Last updated on 2026-10-05 01:52:12 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 | 58.01 | 145.78 | 203.79 | 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 | 141.36 | 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 | 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 | 119.00 | 298.00 | 417.00 | 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)
Traceback:
1: 12: cpp_horseshoe(X, Y, intercept, as.integer(nburn), as.integer(npost), tryCatchOne(expr, names, parentenv, handlers[[1L]]) seed, verbose, as.integer(printevery), as.integer(chain_index))
13:
tryCatchList(expr, classes, parentenv, handlers) 2:
horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn, 14: npost = npost, seed = seed_chain, verbose = output_verbose, tryCatch(expr, error = function(e) { printevery = printevery, chain_index = chain) call <- conditionCall(e)
3: eval(c.expr, envir = args, enclos = envir) if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch))) 4: call <- sys.call(-4L)eval(c.expr, envir = args, enclos = envir) dcall <- deparse(call, nlines = 1L)
prefix <- paste("Error in", dcall, ": ") 5: LONG <- 75LdoTryCatch(return(expr), name, parentenv, handler) sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") 6: if (is.na(w)) tryCatchOne(expr, names, parentenv, handlers[[1L]]) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b") 7: if (w > LONG) tryCatchList(expr, classes, parentenv, handlers) prefix <- paste0(prefix, "\n ")
} 8: else prefix <- "Error : "tryCatch(eval(c.expr, envir = args, enclos = envir), error = function(e) e) msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L])) 9: FUN(X[[i]], ...) if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)10: .Internal(printDeferredWarnings())lapply(X = S, FUN = FUN, ...) }
invisible(structure(msg, class = "try-error", condition = e))11: })doTryCatch(return(expr), name, parentenv, handler)
15: 12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)tryCatchOne(expr, names, parentenv, handlers[[1L]])
16: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
13: 17: tryCatchList(expr, classes, parentenv, handlers)FUN(X[[i]], ...)
14: 18: 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)19: dcall <- deparse(call, nlines = 1L)mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed, prefix <- paste("Error in", dcall, ": ") mc.silent = silent, mc.cores = cores)
LONG <- 75L20: sm <- strsplit(conditionMessage(e), "\n")[[1L]]e$fun(obj, substitute(ex), parent.frame(), e$data) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w)) 21: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], foreach::foreach(chain = 1:nchains, .combine = list, .multicombine = TRUE, type = "b") .maxcombine = ifelse(nchains >= 2, nchains, 2)) %dopar% { if (w > LONG) prefix <- paste0(prefix, "\n ") seed_chain = if (!is.null(seed)) } seed + chain else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") else NULL .Internal(seterrmessage(msg[1L])) return(switch(model, Multi_Laplace = { if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) multi_laplace_mcmc(X, Y, intercept = !standardize, h = extra_parameters$h, .Internal(printDeferredWarnings()) v = extra_parameters$v, nburn = nburn, npost = npost, } seed = seed_chain, verbose = output_verbose, printevery = printevery, invisible(structure(msg, class = "try-error", condition = e)) chain_index = chain)}) }, Horseshoe = {
horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn, 15: npost = npost, seed = seed_chain, verbose = output_verbose, try(lapply(X = S, FUN = FUN, ...), silent = TRUE) 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)16: }, Spike_Laplace = { spike_laplace_partially_mcmc(X, Y, intercept = !standardize, sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) a = extra_parameters$a, b = extra_parameters$b, nburn = nburn, npost = npost, seed = seed_chain, verbose = output_verbose,
printevery = printevery, chain_index = chain)17: }))FUN(X[[i]], ...)}
18: 22: withCallingHandlers(expr, warning = function(w) if (inherits(w, lapply(seq_len(cores), inner.do) classes)) tryInvokeRestart("muffleWarning"))
23: suppressWarnings(foreach::foreach(chain = 1:nchains, .combine = list, .multicombine = TRUE, .maxcombine = ifelse(nchains >= 2, 19: nchains, 2)) %dopar% {mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed, seed_chain = if (!is.null(seed)) mc.silent = silent, mc.cores = cores) seed + chain
else NULL20: return(switch(model, Multi_Laplace = {e$fun(obj, substitute(ex), parent.frame(), e$data) multi_laplace_mcmc(X, Y, intercept = !standardize, h = extra_parameters$h,
