Last updated on 2026-10-05 23:51:08 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.9 | 73.38 | 188.23 | 261.61 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.0.9 | 58.23 | 143.85 | 202.08 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.0.9 | 53.00 | 129.81 | 182.81 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.0.9 | 66.00 | 141.72 | 207.72 | OK | |
| r-devel-windows-x86_64 | 1.0.9 | 88.00 | 311.00 | 399.00 | OK | |
| r-patched-linux-x86_64 | 1.0.9 | 85.21 | 185.68 | 270.89 | OK | |
| r-release-linux-x86_64 | 1.0.9 | OK | ||||
| r-release-macos-arm64 | 1.0.9 | 15.00 | 53.00 | 68.00 | OK | |
| r-release-macos-x86_64 | 1.0.9 | 54.00 | 239.00 | 293.00 | OK | |
| r-release-windows-x86_64 | 1.0.9 | 87.00 | 232.00 | 319.00 | OK | |
| r-oldrel-macos-arm64 | 1.0.9 | ERROR | ||||
| r-oldrel-macos-x86_64 | 1.0.9 | 52.00 | 206.00 | 258.00 | OK | |
| r-oldrel-windows-x86_64 | 1.0.9 | 115.00 | 303.00 | 418.00 | OK |
Version: 1.0.9
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘Introduction.Rmd’ using rmarkdown
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: cpp_horseshoe(X, Y, intercept, as.integer(nburn), as.integer(npost), seed, verbose, as.integer(printevery), as.integer(chain_index))
2: horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn, npost = npost, seed = seed_chain, verbose = output_verbose, printevery = printevery, chain_index = chain)
3: eval(c.expr, envir = args, enclos = envir)
4: eval(c.expr, envir = args, enclos = envir)
5: doTryCatch(return(expr), name, parentenv, handler)
6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
7: tryCatchList(expr, classes, parentenv, handlers)
8: tryCatch(eval(c.expr, envir = args, enclos = envir), error = function(e) e)
9: FUN(X[[i]], ...)
10: lapply(X = S, FUN = FUN, ...)
11: doTryCatch(return(expr), name, parentenv, handler)
12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
13: tryCatchList(expr, classes, parentenv, handlers)
14: 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))})
15: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
16: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
17: FUN(X[[i]], ...)
18: lapply(seq_len(cores), inner.do)
19: mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed, mc.silent = silent, mc.cores = cores)
20: e$fun(obj, substitute(ex), parent.frame(), e$data)
21: foreach::foreach(chain = 1:nchains, .combine = list, .multicombine = TRUE, .maxcombine = ifelse(nchains >= 2, nchains, 2)) %dopar% { seed_chain = if (!is.null(seed)) seed + chain else NULL return(switch(model, Multi_Laplace = { multi_laplace_mcmc(X, Y, intercept = !standardize, h = extra_parameters$h, v = extra_parameters$v, nburn = nburn, npost = npost, seed = seed_chain, verbose = output_verbose, printevery = printevery, chain_index = chain) }, Horseshoe = { horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn, npost = npost, seed = seed_chain, verbose = output_verbose, printevery = printevery, chain_index = chain) }, ARD = { ARD_mcmc(X, Y, intercept = !standardize, nburn = nburn, npost = npost, seed = seed_chain, verbose = output_verbose, printevery = printevery, chain_index = chain) }, Spike_Laplace = { spike_laplace_partially_mcmc(X, Y, intercept = !standardize, a = extra_parameters$a, b = extra_parameters$b, nburn = nburn, npost = npost, seed = seed_chain, verbose = output_verbose, printevery = printevery, chain_index = chain) }))}
