Last updated on 2026-09-26 18:51:31 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 | 58.42 | 143.10 | 201.52 | 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 | 141.02 | 207.02 | 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 | 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 | 22.00 | 59.00 | 81.00 | ERROR | |
| r-oldrel-macos-x86_64 | 1.0.9 | 52.00 | 206.00 | 258.00 | OK | |
| r-oldrel-windows-x86_64 | 1.0.9 | 115.00 | 293.00 | 408.00 | 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))
Traceback:
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 1: type = "b")cpp_horseshoe(X, Y, intercept, as.integer(nburn), as.integer(npost), seed, verbose, as.integer(printevery), as.integer(chain_index)) if (w > LONG)
prefix <- paste0(prefix, "\n ") 2: }horseshoe_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]))
if (!silent && isTRUE(getOption("show.error.messages"))) { 3: cat(msg, file = outFile)eval(c.expr, envir = args, enclos = envir) .Internal(printDeferredWarnings())
} 4: invisible(structure(msg, class = "try-error", condition = e))eval(c.expr, envir = args, enclos = envir)})
5: 15: doTryCatch(return(expr), name, parentenv, handler)try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
6: 16: tryCatchOne(expr, names, parentenv, handlers[[1L]])sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
7: 17: tryCatchList(expr, classes, parentenv, handlers)FUN(X[[i]], ...)
8: 18: tryCatch(eval(c.expr, envir = args, enclos = envir), error = function(e) e)lapply(seq_len(cores), inner.do)
9: 19: FUN(X[[i]], ...)mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed,
mc.silent = silent, mc.cores = cores)10:
lapply(X = S, FUN = FUN, ...)20:
e$fun(obj, substitute(ex), parent.frame(), e$data)11:
doTryCatch(return(expr), name, parentenv, handler)21:
foreach::foreach(chain = 1:nchains, .combine = list, .multicombine = TRUE, 12: .maxcombine = ifelse(nchains >= 2, nchains, 2)) %dopar% {tryCatchOne(expr, names, parentenv, handlers[[1L]]) seed_chain = if (!is.null(seed))
seed + chain else NULL13: return(switch(model, Multi_Laplace = {tryCatchList(expr, classes, parentenv, handlers) multi_laplace_mcmc(X, Y, intercept = !standardize, h = extra_parameters$h,
v = extra_parameters$v, nburn = nburn, npost = npost, 14: seed = seed_chain, verbose = output_verbose, printevery = printevery, tryCatch(expr, error = function(e) { chain_index = chain) call <- conditionCall(e) }, Horseshoe = { if (!is.null(call)) { horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn, if (identical(call[[1L]], quote(doTryCatch))) npost = npost, seed = seed_chain, verbose = output_verbose, call <- sys.call(-4L) printevery = printevery, chain_index = chain) dcall <- deparse(call, nlines = 1L) }, ARD = { prefix <- paste("Error in", dcall, ": ") ARD_mcmc(X, Y, intercept = !standardize, nburn = nburn, LONG <- 75L npost = npost, seed = seed_chain, verbose = output_verbose, sm <- strsplit(conditionMessage(e), "\n")[[1L]] printevery = printevery, chain_index = chain) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") }, Spike_Laplace = { if (is.na(w)) spike_laplace_partially_mcmc(X, Y, intercept = !standardize, w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], a = extra_parameters$a, b = extra_parameters$b, nburn = nburn, type = "b") npost = npost, seed = seed_chain, verbose = output_verbose, if (w > LONG) printevery = printevery, chain_index = chain) prefix <- paste0(prefix, "\n ") })) }}
else prefix <- "Error : "22: msg <- paste0(prefix, conditionMessage(e), "\n")withCallingHandlers(expr, warning = function(w) if (inherits(w, .Internal(seterrmessage(msg[1L])) classes)) tryInvokeRestart("muffleWarning")) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile)
.Internal(printDeferredWarnings())23: }suppressWarnings(foreach::foreach(chain = 1:nchains, .combine = list, invisible(structure(msg, class = "try-error", condition = e)) .multicombine = TRUE, .maxcombine = ifelse(nchains >= 2, }) nchains, 2)) %dopar% { seed_chain = if (!is.null(seed))
seed + chain15: else NULLtry(lapply(X = S, FUN = FUN, ...), silent = TRUE) return(switch(model, Multi_Laplace = {
multi_laplace_mcmc(X, Y, intercept = !standardize, h = extra_parameters$h, 16: v = extra_parameters$v, nburn = nburn, npost = npost, sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) seed = seed_chain, verbose = output_verbose, printevery = printevery,
chain_index = chain)17: }, Horseshoe = {FUN(X[[i]], ...) horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn,
npost = npost, seed = seed_chain, verbose = output_verbose, 18: printevery = printevery, chain_index = chain)lapply(seq_len(cores), inner.do) }, ARD = {
ARD_mcmc(X, Y, intercept = !standardize, nburn = nburn, 19: npost = npost, seed = seed_chain, verbose = output_verbose, mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed, printevery = printevery, chain_index = chain) mc.silent = silent, mc.cores = cores) }, Spike_Laplace = {
