- 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 02:05:58 UTC
- checking for file ‘clustra/DESCRIPTION’ ... OK
- this is package ‘clustra’ version ‘0.2.1’
- 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 ‘clustra’ can be installed ... [1s/1s] 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 ... [1s/1s] 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 ... [1s/1s] OK
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [85s/65s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘clustra_bp_vignette.Rmd’ using rmarkdown
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: Predict.matrix.tprs.smooth(object, dk$data)
Traceback:
1: Predict.matrix.tprs.smooth(object, dk$data)
2: 2: Predict.matrix(object, dk$data)
3: Predict.matrix3(object, data)
4: PredictMat(object$smooth[[i]], dk$mf, n = dk$nr[termk])
5: predict.bamd(object, newdata, type, se.fit, terms, exclude, block.size, newdata.guaranteed, na.action, n.threads, gc.level = gc.level, ...)
6: Predict.matrix(object, dk$data)
3: Predict.matrix3(object, data)mgcv::predict.bam(object = tps, newdata = newdata, type = "response", newdata.guaranteed = TRUE)
7: as.vector(mgcv::predict.bam(object = tps, newdata = newdata, type = "response", newdata.guaranteed = TRUE))
8: FUN(X[[i]], ...)
9:
4: PredictMat(object$smooth[[i]], dk$mf, n = dk$nr[termk])
lapply(X = S, FUN = FUN, ...)
10: doTryCatch(return(expr), name, parentenv, handler)
11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
12: tryCatchList(expr, classes, parentenv, handlers)
5: predict.bamd(object, newdata, type, se.fit, terms, exclude, block.size, newdata.guaranteed, na.action, n.threads, gc.level = gc.level, ...)13: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) {
6: mgcv::predict.bam(object = tps, newdata = newdata, type = "response", newdata.guaranteed = TRUE) 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)
7: as.vector(mgcv::predict.bam(object = tps, newdata = newdata, type = "response", newdata.guaranteed = TRUE))
8: FUN(X[[i]], ...)
9: lapply(X = S, FUN = FUN, ...)
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))})
14: 10: doTryCatch(return(expr), name, parentenv, handler)
11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
12: tryCatchList(expr, classes, parentenv, handlers)
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
15: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
16: FUN(X[[i]], ...)
17: 13: tryCatch(expr, error = function(e) {lapply(seq_len(cores), inner.do)
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], 18: parallel::mclapply(tps, pred_g, newdata = newdata, mc.cores = mccores)
19: trajectories(data, k, group, maxdf, conv, mccores, verbose = verbose, ...)
20: clustra(data, k = 5, maxdf = 30, conv = c(20, 0.5), mccores = mc, verbose = TRUE)
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()) }21: eval(expr, envir)
22: eval(expr, envir)
23: withVisible(eval(expr, envir))
24: 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) { invisible(structure(msg, class = "try-error", condition = e))})
14: 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) {try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
15: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
16: watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd)FUN(X[[i]], ...)
17: switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})lapply(seq_len(cores), inner.do)
18:
25: eval(call)parallel::mclapply(tps, pred_g, newdata = newdata, mc.cores = mccores)
19:
26: eval(call)trajectories(data, k, group, maxdf, conv, mccores, verbose = verbose, ...)
20: clustra(data, k = 5, maxdf = 30, conv = c(20, 0.5), mccores = mc, verbose = TRUE)
27: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE
21: eval(expr, envir)}, handlers)
28:
22: eval(expr, envir)doWithOneRestart(return(expr), restart)
29:
23: withVisible(eval(expr, envir))withOneRestart(expr, restarts[[1L]])
30:
24: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output()withRestartList(expr, restarts[-nr])
31: if (on_message$capture) { watcher$push(cnd) }doWithOneRestart(return(expr), restart)
32: if (on_message$silence) { invokeRestart("muffleMessage") }withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
33: }, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output()withRestartList(expr, restarts)
34: if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd)withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } } if (on_warning$silence) { invokeRestart("muffleWarning") TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
}}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd)35: evaluate::evaluate(...)