22: withCallingHandlers(expr, warning = function(w) if (inherits(w, classes)) tryInvokeRestart("muffleWarning"))
23: suppressWarnings(foreach::foreach(chain = 1:nchains, .combine = list, .multicombine = TRUE, .maxcombine = ifelse(nchains >= 2, nchains, 2)) %dopar% { seed_chain = if (!is.null(seed)) seed + chain else NULL return(switch(model, Multi_Laplace = { multi_laplace_mcmc(X, Y, intercept = !standardize, h = extra_parameters$h, v = extra_parameters$v, nburn = nburn, npost = npost, seed = seed_chain, verbose = output_verbose, printevery = printevery, chain_index = chain) }, Horseshoe = { horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn, npost = npost, seed = seed_chain, verbose = output_verbose, printevery = printevery, chain_index = chain) }, ARD = { ARD_mcmc(X, Y, intercept = !standardize, nburn = nburn, npost = npost, seed = seed_chain, verbose = output_verbose, printevery = printevery, chain_index = chain) }, Spike_Laplace = { spike_laplace_partially_mcmc(X, Y, intercept = !standardize, a = extra_parameters$a, b = extra_parameters$b, nburn = nburn, npost = npost, seed = seed_chain, verbose = output_verbose, printevery = printevery, chain_index = chain) }))})
24: BMI_LASSO(data$data_MI$X, data$data_MI$Y, model = "Horseshoe", nburn = 4000, npost = 4000, output_verbose = FALSE, nchains = 2, ncores = 2, seed = seed)
25: eval(expr, envir)
26: eval(expr, envir)
27: withVisible(eval(expr, envir))
28: 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)
Traceback:
{ 1: if (getOption("warn") >= 2 || getOption("warn") < 0) {cpp_horseshoe(X, Y, intercept, as.integer(nburn), as.integer(npost), return() seed, verbose, as.integer(printevery), as.integer(chain_index)) }
watcher$capture_plot_and_output() 2: if (on_warning$capture) {horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn, cnd <- sanitize_call(cnd) npost = npost, seed = seed_chain, verbose = output_verbose, watcher$push(cnd) printevery = printevery, chain_index = chain) }
if (on_warning$silence) { 3: invokeRestart("muffleWarning")eval(c.expr, envir = args, enclos = envir) }
}, error = function (cnd) { 4: watcher$capture_plot_and_output()eval(c.expr, envir = args, enclos = envir) cnd <- sanitize_call(cnd)
watcher$push(cnd) 5: switch(on_error, continue = invokeRestart("eval_continue"), doTryCatch(return(expr), name, parentenv, handler) stop = invokeRestart("eval_stop"), error = NULL)
})
6: 29: tryCatchOne(expr, names, parentenv, handlers[[1L]])eval(call)
7: 30: tryCatchList(expr, classes, parentenv, handlers)eval(call)
8: 31: tryCatch(eval(c.expr, envir = args, enclos = envir), error = function(e) e)with_handlers({ for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir)) 9: watcher$capture_plot_and_output()FUN(X[[i]], ...) watcher$print_value(ev$value, ev$visible, envir)
}10: TRUE}, handlers)lapply(X = S, FUN = FUN, ...)