spike_laplace_partially_mcmc(X, Y, intercept = !standardize, 20: a = extra_parameters$a, b = extra_parameters$b, nburn = nburn, e$fun(obj, substitute(ex), parent.frame(), e$data) npost = npost, seed = seed_chain, verbose = output_verbose,
printevery = printevery, chain_index = chain)21: }))foreach::foreach(chain = 1:nchains, .combine = list, .multicombine = TRUE, }) .maxcombine = ifelse(nchains >= 2, nchains, 2)) %dopar% { seed_chain = if (!is.null(seed))
seed + chain24: else NULLBMI_LASSO(data$data_MI$X, data$data_MI$Y, model = "Horseshoe", return(switch(model, Multi_Laplace = { nburn = 4000, npost = 4000, output_verbose = FALSE, nchains = 2, multi_laplace_mcmc(X, Y, intercept = !standardize, h = extra_parameters$h, ncores = 2, seed = seed)
v = extra_parameters$v, nburn = nburn, npost = npost, 25: seed = seed_chain, verbose = output_verbose, printevery = printevery, eval(expr, envir)
chain_index = chain)26: }, Horseshoe = {eval(expr, envir)
horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn, 27: npost = npost, seed = seed_chain, verbose = output_verbose, withVisible(eval(expr, envir)) printevery = printevery, chain_index = chain)
}, ARD = {28: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { ARD_mcmc(X, Y, intercept = !standardize, nburn = nburn, watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) npost = npost, seed = seed_chain, verbose = output_verbose, printevery = printevery, chain_index = chain) }, Spike_Laplace = { } spike_laplace_partially_mcmc(X, Y, intercept = !standardize, a = extra_parameters$a, b = extra_parameters$b, nburn = nburn, npost = npost, seed = seed_chain, verbose = output_verbose, if (on_message$silence) { printevery = printevery, chain_index = chain) invokeRestart("muffleMessage") })) }}}, warning = function (cnd)
{22: if (getOption("warn") >= 2 || getOption("warn") < 0) {withCallingHandlers(expr, warning = function(w) if (inherits(w, return() classes)) tryInvokeRestart("muffleWarning")) }
watcher$capture_plot_and_output()23: if (on_warning$capture) {suppressWarnings(foreach::foreach(chain = 1:nchains, .combine = list, .multicombine = TRUE, .maxcombine = ifelse(nchains >= 2, cnd <- sanitize_call(cnd) nchains, 2)) %dopar% { watcher$push(cnd) seed_chain = if (!is.null(seed)) } seed + chain if (on_warning$silence) { else NULL invokeRestart("muffleWarning") return(switch(model, Multi_Laplace = { } multi_laplace_mcmc(X, Y, intercept = !standardize, h = extra_parameters$h, }, error = function (cnd) v = extra_parameters$v, nburn = nburn, npost = npost, { seed = seed_chain, verbose = output_verbose, printevery = printevery, watcher$capture_plot_and_output() chain_index = chain) cnd <- sanitize_call(cnd) }, Horseshoe = { watcher$push(cnd) horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn, switch(on_error, continue = invokeRestart("eval_continue"), npost = npost, seed = seed_chain, verbose = output_verbose, stop = invokeRestart("eval_stop"), error = NULL) printevery = printevery, chain_index = chain)}) }, ARD = {
ARD_mcmc(X, Y, intercept = !standardize, nburn = nburn, 29: npost = npost, seed = seed_chain, verbose = output_verbose, eval(call) printevery = printevery, chain_index = chain)
}, Spike_Laplace = {30: spike_laplace_partially_mcmc(X, Y, intercept = !standardize, eval(call) a = extra_parameters$a, b = extra_parameters$b, nburn = nburn,
npost = npost, seed = seed_chain, verbose = output_verbose, printevery = printevery, chain_index = chain)31: }))with_handlers({}) for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir))24: watcher$capture_plot_and_output()BMI_LASSO(data$data_MI$X, data$data_MI$Y, model = "Horseshoe", watcher$print_value(ev$value, ev$visible, envir) nburn = 4000, npost = 4000, output_verbose = FALSE, nchains = 2, } ncores = 2, seed = seed) TRUE
}, handlers)25:
eval(expr, envir)
32: 26: doWithOneRestart(return(expr), restart)eval(expr, envir)
33: 27: withOneRestart(expr, restarts[[1L]])withVisible(eval(expr, envir))
34: 28: withRestartList(expr, restarts[-nr])withCallingHandlers(code, error = function (e)
rlang::entrace(e), message = function (cnd) {35: watcher$capture_plot_and_output()doWithOneRestart(return(expr), restart) if (on_message$capture) {
watcher$push(cnd)36: }withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
if (on_message$silence) {37: invokeRestart("muffleMessage") }withRestartList(expr, restarts)}, warning = function (cnd)
{ if (getOption("warn") >= 2 || getOption("warn") < 0) {38: return()withRestarts(with_handlers({ for (expr in tle$exprs) { } ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$capture_plot_and_output() if (on_warning$capture) { watcher$print_value(ev$value, ev$visible, envir) cnd <- sanitize_call(cnd) watcher$push(cnd) } } TRUE if (on_warning$silence) {}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) invokeRestart("muffleWarning")
}39: }, error = function (cnd) evaluate::evaluate(...){
