Last updated on 2026-10-01 05:01:46 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.9 | 75.96 | 187.06 | 263.02 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.0.9 | 57.90 | 144.46 | 202.36 | 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 | 85.21 | 185.68 | 270.89 | 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 | 87.00 | 232.00 | 319.00 | OK | |
| r-oldrel-macos-arm64 | 1.0.9 | 19.00 | 55.00 | 74.00 | 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: 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$capture_plot_and_output()
if (on_warning$capture) { 2: cnd <- sanitize_call(cnd)horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn, watcher$push(cnd) npost = npost, seed = seed_chain, verbose = output_verbose, } printevery = printevery, chain_index = chain) if (on_warning$silence) {
invokeRestart("muffleWarning") 3: }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) switch(on_error, continue = invokeRestart("eval_continue"), 5: doTryCatch(return(expr), name, parentenv, handler) stop = invokeRestart("eval_stop"), error = NULL)
}) 6:
tryCatchOne(expr, names, parentenv, handlers[[1L]])29:
eval(call) 7:
tryCatchList(expr, classes, parentenv, handlers)30:
eval(call) 8:
tryCatch(eval(c.expr, envir = args, enclos = envir), error = function(e) e)31:
with_handlers({ for (expr in tle$exprs) { 9: ev <- withVisible(eval(expr, envir))FUN(X[[i]], ...) watcher$capture_plot_and_output()
watcher$print_value(ev$value, ev$visible, envir)10: }lapply(X = S, FUN = FUN, ...) TRUE
}, handlers)
11: 32: doWithOneRestart(return(expr), restart)
doTryCatch(return(expr), name, parentenv, handler)33:
withOneRestart(expr, restarts[[1L]])
12: 34: tryCatchOne(expr, names, parentenv, handlers[[1L]])withRestartList(expr, restarts[-nr])
13: 35: tryCatchList(expr, classes, parentenv, handlers)doWithOneRestart(return(expr), restart)
14: 36: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])tryCatch(expr, error = function(e) {
call <- conditionCall(e)37: if (!is.null(call)) {withRestartList(expr, restarts) if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L)
dcall <- deparse(call, nlines = 1L)38: prefix <- paste("Error in", dcall, ": ")withRestarts(with_handlers({ LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] for (expr in tle$exprs) { w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") ev <- withVisible(eval(expr, envir)) if (is.na(w)) watcher$capture_plot_and_output() w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], watcher$print_value(ev$value, ev$visible, envir) type = "b") if (w > LONG) } prefix <- paste0(prefix, "\n ") TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) }
else prefix <- "Error : "39: msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L]))evaluate::evaluate(...) if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)40: .Internal(printDeferredWarnings())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 { invisible(structure(msg, class = "try-error", condition = e)) if (options$error && options$include) 0L}) else 2L
}, output_handler = knit_handlers(options$render, options))15:
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)41:
16: in_dir(input_dir(), expr)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
42:
in_input_dir(evaluate(code, envir = env, new_device = FALSE, 17: keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, FUN(X[[i]], ...)