32: 11: doWithOneRestart(return(expr), restart)doTryCatch(return(expr), name, parentenv, handler)
12: 33: tryCatchOne(expr, names, parentenv, handlers[[1L]])withOneRestart(expr, restarts[[1L]])
13: 34: tryCatchList(expr, classes, parentenv, handlers)withRestartList(expr, restarts[-nr])
14: 35: tryCatch(expr, error = function(e) {doWithOneRestart(return(expr), restart)
call <- conditionCall(e)36: if (!is.null(call)) {withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)37: dcall <- deparse(call, nlines = 1L)withRestartList(expr, restarts) prefix <- paste("Error in", dcall, ": ")
LONG <- 75L38: sm <- strsplit(conditionMessage(e), "\n")[[1L]]withRestarts(with_handlers({ w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) for (expr in tle$exprs) { w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") ev <- withVisible(eval(expr, envir)) if (w > LONG) watcher$capture_plot_and_output() prefix <- paste0(prefix, "\n ") watcher$print_value(ev$value, ev$visible, envir) } } TRUE else prefix <- "Error : "}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))39: if (!silent && isTRUE(getOption("show.error.messages"))) {evaluate::evaluate(...) cat(msg, file = outFile)
.Internal(printDeferredWarnings())40: }evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, invisible(structure(msg, class = "try-error", condition = e)) 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) 15: 0Ltry(lapply(X = S, FUN = FUN, ...), silent = TRUE) else 2L
}, output_handler = knit_handlers(options$render, options))16:
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))41: in_dir(input_dir(), expr)
17: 42: FUN(X[[i]], ...)in_input_dir(evaluate(code, envir = env, new_device = FALSE,
keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 18: keep_message = if (is.numeric(options$message)) TRUE else options$message, lapply(seq_len(cores), inner.do) stop_on_error = if (is.numeric(options$error)) options$error else {
if (options$error && options$include) 19: 0Lmclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed, else 2L mc.silent = silent, mc.cores = cores) }, output_handler = knit_handlers(options$render, options)))
20: 43: e$fun(obj, substitute(ex), parent.frame(), e$data)eng_r(options)
44: 21: block_exec(params)foreach::foreach(chain = 1:nchains, .combine = list, .multicombine = TRUE,
.maxcombine = ifelse(nchains >= 2, nchains, 2)) %dopar% {45: seed_chain = if (!is.null(seed)) call_block(x) seed + chain
else NULL46: return(switch(model, Multi_Laplace = {process_group(group) multi_laplace_mcmc(X, Y, intercept = !standardize, h = extra_parameters$h,
v = extra_parameters$v, nburn = nburn, npost = npost, 47: seed = seed_chain, verbose = output_verbose, printevery = printevery, chain_index = chain)withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), }, Horseshoe = { error = function(e) { horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn, if (progress && is.function(pb$interrupt)) pb$interrupt() npost = npost, seed = seed_chain, verbose = output_verbose, if (is_R_CMD_build() || is_R_CMD_check()) printevery = printevery, chain_index = chain) error <<- format(e) }, ARD = { })
ARD_mcmc(X, Y, intercept = !standardize, nburn = nburn, 48: npost = npost, seed = seed_chain, verbose = output_verbose, with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), printevery = printevery, chain_index = chain) error = function(e) { if (progress && is.function(pb$interrupt)) }, Spike_Laplace = { pb$interrupt() spike_laplace_partially_mcmc(X, Y, intercept = !standardize, a = extra_parameters$a, b = extra_parameters$b, nburn = nburn, if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) npost = npost, seed = seed_chain, verbose = output_verbose, }), list(rlang_trace_top_env = knit_global())) printevery = printevery, chain_index = chain)
}))49: }xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {22: if (progress && is.function(pb$interrupt)) withCallingHandlers(expr, warning = function(w) if (inherits(w, pb$interrupt() classes)) tryInvokeRestart("muffleWarning")) if (is_R_CMD_build() || is_R_CMD_check())
error <<- format(e)23: }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd)suppressWarnings(foreach::foreach(chain = 1:nchains, .combine = list, write_utf8(res, output %n% stdout()) .multicombine = TRUE, .maxcombine = ifelse(nchains >= 2, paste0("\nQuitting from ", loc, if (!is.null(error)) nchains, 2)) %dopar% { paste0("\n", rule(), error, "\n", rule())) seed_chain = if (!is.null(seed)) }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) seed + chain
else NULL50: return(switch(model, Multi_Laplace = {process_file(text, output) multi_laplace_mcmc(X, Y, intercept = !standardize, h = extra_parameters$h,