watcher$capture_plot_and_output()40: cnd <- sanitize_call(cnd)evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, watcher$push(cnd) keep_message = if (is.numeric(options$message)) TRUE else options$message, switch(on_error, continue = invokeRestart("eval_continue"), stop_on_error = if (is.numeric(options$error)) options$error else { stop = invokeRestart("eval_stop"), error = NULL) if (options$error && options$include) }) 0L
else 2L29: }, output_handler = knit_handlers(options$render, options))eval(call)
41: 30: in_dir(input_dir(), expr)eval(call)
42: 31: in_input_dir(evaluate(code, envir = env, new_device = FALSE, with_handlers({ keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) keep_message = if (is.numeric(options$message)) TRUE else options$message, watcher$capture_plot_and_output() stop_on_error = if (is.numeric(options$error)) options$error else { watcher$print_value(ev$value, ev$visible, envir) if (options$error && options$include) } 0L TRUE else 2L}, handlers) }, output_handler = knit_handlers(options$render, options)))
32:
doWithOneRestart(return(expr), restart)43:
eng_r(options)33: withOneRestart(expr, restarts[[1L]])
44: 34: block_exec(params)withRestartList(expr, restarts[-nr])
45: 35: call_block(x)doWithOneRestart(return(expr), restart)
46: 36: process_group(group)withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
47: 37: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), withRestartList(expr, restarts) error = function(e) {
38: if (progress && is.function(pb$interrupt)) withRestarts(with_handlers({ pb$interrupt() for (expr in tle$exprs) { if (is_R_CMD_build() || is_R_CMD_check()) ev <- withVisible(eval(expr, envir)) error <<- format(e) watcher$capture_plot_and_output() }) watcher$print_value(ev$value, ev$visible, envir) }
TRUE48: }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {39: if (progress && is.function(pb$interrupt)) evaluate::evaluate(...) pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) 40: error <<- format(e)evaluate(code, envir = env, new_device = FALSE, 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,
49: stop_on_error = if (is.numeric(options$error)) options$error else {xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), if (options$error && options$include) error = function(e) { 0L if (progress && is.function(pb$interrupt)) else 2L pb$interrupt() }, output_handler = knit_handlers(options$render, options)) if (is_R_CMD_build() || is_R_CMD_check())
error <<- format(e)41: }), list(rlang_trace_top_env = knit_global())), function(loc) {in_dir(input_dir(), expr) setwd(wd)
write_utf8(res, output %n% stdout())42: paste0("\nQuitting from ", loc, if (!is.null(error)) in_input_dir(evaluate(code, envir = env, new_device = FALSE, paste0("\n", rule(), error, "\n", rule())) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) stop_on_error = if (is.numeric(options$error)) options$error else {
if (options$error && options$include) 50: 0Lprocess_file(text, output) else 2L
}, output_handler = knit_handlers(options$render, options)))51: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
43: eng_r(options)52:
rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 44: output_dir = getwd(), ...)block_exec(params)
53: 45: vweave_rmarkdown(...)call_block(x)
54: 46: engine$weave(file, quiet = quiet, encoding = enc)
process_group(group)55:
doTryCatch(return(expr), name, parentenv, handler)47:
withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 56: error = function(e) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (progress && is.function(pb$interrupt))
pb$interrupt()57: if (is_R_CMD_build() || is_R_CMD_check()) tryCatchList(expr, classes, parentenv, handlers) error <<- format(e)
})
58: 48: tryCatch({with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), engine$weave(file, quiet = quiet, encoding = enc) error = function(e) { setwd(startdir) if (progress && is.function(pb$interrupt)) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { pb$interrupt() texi2pdf(file = output, clean = FALSE, quiet = quiet) if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) output <- find_vignette_product(name, by = "texi2pdf", }), list(rlang_trace_top_env = knit_global())) engine = engine)
49: }xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), outputs <- c(outputs, output) error = function(e) {}, error = function(e) { if (progress && is.function(pb$interrupt)) thisOK <<- FALSE pb$interrupt() fails <<- c(fails, file) if (is_R_CMD_build() || is_R_CMD_check()) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", error <<- format(e) file, conditionMessage(e))) }), list(rlang_trace_top_env = knit_global())), function(loc) {})
setwd(wd)59: write_utf8(res, output %n% stdout())tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/BMIselect.Rcheck/vign_test/BMIselect", paste0("\nQuitting from ", loc, if (!is.null(error)) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp6laTQx/file13c7926736f0b.rds") paste0("\n", rule(), error, "\n", rule()))
}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)An irrecoverable exception occurred. R is aborting now ...
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/Rtmp6laTQx/file13c7926736f0b.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