Last updated on 2026-09-23 16:51:00 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.9 | 72.29 | 186.55 | 258.84 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.0.9 | 57.17 | 144.42 | 201.59 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.0.9 | 54.00 | 129.32 | 183.32 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.0.9 | 66.00 | 141.02 | 207.02 | OK | |
| r-devel-windows-x86_64 | 1.0.9 | 88.00 | 313.00 | 401.00 | OK | |
| r-patched-linux-x86_64 | 1.0.9 | 74.22 | 182.74 | 256.96 | OK | |
| r-release-linux-x86_64 | 1.0.9 | 76.25 | 184.95 | 261.20 | 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 | ERROR | ||||
| r-oldrel-macos-x86_64 | 1.0.9 | 52.00 | 206.00 | 258.00 | OK | |
| r-oldrel-windows-x86_64 | 1.0.9 | 118.00 | 301.00 | 419.00 | 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)
Traceback:
1: dcall <- deparse(call, nlines = 1L)cpp_horseshoe(X, Y, intercept, as.integer(nburn), as.integer(npost), prefix <- paste("Error in", dcall, ": ") seed, verbose, as.integer(printevery), as.integer(chain_index))
LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] 2: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn, npost = npost, seed = seed_chain, verbose = output_verbose, w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) printevery = printevery, chain_index = chain)
prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " 3: eval(c.expr, envir = args, enclos = envir) msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L]))
4: if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile)eval(c.expr, envir = args, enclos = envir) .Internal(printDeferredWarnings())
} 5: invisible(structure(msg, class = "try-error", condition = e))doTryCatch(return(expr), name, parentenv, handler)})
6: 15: tryCatchOne(expr, names, parentenv, handlers[[1L]])try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
16: 7: tryCatchList(expr, classes, parentenv, handlers)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
8: 17: tryCatch(eval(c.expr, envir = args, enclos = envir), error = function(e) e)FUN(X[[i]], ...)
9: FUN(X[[i]], ...)18:
lapply(seq_len(cores), inner.do)10:
lapply(X = S, FUN = FUN, ...)19:
mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed, 11: mc.silent = silent, mc.cores = cores)doTryCatch(return(expr), name, parentenv, handler)
20: 12: e$fun(obj, substitute(ex), parent.frame(), e$data)tryCatchOne(expr, names, parentenv, handlers[[1L]])
21: 13: foreach::foreach(chain = 1:nchains, .combine = list, .multicombine = TRUE, tryCatchList(expr, classes, parentenv, handlers) .maxcombine = ifelse(nchains >= 2, nchains, 2)) %dopar% {
seed_chain = if (!is.null(seed)) 14: seed + chaintryCatch(expr, error = function(e) { else NULL call <- conditionCall(e) return(switch(model, Multi_Laplace = { if (!is.null(call)) { multi_laplace_mcmc(X, Y, intercept = !standardize, h = extra_parameters$h, if (identical(call[[1L]], quote(doTryCatch))) v = extra_parameters$v, nburn = nburn, npost = npost, call <- sys.call(-4L) seed = seed_chain, verbose = output_verbose, printevery = printevery, dcall <- deparse(call, nlines = 1L) chain_index = chain) prefix <- paste("Error in", dcall, ": ") }, Horseshoe = { LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn, if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], npost = npost, seed = seed_chain, verbose = output_verbose, type = "b") if (w > LONG) printevery = printevery, chain_index = chain) prefix <- paste0(prefix, "\n ") }, ARD = { } ARD_mcmc(X, Y, intercept = !standardize, nburn = nburn, else prefix <- "Error : " npost = npost, seed = seed_chain, verbose = output_verbose, msg <- paste0(prefix, conditionMessage(e), "\n") printevery = printevery, chain_index = chain) .Internal(seterrmessage(msg[1L])) }, Spike_Laplace = { if (!silent && isTRUE(getOption("show.error.messages"))) { spike_laplace_partially_mcmc(X, Y, intercept = !standardize, cat(msg, file = outFile) a = extra_parameters$a, b = extra_parameters$b, nburn = nburn, .Internal(printDeferredWarnings()) npost = npost, seed = seed_chain, verbose = output_verbose, } printevery = printevery, chain_index = chain) invisible(structure(msg, class = "try-error", condition = e)) }))})}
15: 22: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)withCallingHandlers(expr, warning = function(w) if (inherits(w,
classes)) tryInvokeRestart("muffleWarning"))16:
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))23:
17: suppressWarnings(foreach::foreach(chain = 1:nchains, .combine = list, FUN(X[[i]], ...) .multicombine = TRUE, .maxcombine = ifelse(nchains >= 2,
nchains, 2)) %dopar% {18: seed_chain = if (!is.null(seed)) lapply(seq_len(cores), inner.do) seed + chain
else NULL19: return(switch(model, Multi_Laplace = {mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed, multi_laplace_mcmc(X, Y, intercept = !standardize, h = extra_parameters$h, mc.silent = silent, mc.cores = cores) v = extra_parameters$v, nburn = nburn, npost = npost,
seed = seed_chain, verbose = output_verbose, printevery = printevery, 20: chain_index = chain)e$fun(obj, substitute(ex), parent.frame(), e$data) }, Horseshoe = {