keep_message = if (is.numeric(options$message)) TRUE else options$message, 18: stop_on_error = if (is.numeric(options$error)) options$error else {lapply(seq_len(cores), inner.do) if (options$error && options$include)
0L19: else 2Lmclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed, }, output_handler = knit_handlers(options$render, options))) mc.silent = silent, mc.cores = cores)
43: 20: eng_r(options)e$fun(obj, substitute(ex), parent.frame(), e$data)
44:
block_exec(params)21:
foreach::foreach(chain = 1:nchains, .combine = list, .multicombine = TRUE, 45: .maxcombine = ifelse(nchains >= 2, nchains, 2)) %dopar% {call_block(x)
seed_chain = if (!is.null(seed)) 46: seed + chainprocess_group(group) else NULL
return(switch(model, Multi_Laplace = {47: multi_laplace_mcmc(X, Y, intercept = !standardize, h = extra_parameters$h, withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), v = extra_parameters$v, nburn = nburn, npost = npost, error = function(e) { seed = seed_chain, verbose = output_verbose, printevery = printevery, if (progress && is.function(pb$interrupt)) chain_index = chain) pb$interrupt() }, Horseshoe = { if (is_R_CMD_build() || is_R_CMD_check()) horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn, error <<- format(e) npost = npost, seed = seed_chain, verbose = output_verbose, }) printevery = printevery, chain_index = chain)
}, ARD = {48: ARD_mcmc(X, Y, intercept = !standardize, nburn = nburn, 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) { }, Spike_Laplace = { if (progress && is.function(pb$interrupt)) spike_laplace_partially_mcmc(X, Y, intercept = !standardize, pb$interrupt() a = extra_parameters$a, b = extra_parameters$b, 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())) }))
}49:
xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 22: error = function(e) {withCallingHandlers(expr, warning = function(w) if (inherits(w, if (progress && is.function(pb$interrupt)) classes)) tryInvokeRestart("muffleWarning")) pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) 23: error <<- format(e)suppressWarnings(foreach::foreach(chain = 1:nchains, .combine = list, }), list(rlang_trace_top_env = knit_global())), function(loc) { .multicombine = TRUE, .maxcombine = ifelse(nchains >= 2, setwd(wd) nchains, 2)) %dopar% { write_utf8(res, output %n% stdout()) seed_chain = if (!is.null(seed)) paste0("\nQuitting from ", loc, if (!is.null(error)) seed + chain paste0("\n", rule(), error, "\n", rule())) else NULL}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) return(switch(model, Multi_Laplace = {
multi_laplace_mcmc(X, Y, intercept = !standardize, h = extra_parameters$h, 50: v = extra_parameters$v, nburn = nburn, npost = npost, process_file(text, output) seed = seed_chain, verbose = output_verbose, printevery = printevery,
chain_index = chain)51: }, Horseshoe = {knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn,
52: npost = npost, seed = seed_chain, verbose = output_verbose, rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), printevery = printevery, chain_index = chain) output_dir = getwd(), ...) }, ARD = {
ARD_mcmc(X, Y, intercept = !standardize, nburn = nburn, 53: npost = npost, seed = seed_chain, verbose = output_verbose, vweave_rmarkdown(...) printevery = printevery, chain_index = chain)
}, Spike_Laplace = {54: spike_laplace_partially_mcmc(X, Y, intercept = !standardize, engine$weave(file, quiet = quiet, encoding = enc) a = extra_parameters$a, b = extra_parameters$b, nburn = nburn,
npost = npost, seed = seed_chain, verbose = output_verbose, 55: printevery = printevery, chain_index = chain)doTryCatch(return(expr), name, parentenv, handler) }))
})56:
tryCatchOne(expr, names, parentenv, handlers[[1L]])24:
BMI_LASSO(data$data_MI$X, data$data_MI$Y, model = "Horseshoe", 57: nburn = 4000, npost = 4000, output_verbose = FALSE, nchains = 2, tryCatchList(expr, classes, parentenv, handlers) ncores = 2, seed = seed)
58: 25: tryCatch({eval(expr, envir) engine$weave(file, quiet = quiet, encoding = enc)
setwd(startdir)26: output <- find_vignette_product(name, by = "weave", engine = engine)eval(expr, envir) if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet)27: output <- find_vignette_product(name, by = "texi2pdf", withVisible(eval(expr, envir)) engine = engine)
}28: outputs <- c(outputs, output)withCallingHandlers(code, error = function (e) }, error = function(e) {rlang::entrace(e), message = function (cnd) thisOK <<- FALSE{ fails <<- c(fails, file) watcher$capture_plot_and_output() message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e))) if (on_message$capture) {}) watcher$push(cnd)
}59: if (on_message$silence) { invokeRestart("muffleMessage")tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/BMIselect.Rcheck/vign_test/BMIselect", } skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp32Lohg/file10a812148b375.rds")}, warning = function (cnd)
{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/Rtmp32Lohg/file10a812148b375.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