36: 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 switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)}) else 2L }, output_handler = knit_handlers(options$render, options))
25: eval(call)37: in_dir(input_dir(), expr)
26: eval(call)38: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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$include)
27: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE 0L else 2L }, output_handler = knit_handlers(options$render, options)))
39: eng_r(options)
40: block_exec(params)
41: }, handlers)
28: doWithOneRestart(return(expr), restart)
29: call_block(x)
42: process_group(group)
43: withOneRestart(expr, restarts[[1L]])
30: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) withRestartList(expr, restarts[-nr])
31: doWithOneRestart(return(expr), restart)
32: pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
44: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
33: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) withRestartList(expr, restarts)
34: pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } }), list(rlang_trace_top_env = knit_global()))
45: TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) 35: evaluate::evaluate(...)
pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)36: 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 }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) else 2L }, output_handler = knit_handlers(options$render, options))
paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)37: in_dir(input_dir(), expr)
46: process_file(text, output)38: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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$include)
47: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
48: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
39: eng_r(options) output_dir = getwd(), ...)
49:
40: block_exec(params)vweave_rmarkdown(...)
50:
41: call_block(x)
42: process_group(group)engine$weave(file, quiet = quiet, encoding = enc)
51: doTryCatch(return(expr), name, parentenv, handler)
52:
43: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt()tryCatchOne(expr, names, parentenv, handlers[[1L]])
53: if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })tryCatchList(expr, classes, parentenv, handlers)
54:
44: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), tryCatch({ engine$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) error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() 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)))})
if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
45: 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()55: tools:::.buildOneVignette("clustra_bp_vignette.Rmd", "/Volumes/Builds/packages/sonoma-arm64/results/4.6/clustra.Rcheck/vign_test/clustra", TRUE, FALSE, "clustra_bp_vignette", "UTF-8", "/Volumes/Temp/tmp/RtmphL3YLn/file1a353971c7f0.rds")
An irrecoverable exception occurred. R is aborting now ...
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)
46: process_file(text, output)
47: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
48: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
49: vweave_rmarkdown(...)
50: engine$weave(file, quiet = quiet, encoding = enc)
51: doTryCatch(return(expr), name, parentenv, handler)
52: tryCatchOne(expr, names, parentenv, handlers[[1L]])
53: tryCatchList(expr, classes, parentenv, handlers)
54: tryCatch({ engine$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)))})
55: tools:::.buildOneVignette("clustra_bp_vignette.Rmd", "/Volumes/Builds/packages/sonoma-arm64/results/4.6/clustra.Rcheck/vign_test/clustra", TRUE, FALSE, "clustra_bp_vignette", "UTF-8", "/Volumes/Temp/tmp/RtmphL3YLn/file1a353971c7f0.rds")
An irrecoverable exception occurred. R is aborting now ...
Quitting from clustra_bp_vignette.Rmd:71-74 [run5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `apply()`:
! dim(X) must have a positive length
---
Backtrace:
▆
1. └─clustra::clustra(...)
2. └─clustra::trajectories(...)
3. └─base::apply(loss, 1, which.min)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'clustra_bp_vignette.Rmd' failed with diagnostics:
dim(X) must have a positive length
--- failed re-building ‘clustra_bp_vignette.Rmd’
--- re-building ‘clustra_vignette.Rmd’ using rmarkdown
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: predict.gam(object, newdata = newdata, type = type, se.fit = se.fit, terms = terms, exclude = exclude, block.size = block.size, newdata.guaranteed = newdata.guaranteed, na.action = na.action, ...)
2: mgcv::predict.bam(object = tps, newdata = newdata, type = "response", newdata.guaranteed = TRUE)
3: as.vector(mgcv::predict.bam(object = tps, newdata = newdata, type = "response", newdata.guaranteed = TRUE))
4: FUN(X[[i]], ...)
5: lapply(X = S, FUN = FUN, ...)
6: doTryCatch(return(expr), name, parentenv, handler)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: tryCatchList(expr, classes, parentenv, handlers)
9: 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))})
10: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
11: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
12: FUN(X[[i]], ...)
13: lapply(seq_len(cores), inner.do)
14: parallel::mclapply(sfit, pred_g, newdata = newdata, mc.cores = mccores)
15: start_groups(k, data, starts, maxdf, conv, mccores, verbose = verbose)
16: clustra(data, k = 40, starts = "distant", maxdf = 10, conv = c(10, 0), mccores = mc, verbose = TRUE)
17: eval(expr, envir)
18: eval(expr, envir)
19: withVisible(eval(expr, envir))
20: 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)})
21: eval(call)
22: eval(call)
23: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
24: doWithOneRestart(return(expr), restart)
25: withOneRestart(expr, restarts[[1L]])
26: withRestartList(expr, restarts[-nr])
27: doWithOneRestart(return(expr), restart)
28: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
29: withRestartList(expr, restarts)
30: withRestarts(with_handlers({ for (expr in tle$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)
31: evaluate::evaluate(...)
