(structure(msg, class = "try-error", condition = e)) 55: })tryCatchOne(expr, names, parentenv, handlers[[1L]]) 12: tryCatchList(expr, classes, parentenv, handlers)try(lapply(X = S, FUN = FUN, ...), silent = TRUE)56: tryCatchList(expr, classes, parentenv, handlers)57: tryCatch({ 57: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc)13: setwd(startdir) engine$weave(file, quiet = quiet, encoding = enc)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) output <- find_vignette_product(name, by = "weave", engine = engine) setwd(startdir) if (!have.makefile && vignette_is_tex(output)) {14: output <- find_vignette_product(name, by = "weave", engine = engine) texi2pdf(file = output, clean = FALSE, quiet = quiet) if (!have.makefile && vignette_is_tex(output)) {FUN(X[[i]], ...) texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) output <- find_vignette_product(name, by = "texi2pdf", 15: } engine = engine)lapply(seq_len(cores), inner.do) } outputs <- c(outputs, output) }, error = function(e) {16: outputs <- c(outputs, output)parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) thisOK <<- FALSE17: fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))doTryCatch(return(expr), name, parentenv, handler)}) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", 58: file, conditionMessage(e))) tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", 18: }) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpUd2XsP/file93027e8fdc2b.rds")tryCatchOne(expr, names, parentenv, handlers[[1L]]) 58: An irrecoverable exception occurred. R is aborting now ... 19: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpUd2XsP/file93027e8fdc2b.rds")tryCatchList(expr, classes, parentenv, handlers) 20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)An irrecoverable exception occurred. R is aborting now ... 21: SweepApply(theta, worker, numProcess) 22: unlist(SweepApply(theta, worker, numProcess)) 23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE) 24: eval(expr, envir) 25: eval(expr, envir) 26: withVisible(eval(expr, envir)) 27: 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)}) 28: eval(call) 29: eval(call) 30: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers) 31: doWithOneRestart(return(expr), restart) 32: withOneRestart(expr, restarts[[1L]]) 33: withRestartList(expr, restarts[-nr]) 34: doWithOneRestart(return(expr), restart) 35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 36: withRestartList(expr, restarts) 37: withRestarts(with_handlers({ for (expr in tle$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) 38: evaluate::evaluate(...) 39: 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$render, options)) 40: in_dir(input_dir(), expr) 41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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))) 42: eng_r(options) 43: block_exec(params) 44: call_block(x) 45: process_group(group) 46: 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) }) 47: 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())) 48: 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) 49: process_file(text, output) 50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) 52: vweave_rmarkdown(...) 53: engine$weave(file, quiet = quiet, encoding = enc) 54: doTryCatch(return(expr), name, parentenv, handler) 55: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 56: tryCatchList(expr, classes, parentenv, handlers) 57: tryCatch({ engine$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)))}) 58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpUd2XsP/file93027e8fdc2b.rds") An irrecoverable exception occurred. R is aborting now ... Quitting from rEDM-tutorial.Rmd:466-469 [smap_thrips] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `data.frame()`: ! arguments imply differing number of rows: 15, 0 --- Backtrace: ▆ 1. └─rEDM::PredictNonlinear(...) 2. └─base::data.frame(Theta = theta, rho = rho) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'rEDM-tutorial.Rmd' failed with diagnostics: arguments imply differing number of rows: 15, 0 --- failed re-building ‘rEDM-tutorial.Rmd’ SUMMARY: processing the following file failed: ‘rEDM-tutorial.Rmd’ Error: Vignette re-building failed. Execution halted
checking PDF version of manual ... [5s/5s] OK
DONE

Status: 1 ERROR