21: horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn, foreach::foreach(chain = 1:nchains, .combine = list, .multicombine = TRUE, .maxcombine = ifelse(nchains >= 2, nchains, 2)) %dopar% { seed_chain = if (!is.null(seed)) npost = npost, seed = seed_chain, verbose = output_verbose, seed + chain printevery = printevery, chain_index = chain) }, ARD = { else NULL ARD_mcmc(X, Y, intercept = !standardize, nburn = nburn, return(switch(model, Multi_Laplace = { npost = npost, seed = seed_chain, verbose = output_verbose, multi_laplace_mcmc(X, Y, intercept = !standardize, h = extra_parameters$h, printevery = printevery, chain_index = chain) v = extra_parameters$v, nburn = nburn, npost = npost, }, Spike_Laplace = { seed = seed_chain, verbose = output_verbose, printevery = printevery, spike_laplace_partially_mcmc(X, Y, intercept = !standardize, chain_index = chain) a = extra_parameters$a, b = extra_parameters$b, nburn = nburn, }, Horseshoe = { npost = npost, seed = seed_chain, verbose = output_verbose, horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn, printevery = printevery, chain_index = chain) 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, 24: printevery = printevery, chain_index = chain)BMI_LASSO(data$data_MI$X, data$data_MI$Y, model = "Horseshoe", }, Spike_Laplace = { nburn = 4000, npost = 4000, output_verbose = FALSE, nchains = 2, spike_laplace_partially_mcmc(X, Y, intercept = !standardize, ncores = 2, seed = seed) a = extra_parameters$a, b = extra_parameters$b, nburn = nburn,
npost = npost, seed = seed_chain, verbose = output_verbose, 25: printevery = printevery, chain_index = chain)eval(expr, envir) }))
}26:
eval(expr, envir)22:
withCallingHandlers(expr, warning = function(w) if (inherits(w, 27: classes)) tryInvokeRestart("muffleWarning"))withVisible(eval(expr, envir))
23: 28: suppressWarnings(foreach::foreach(chain = 1:nchains, .combine = list, withCallingHandlers(code, error = function (e) .multicombine = TRUE, .maxcombine = ifelse(nchains >= 2, rlang::entrace(e), message = function (cnd) nchains, 2)) %dopar% {{ watcher$capture_plot_and_output() seed_chain = if (!is.null(seed)) if (on_message$capture) { seed + chain watcher$push(cnd) else NULL } return(switch(model, Multi_Laplace = { if (on_message$silence) { multi_laplace_mcmc(X, Y, intercept = !standardize, h = extra_parameters$h, invokeRestart("muffleMessage") v = extra_parameters$v, nburn = nburn, npost = npost, } seed = seed_chain, verbose = output_verbose, printevery = printevery, }, warning = function (cnd) chain_index = chain){ }, Horseshoe = { if (getOption("warn") >= 2 || getOption("warn") < 0) { horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn, return() npost = npost, seed = seed_chain, verbose = output_verbose, } printevery = printevery, chain_index = chain) watcher$capture_plot_and_output() }, ARD = { ARD_mcmc(X, Y, intercept = !standardize, nburn = nburn, if (on_warning$capture) { npost = npost, seed = seed_chain, verbose = output_verbose, cnd <- sanitize_call(cnd) printevery = printevery, chain_index = chain) watcher$push(cnd) }, Spike_Laplace = { } spike_laplace_partially_mcmc(X, Y, intercept = !standardize, if (on_warning$silence) { a = extra_parameters$a, b = extra_parameters$b, nburn = nburn, invokeRestart("muffleWarning") npost = npost, seed = seed_chain, verbose = output_verbose, printevery = printevery, chain_index = chain) } }))}, error = function (cnd) }){
watcher$capture_plot_and_output()24: cnd <- sanitize_call(cnd)BMI_LASSO(data$data_MI$X, data$data_MI$Y, model = "Horseshoe", watcher$push(cnd) nburn = 4000, npost = 4000, output_verbose = FALSE, nchains = 2, switch(on_error, continue = invokeRestart("eval_continue"), ncores = 2, seed = seed) stop = invokeRestart("eval_stop"), error = NULL)
})25:
eval(expr, envir)29:
eval(call)26:
eval(expr, envir)30:
27: eval(call)withVisible(eval(expr, envir))
31: 28: withCallingHandlers(code, error = function (e) with_handlers({ for (expr in tle$exprs) {rlang::entrace(e), message = function (cnd) ev <- withVisible(eval(expr, envir)){ watcher$capture_plot_and_output() watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) if (on_message$capture) { } watcher$push(cnd) TRUE }}, handlers) if (on_message$silence) {
invokeRestart("muffleMessage")32: }doWithOneRestart(return(expr), restart)}, warning = function (cnd)
{33: if (getOption("warn") >= 2 || getOption("warn") < 0) {withOneRestart(expr, restarts[[1L]]) return() }
watcher$capture_plot_and_output()34: if (on_warning$capture) {withRestartList(expr, restarts[-nr]) cnd <- sanitize_call(cnd)
watcher$push(cnd) }35: if (on_warning$silence) { invokeRestart("muffleWarning")doWithOneRestart(return(expr), restart) }
}, error = function (cnd) 36: {withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) watcher$capture_plot_and_output()
cnd <- sanitize_call(cnd)37: watcher$push(cnd)withRestartList(expr, restarts) switch(on_error, continue = invokeRestart("eval_continue"),
stop = invokeRestart("eval_stop"), error = NULL)38: })withRestarts(with_handlers({
for (expr in tle$exprs) {29: ev <- withVisible(eval(expr, envir))eval(call) watcher$capture_plot_and_output()