v = extra_parameters$v, nburn = nburn, npost = npost, 21: seed = seed_chain, verbose = output_verbose, printevery = printevery, foreach::foreach(chain = 1:nchains, .combine = list, .multicombine = TRUE, chain_index = chain) .maxcombine = ifelse(nchains >= 2, nchains, 2)) %dopar% { }, Horseshoe = { seed_chain = if (!is.null(seed)) horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn, seed + chain else NULL npost = npost, seed = seed_chain, verbose = output_verbose, return(switch(model, Multi_Laplace = { printevery = printevery, chain_index = chain) multi_laplace_mcmc(X, Y, intercept = !standardize, h = extra_parameters$h, }, ARD = { v = extra_parameters$v, nburn = nburn, npost = npost, ARD_mcmc(X, Y, intercept = !standardize, nburn = nburn, npost = npost, seed = seed_chain, verbose = output_verbose, seed = seed_chain, verbose = output_verbose, printevery = printevery, printevery = printevery, chain_index = chain) chain_index = chain) }, Spike_Laplace = { spike_laplace_partially_mcmc(X, Y, intercept = !standardize, }, Horseshoe = { a = extra_parameters$a, b = extra_parameters$b, nburn = nburn, horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn, npost = npost, seed = seed_chain, verbose = output_verbose, npost = npost, seed = seed_chain, verbose = output_verbose, printevery = printevery, chain_index = chain) 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)24: }, Spike_Laplace = { spike_laplace_partially_mcmc(X, Y, intercept = !standardize, BMI_LASSO(data$data_MI$X, data$data_MI$Y, model = "Horseshoe", a = extra_parameters$a, b = extra_parameters$b, nburn = nburn, npost = npost, seed = seed_chain, verbose = output_verbose, nburn = 4000, npost = 4000, output_verbose = FALSE, nchains = 2, printevery = printevery, chain_index = chain) ncores = 2, seed = seed) }))
}
25: 22: eval(expr, envir)withCallingHandlers(expr, warning = function(w) if (inherits(w,
classes)) tryInvokeRestart("muffleWarning"))26:
23: eval(expr, envir)suppressWarnings(foreach::foreach(chain = 1:nchains, .combine = list,
.multicombine = TRUE, .maxcombine = ifelse(nchains >= 2, 27: nchains, 2)) %dopar% {withVisible(eval(expr, envir)) seed_chain = if (!is.null(seed))
seed + chain28: else NULLwithCallingHandlers(code, error = function (e) return(switch(model, Multi_Laplace = {rlang::entrace(e), message = function (cnd) 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, watcher$capture_plot_and_output() chain_index = chain) }, Horseshoe = { if (on_message$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) { }, ARD = { invokeRestart("muffleMessage") ARD_mcmc(X, Y, intercept = !standardize, nburn = nburn, } npost = npost, seed = seed_chain, verbose = output_verbose, }, warning = function (cnd) printevery = printevery, chain_index = chain){ }, Spike_Laplace = { if (getOption("warn") >= 2 || getOption("warn") < 0) { spike_laplace_partially_mcmc(X, Y, intercept = !standardize, return() a = extra_parameters$a, b = extra_parameters$b, nburn = nburn, } npost = npost, seed = seed_chain, verbose = output_verbose, watcher$capture_plot_and_output() printevery = printevery, chain_index = chain) if (on_warning$capture) { })) cnd <- sanitize_call(cnd)}) watcher$push(cnd)
}24: if (on_warning$silence) { invokeRestart("muffleWarning")BMI_LASSO(data$data_MI$X, data$data_MI$Y, model = "Horseshoe", } nburn = 4000, npost = 4000, output_verbose = FALSE, nchains = 2, }, error = function (cnd) ncores = 2, seed = seed){
watcher$capture_plot_and_output()25: cnd <- sanitize_call(cnd)eval(expr, envir) watcher$push(cnd)
switch(on_error, continue = invokeRestart("eval_continue"), 26: stop = invokeRestart("eval_stop"), error = NULL)eval(expr, envir)})
27:
withVisible(eval(expr, envir))29:
28: eval(call)withCallingHandlers(code, error = function (e)
rlang::entrace(e), message = function (cnd) 30: eval(call){
watcher$capture_plot_and_output()31: if (on_message$capture) {with_handlers({ watcher$push(cnd) } for (expr in tle$exprs) { if (on_message$silence) { ev <- withVisible(eval(expr, envir)) invokeRestart("muffleMessage") watcher$capture_plot_and_output() } watcher$print_value(ev$value, ev$visible, envir)}, warning = function (cnd) }{ TRUE if (getOption("warn") >= 2 || getOption("warn") < 0) {}, handlers) return()
}32: watcher$capture_plot_and_output()doWithOneRestart(return(expr), restart) if (on_warning$capture) {
cnd <- sanitize_call(cnd)33: watcher$push(cnd)withOneRestart(expr, restarts[[1L]]) }
if (on_warning$silence) {34: invokeRestart("muffleWarning") }withRestartList(expr, restarts[-nr])
}, error = function (cnd) 35: {doWithOneRestart(return(expr), restart) watcher$capture_plot_and_output()
cnd <- sanitize_call(cnd)36: watcher$push(cnd)withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
29: 37: eval(call)withRestartList(expr, restarts)
30:
eval(call)38:
withRestarts(with_handlers({31: for (expr in tle$exprs) {with_handlers({ ev <- withVisible(eval(expr, envir)) for (expr in tle$exprs) { watcher$capture_plot_and_output() ev <- withVisible(eval(expr, envir)) watcher$print_value(ev$value, ev$visible, envir) watcher$capture_plot_and_output() } watcher$print_value(ev$value, ev$visible, envir) TRUE }}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) TRUE
}, handlers)39:
evaluate::evaluate(...)32:
doWithOneRestart(return(expr), restart)40:
evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 33: keep_message = if (is.numeric(options$message)) TRUE else options$message, withOneRestart(expr, restarts[[1L]]) stop_on_error = if (is.numeric(options$error)) options$error else {