32: 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$render, options))
33: in_dir(input_dir(), expr)
34: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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)))
35: eng_r(options)
36: block_exec(params)
37: call_block(x)
38: process_group(group)
39: 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) })
40: 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()))
41: 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)
42: process_file(text, output)
43: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
44: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
45: vweave_rmarkdown(...)
46: engine$weave(file, quiet = quiet, encoding = enc)
47: doTryCatch(return(expr), name, parentenv, handler)
48: tryCatchOne(expr, names, parentenv, handlers[[1L]])
49: tryCatchList(expr, classes, parentenv, handlers)
50: tryCatch({ engine$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)))})
51: tools:::.buildOneVignette("clustra_vignette.Rmd", "/Volumes/Builds/packages/sonoma-arm64/results/4.6/clustra.Rcheck/vign_test/clustra", TRUE, FALSE, "clustra_vignette", "UTF-8", "/Volumes/Temp/tmp/RtmphL3YLn/file1a353bbf7ea2.rds")
An irrecoverable exception occurred. R is aborting now ...
Traceback:
1: predict.gam(object, newdata = newdata, type = type, se.fit = se.fit, terms = terms, exclude = exclude, block.size = block.size, newdata.guaranteed = newdata.guaranteed, na.action = na.action, ...)
2: mgcv::predict.bam(object = tps, newdata = newdata, type = "response", newdata.guaranteed = TRUE)
3: as.vector(mgcv::predict.bam(object = tps, newdata = newdata, type = "response", newdata.guaranteed = TRUE))
4: FUN(X[[i]], ...)
5: lapply(X = S, FUN = FUN, ...)
6: doTryCatch(return(expr), name, parentenv, handler)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: tryCatchList(expr, classes, parentenv, handlers)
9: 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))})
10: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
11: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
12: FUN(X[[i]], ...)
13: lapply(seq_len(cores), inner.do)
14: parallel::mclapply(sfit, pred_g, newdata = newdata, mc.cores = mccores)
15: start_groups(k, data, starts, maxdf, conv, mccores, verbose = verbose)
16: clustra(data, k = 40, starts = "distant", maxdf = 10, conv = c(10, 0), mccores = mc, verbose = TRUE)
17: eval(expr, envir)
18: eval(expr, envir)
19: withVisible(eval(expr, envir))
20: 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)})
21: eval(call)
22: eval(call)
23: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
24: doWithOneRestart(return(expr), restart)
25: withOneRestart(expr, restarts[[1L]])
26: withRestartList(expr, restarts[-nr])
27: doWithOneRestart(return(expr), restart)
28: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
29: withRestartList(expr, restarts)
30: withRestarts(with_handlers({ for (expr in tle$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)
31: evaluate::evaluate(...)
32: 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$render, options))
33: in_dir(input_dir(), expr)
34: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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)))
35: eng_r(options)
36: block_exec(params)
37: call_block(x)
38: process_group(group)
39: 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) })
40: 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()))
41: 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)
42: process_file(text, output)
43: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
44: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
45: vweave_rmarkdown(...)
46: engine$weave(file, quiet = quiet, encoding = enc)
47: doTryCatch(return(expr), name, parentenv, handler)
48: tryCatchOne(expr, names, parentenv, handlers[[1L]])
49: tryCatchList(expr, classes, parentenv, handlers)
50: tryCatch({ engine$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)))})
51: tools:::.buildOneVignette("clustra_vignette.Rmd", "/Volumes/Builds/packages/sonoma-arm64/results/4.6/clustra.Rcheck/vign_test/clustra", TRUE, FALSE, "clustra_vignette", "UTF-8", "/Volumes/Temp/tmp/RtmphL3YLn/file1a353bbf7ea2.rds")
An irrecoverable exception occurred. R is aborting now ...
Quitting from clustra_vignette.Rmd:129-139 [hclust_d]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `apply()`:
! dim(X) must have a positive length
---
Backtrace:
▆
1. └─clustra::clustra(...)
2. └─clustra:::start_groups(...)
3. └─base::apply(loss, 1, which.min)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'clustra_vignette.Rmd' failed with diagnostics:
dim(X) must have a positive length
--- failed re-building ‘clustra_vignette.Rmd’
SUMMARY: processing the following files failed:
‘clustra_bp_vignette.Rmd’ ‘clustra_vignette.Rmd’
Error: Vignette re-building failed.
Execution halted
- checking PDF version of manual ... [2s/2s] OK
- DONE
Status: 1 ERROR
- using check arguments '--no-clean-on-error '