Last updated on 2026-09-29 06:51:33 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.9 | 81.17 | 183.62 | 264.79 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.0.9 | 56.06 | 142.78 | 198.84 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.0.9 | 53.00 | 131.74 | 184.74 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.0.9 | 66.00 | 141.36 | 207.36 | OK | |
| r-devel-windows-x86_64 | 1.0.9 | 88.00 | 311.00 | 399.00 | OK | |
| r-patched-linux-x86_64 | 1.0.9 | 77.52 | 185.85 | 263.37 | OK | |
| r-release-linux-x86_64 | 1.0.9 | 74.01 | 183.92 | 257.93 | 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 | 88.00 | 238.00 | 326.00 | OK | |
| r-oldrel-macos-arm64 | 1.0.9 | 18.00 | 61.00 | 79.00 | ERROR | |
| r-oldrel-macos-x86_64 | 1.0.9 | 52.00 | 206.00 | 258.00 | OK | |
| r-oldrel-windows-x86_64 | 1.0.9 | 114.00 | 290.00 | 404.00 | 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:
Traceback:
withCallingHandlers(code, error = function (e) 1: rlang::entrace(e), message = function (cnd) cpp_horseshoe(X, Y, intercept, as.integer(nburn), as.integer(npost), { seed, verbose, as.integer(printevery), as.integer(chain_index))
watcher$capture_plot_and_output() 2: if (on_message$capture) {horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn, watcher$push(cnd) npost = npost, seed = seed_chain, verbose = output_verbose, } printevery = printevery, chain_index = chain) if (on_message$silence) {
invokeRestart("muffleMessage") 3: }}, warning = function (cnd) eval(c.expr, envir = args, enclos = envir){
if (getOption("warn") >= 2 || getOption("warn") < 0) { 4: return()eval(c.expr, envir = args, enclos = envir) }
watcher$capture_plot_and_output() 5: if (on_warning$capture) {doTryCatch(return(expr), name, parentenv, handler) cnd <- sanitize_call(cnd) watcher$push(cnd)
} 6: if (on_warning$silence) {tryCatchOne(expr, names, parentenv, handlers[[1L]])
invokeRestart("muffleWarning") 7: }tryCatchList(expr, classes, parentenv, handlers)}, error = function (cnd)
{ 8: tryCatch(eval(c.expr, envir = args, enclos = envir), error = function(e) e) watcher$capture_plot_and_output()
cnd <- sanitize_call(cnd) 9: FUN(X[[i]], ...) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"),
stop = invokeRestart("eval_stop"), error = NULL)})10:
lapply(X = S, FUN = FUN, ...)29:
11: eval(call)doTryCatch(return(expr), name, parentenv, handler)
30: 12: eval(call)tryCatchOne(expr, names, parentenv, handlers[[1L]])
31: 13: with_handlers({tryCatchList(expr, classes, parentenv, handlers) for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir))14: watcher$capture_plot_and_output()tryCatch(expr, error = function(e) { watcher$print_value(ev$value, ev$visible, envir) call <- conditionCall(e) } if (!is.null(call)) { TRUE if (identical(call[[1L]], quote(doTryCatch))) }, handlers) call <- sys.call(-4L)
32: doWithOneRestart(return(expr), restart) dcall <- deparse(call, nlines = 1L)
prefix <- paste("Error in", dcall, ": ")33: LONG <- 75LwithOneRestart(expr, restarts[[1L]])
sm <- strsplit(conditionMessage(e), "\n")[[1L]]34: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")withRestartList(expr, restarts[-nr]) if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 35: type = "b")doWithOneRestart(return(expr), restart) if (w > LONG)
prefix <- paste0(prefix, "\n ")36: }withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")37: .Internal(seterrmessage(msg[1L]))withRestartList(expr, restarts) if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)38: .Internal(printDeferredWarnings())withRestarts(with_handlers({ } for (expr in tle$exprs) { invisible(structure(msg, class = "try-error", condition = e)) ev <- withVisible(eval(expr, envir))}) watcher$capture_plot_and_output()
watcher$print_value(ev$value, ev$visible, envir)15: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) }
TRUE16: }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
39: 17: evaluate::evaluate(...)FUN(X[[i]], ...)