watcher$print_value(ev$value, ev$visible, envir)30: }eval(call) TRUE
}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)31:
with_handlers({39: for (expr in tle$exprs) {evaluate::evaluate(...) ev <- withVisible(eval(expr, envir))
watcher$capture_plot_and_output()40: watcher$print_value(ev$value, ev$visible, envir)evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, } keep_message = if (is.numeric(options$message)) TRUE else options$message, TRUE stop_on_error = if (is.numeric(options$error)) options$error else {}, handlers) if (options$error && options$include)
0L32: else 2LdoWithOneRestart(return(expr), restart) }, output_handler = knit_handlers(options$render, options))
33: 41: withOneRestart(expr, restarts[[1L]])
in_dir(input_dir(), expr)34:
withRestartList(expr, restarts[-nr])42:
in_input_dir(evaluate(code, envir = env, new_device = FALSE, 35: keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, doWithOneRestart(return(expr), restart) keep_message = if (is.numeric(options$message)) TRUE else options$message,
stop_on_error = if (is.numeric(options$error)) options$error else {36: if (options$error && options$include) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
0L37: else 2LwithRestartList(expr, restarts) }, 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$capture_plot_and_output()block_exec(params) watcher$print_value(ev$value, ev$visible, envir)
}45: TRUEcall_block(x)}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
46: 39: process_group(group)evaluate::evaluate(...)
47: 40: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 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, error = function(e) { stop_on_error = if (is.numeric(options$error)) options$error else { if (progress && is.function(pb$interrupt)) if (options$error && options$include) pb$interrupt() 0L if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }) else 2L
}, output_handler = knit_handlers(options$render, options))48:
with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 41: error = function(e) {in_dir(input_dir(), expr)
if (progress && is.function(pb$interrupt)) 42: pb$interrupt()in_input_dir(evaluate(code, envir = env, new_device = FALSE, if (is_R_CMD_build() || is_R_CMD_check()) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, error <<- format(e) keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { }), list(rlang_trace_top_env = knit_global())) if (options$error && options$include)
0L49: else 2Lxfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), }, output_handler = knit_handlers(options$render, options))) error = function(e) {
if (progress && is.function(pb$interrupt)) 43: pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) eng_r(options) error <<- format(e)
}), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout())44: paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))block_exec(params)
}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)45:
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$interrupt)) pb$interrupt() output_dir = getwd(), ...)
if (is_R_CMD_build() || is_R_CMD_check()) 53: error <<- format(e)vweave_rmarkdown(...) })
54:
48: engine$weave(file, quiet = quiet, encoding = enc)with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) { if (progress && is.function(pb$interrupt)) 55: doTryCatch(return(expr), name, parentenv, handler) pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) 56: error <<- format(e)tryCatchOne(expr, names, parentenv, handlers[[1L]]) }), list(rlang_trace_top_env = knit_global()))
49: 57: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {tryCatchList(expr, classes, parentenv, handlers)
if (progress && is.function(pb$interrupt)) pb$interrupt()58: if (is_R_CMD_build() || is_R_CMD_check()) tryCatch({ error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { engine$weave(file, quiet = quiet, encoding = enc) setwd(wd) write_utf8(res, output %n% stdout()) setwd(startdir) paste0("\nQuitting from ", loc, if (!is.null(error)) output <- find_vignette_product(name, by = "weave", engine = engine) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet)50: output <- find_vignette_product(name, by = "texi2pdf", process_file(text, output) engine = engine) }
51: outputs <- c(outputs, output)}, error = function(e) {knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
thisOK <<- FALSE52: fails <<- c(fails, file)rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e))) output_dir = getwd(), ...)
53: })
59: vweave_rmarkdown(...)tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/BMIselect.Rcheck/vign_test/BMIselect",
skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpH4dHUT/file15096763a955c.rds")54:
engine$weave(file, quiet = quiet, encoding = enc)An irrecoverable exception occurred. R is aborting now ...
55: doTryCatch(return(expr), name, parentenv, handler)
56: tryCatchOne(expr, names, parentenv, handlers[[1L]])
57: tryCatchList(expr, classes, parentenv, handlers)
58: tryCatch({ engine$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/RtmpH4dHUT/file15096763a955c.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