if (options$error && options$include) 0L34: else 2LwithRestartList(expr, restarts[-nr]) }, output_handler = knit_handlers(options$render, options))
35: 41: doWithOneRestart(return(expr), restart)in_dir(input_dir(), expr)
36: 42: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])in_input_dir(evaluate(code, envir = env, new_device = FALSE,
keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 37: 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) withRestartList(expr, restarts) 0L else 2L
}, output_handler = knit_handlers(options$render, options)))38:
43: withRestarts(with_handlers({eng_r(options) for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir))44: watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir)block_exec(params) }
TRUE45: }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)call_block(x)
46: process_group(group)39:
evaluate::evaluate(...)47:
40: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, if (progress && is.function(pb$interrupt)) keep_message = if (is.numeric(options$message)) TRUE else options$message, pb$interrupt() stop_on_error = if (is.numeric(options$error)) options$error else { if (is_R_CMD_build() || is_R_CMD_check()) if (options$error && options$include) error <<- format(e) 0L }) else 2L
}, output_handler = knit_handlers(options$render, options))48:
with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {41: if (progress && is.function(pb$interrupt)) in_dir(input_dir(), expr) pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) 42: in_input_dir(evaluate(code, envir = env, new_device = FALSE, error <<- format(e) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, }), list(rlang_trace_top_env = knit_global())) keep_message = if (is.numeric(options$message)) TRUE else options$message,
stop_on_error = if (is.numeric(options$error)) options$error else {49: if (options$error && options$include) xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 0L error = function(e) { else 2L if (progress && is.function(pb$interrupt)) }, output_handler = knit_handlers(options$render, options))) pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) 43: error <<- format(e)eng_r(options) }), list(rlang_trace_top_env = knit_global())), function(loc) {
setwd(wd)44: write_utf8(res, output %n% stdout())block_exec(params) paste0("\nQuitting from ", loc, if (!is.null(error))
paste0("\n", rule(), error, "\n", rule()))45: }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)call_block(x)
50: process_file(text, output)46:
process_group(group)51:
knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)47:
withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 52: error = function(e) {rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), if (progress && is.function(pb$interrupt)) output_dir = getwd(), ...) pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) 53: error <<- format(e)vweave_rmarkdown(...) })
54: 48: engine$weave(file, quiet = quiet, encoding = enc)with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
55: error = function(e) {doTryCatch(return(expr), name, parentenv, handler) if (progress && is.function(pb$interrupt))
56: pb$interrupt()tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (is_R_CMD_build() || is_R_CMD_check())
error <<- format(e)57: tryCatchList(expr, classes, parentenv, handlers) }), list(rlang_trace_top_env = knit_global()))
58: 49: tryCatch({xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { engine$weave(file, quiet = quiet, encoding = enc) if (progress && is.function(pb$interrupt)) setwd(startdir) pb$interrupt() output <- find_vignette_product(name, by = "weave", engine = engine) if (is_R_CMD_build() || is_R_CMD_check()) if (!have.makefile && vignette_is_tex(output)) { error <<- format(e) texi2pdf(file = output, clean = FALSE, quiet = quiet) }), list(rlang_trace_top_env = knit_global())), function(loc) { output <- find_vignette_product(name, by = "texi2pdf", setwd(wd) engine = engine) write_utf8(res, output %n% stdout()) } paste0("\nQuitting from ", loc, if (!is.null(error)) outputs <- c(outputs, output) paste0("\n", rule(), error, "\n", rule()))}, error = function(e) {}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) thisOK <<- FALSE
fails <<- c(fails, file)50: message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", process_file(text, output) file, conditionMessage(e)))
})51:
knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)59:
tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/BMIselect.Rcheck/vign_test/BMIselect", 52: skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmprbeqc4/filee18c3faf2c5d.rds")rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
output_dir = getwd(), ...)An irrecoverable exception occurred. R is aborting now ...
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/Rtmprbeqc4/filee18c3faf2c5d.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