40: 18: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, lapply(seq_len(cores), inner.do) keep_message = if (is.numeric(options$message)) TRUE else options$message,
stop_on_error = if (is.numeric(options$error)) options$error else {19: if (options$error && options$include) mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed, 0L mc.silent = silent, mc.cores = cores) else 2L
}, output_handler = knit_handlers(options$render, options))20:
e$fun(obj, substitute(ex), parent.frame(), e$data)41:
in_dir(input_dir(), expr)21:
foreach::foreach(chain = 1:nchains, .combine = list, .multicombine = TRUE, 42: .maxcombine = ifelse(nchains >= 2, nchains, 2)) %dopar% {in_input_dir(evaluate(code, envir = env, new_device = FALSE, seed_chain = if (!is.null(seed)) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, seed + chain keep_message = if (is.numeric(options$message)) TRUE else options$message, else NULL stop_on_error = if (is.numeric(options$error)) options$error else { return(switch(model, Multi_Laplace = { if (options$error && options$include) multi_laplace_mcmc(X, Y, intercept = !standardize, h = extra_parameters$h, 0L v = extra_parameters$v, nburn = nburn, npost = npost, else 2L seed = seed_chain, verbose = output_verbose, printevery = printevery, }, output_handler = knit_handlers(options$render, options))) chain_index = chain)
}, Horseshoe = {43: horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn, eng_r(options) npost = npost, seed = seed_chain, verbose = output_verbose,
printevery = printevery, chain_index = chain)44: }, ARD = {block_exec(params) ARD_mcmc(X, Y, intercept = !standardize, nburn = nburn,
npost = npost, seed = seed_chain, verbose = output_verbose, 45: printevery = printevery, chain_index = chain)call_block(x) }, Spike_Laplace = {
spike_laplace_partially_mcmc(X, Y, intercept = !standardize, 46: a = extra_parameters$a, b = extra_parameters$b, nburn = nburn, process_group(group) npost = npost, seed = seed_chain, verbose = output_verbose,
printevery = printevery, chain_index = chain)47: }))withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), } error = function(e) {
if (progress && is.function(pb$interrupt)) 22: pb$interrupt()withCallingHandlers(expr, warning = function(w) if (inherits(w, if (is_R_CMD_build() || is_R_CMD_check()) classes)) tryInvokeRestart("muffleWarning")) error <<- format(e)
23: })
suppressWarnings(foreach::foreach(chain = 1:nchains, .combine = list, .multicombine = TRUE, .maxcombine = ifelse(nchains >= 2, 48: nchains, 2)) %dopar% {with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), seed_chain = if (!is.null(seed)) error = function(e) { seed + chain if (progress && is.function(pb$interrupt)) else NULL pb$interrupt() return(switch(model, Multi_Laplace = { if (is_R_CMD_build() || is_R_CMD_check()) multi_laplace_mcmc(X, Y, intercept = !standardize, h = extra_parameters$h, error <<- format(e) v = extra_parameters$v, nburn = nburn, npost = npost, }), list(rlang_trace_top_env = knit_global())) seed = seed_chain, verbose = output_verbose, printevery = printevery,
chain_index = chain)49: }, Horseshoe = {xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn, error = function(e) { npost = npost, seed = seed_chain, verbose = output_verbose, if (progress && is.function(pb$interrupt)) printevery = printevery, chain_index = chain) }, ARD = { pb$interrupt() ARD_mcmc(X, Y, intercept = !standardize, nburn = nburn, if (is_R_CMD_build() || is_R_CMD_check()) npost = npost, seed = seed_chain, verbose = output_verbose, error <<- format(e) printevery = printevery, chain_index = chain) }), list(rlang_trace_top_env = knit_global())), function(loc) { }, Spike_Laplace = { setwd(wd) spike_laplace_partially_mcmc(X, Y, intercept = !standardize, write_utf8(res, output %n% stdout()) a = extra_parameters$a, b = extra_parameters$b, nburn = nburn, paste0("\nQuitting from ", loc, if (!is.null(error)) npost = npost, seed = seed_chain, verbose = output_verbose, paste0("\n", rule(), error, "\n", rule())) printevery = printevery, chain_index = chain)}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) }))
})50:
process_file(text, output)24:
BMI_LASSO(data$data_MI$X, data$data_MI$Y, model = "Horseshoe", 51: nburn = 4000, npost = 4000, output_verbose = FALSE, nchains = 2, knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) ncores = 2, seed = seed)
25: 52: eval(expr, envir)rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
output_dir = getwd(), ...)26:
eval(expr, envir)53:
vweave_rmarkdown(...)27:
withVisible(eval(expr, envir))54:
engine$weave(file, quiet = quiet, encoding = enc)28:
withCallingHandlers(code, error = function (e) 55: rlang::entrace(e), message = function (cnd) doTryCatch(return(expr), name, parentenv, handler){
watcher$capture_plot_and_output()56: if (on_message$capture) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) watcher$push(cnd)
}57: if (on_message$silence) {tryCatchList(expr, classes, parentenv, handlers) invokeRestart("muffleMessage")
}58: }, warning = function (cnd) tryCatch({{ engine$weave(file, quiet = quiet, encoding = enc) if (getOption("warn") >= 2 || getOption("warn") < 0) { setwd(startdir) return() output <- find_vignette_product(name, by = "weave", engine = engine) } if (!have.makefile && vignette_is_tex(output)) { watcher$capture_plot_and_output() texi2pdf(file = output, clean = FALSE, quiet = quiet) if (on_warning$capture) { output <- find_vignette_product(name, by = "texi2pdf", cnd <- sanitize_call(cnd) engine = engine) watcher$push(cnd) } } outputs <- c(outputs, output) if (on_warning$silence) {}, error = function(e) { invokeRestart("muffleWarning") thisOK <<- FALSE } fails <<- c(fails, file)}, error = function (cnd) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", { file, conditionMessage(e))) watcher$capture_plot_and_output()}) cnd <- sanitize_call(cnd)
watcher$push(cnd)59: switch(on_error, continue = invokeRestart("eval_continue"), tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/BMIselect.Rcheck/vign_test/BMIselect", stop = invokeRestart("eval_stop"), error = NULL) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpafH4ZQ/file17b5a7bd4ca3.rds")})
An irrecoverable exception occurred. R is aborting now ...
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/RtmpafH4ZQ/file17b5a7bd4ca3.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