v = extra_parameters$v, nburn = nburn, npost = npost, 51: seed = seed_chain, verbose = output_verbose, printevery = printevery, knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) chain_index = chain)
52: }, Horseshoe = {rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn, npost = npost, seed = seed_chain, verbose = output_verbose, output_dir = getwd(), ...) printevery = printevery, chain_index = chain)
}, ARD = {53: ARD_mcmc(X, Y, intercept = !standardize, nburn = nburn, vweave_rmarkdown(...) npost = npost, seed = seed_chain, verbose = output_verbose,
printevery = printevery, chain_index = chain)54: }, Spike_Laplace = {engine$weave(file, quiet = quiet, encoding = enc) spike_laplace_partially_mcmc(X, Y, intercept = !standardize,
55: a = extra_parameters$a, b = extra_parameters$b, nburn = nburn, doTryCatch(return(expr), name, parentenv, handler) npost = npost, seed = seed_chain, verbose = output_verbose,
printevery = printevery, chain_index = chain)56: }))})tryCatchOne(expr, names, parentenv, handlers[[1L]])
24: 57: BMI_LASSO(data$data_MI$X, data$data_MI$Y, model = "Horseshoe", tryCatchList(expr, classes, parentenv, handlers)
nburn = 4000, npost = 4000, output_verbose = FALSE, nchains = 2, 58: ncores = 2, seed = seed)tryCatch({
engine$weave(file, quiet = quiet, encoding = enc)25: setwd(startdir)eval(expr, envir)
output <- find_vignette_product(name, by = "weave", engine = engine)26: if (!have.makefile && vignette_is_tex(output)) {eval(expr, envir) texi2pdf(file = output, clean = FALSE, quiet = quiet)
output <- find_vignette_product(name, by = "texi2pdf", 27: engine = engine)withVisible(eval(expr, envir)) }
outputs <- c(outputs, output)28: }, error = function(e) {withCallingHandlers(code, error = function (e) thisOK <<- FALSErlang::entrace(e), message = function (cnd) fails <<- c(fails, file){ watcher$capture_plot_and_output() message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", if (on_message$capture) { file, conditionMessage(e))) watcher$push(cnd)}) }
if (on_message$silence) {59: invokeRestart("muffleMessage")tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/BMIselect.Rcheck/vign_test/BMIselect", }}, warning = function (cnd) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpkMfhZH/file1346b61c8e03a.rds")
{An irrecoverable exception occurred. R is aborting now ...
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)})
29: eval(call)
30: eval(call)
31: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
32: doWithOneRestart(return(expr), restart)
33: withOneRestart(expr, restarts[[1L]])
34: withRestartList(expr, restarts[-nr])
35: doWithOneRestart(return(expr), restart)
36: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
37: withRestartList(expr, restarts)
38: withRestarts(with_handlers({ for (expr in tle$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)
39: evaluate::evaluate(...)
40: 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$render, options))
41: in_dir(input_dir(), expr)
42: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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)))
43: eng_r(options)
44: block_exec(params)
45: call_block(x)
46: process_group(group)
47: 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) })
48: 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()))
49: 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)
50: process_file(text, output)
51: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
52: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
53: vweave_rmarkdown(...)
54: engine$weave(file, quiet = quiet, encoding = enc)
55: doTryCatch(return(expr), name, parentenv, handler)
56: tryCatchOne(expr, names, parentenv, handlers[[1L]])
57: tryCatchList(expr, classes, parentenv, handlers)
58: tryCatch({ engine$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)))})
59: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/BMIselect.Rcheck/vign_test/BMIselect", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpkMfhZH/file1346b61c8e03a.rds")
An irrecoverable exception occurred. R is aborting now ...
Quitting from Introduction.Rmd:174-189 [unnamed-chunk-6]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `apply()`:
! dim(X) must have a positive length
---
Backtrace:
▆
1. └─BMIselect::BMI_LASSO(...)
2. └─base::lapply(...)
3. └─BMIselect (local) FUN(X[[i]], ...)
4. ├─base::unique(...)
5. ├─base::t(...)
6. └─base::sapply(...)
7. └─base::lapply(X = X, FUN = FUN, ...)
8. └─BMIselect (local) FUN(X[[i]], ...)
9. └─base::apply(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
dim(X) must have a positive length
--- failed re-building ‘Introduction.Rmd’
SUMMARY: processing the following file failed:
‘Introduction.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-macos-arm64