Last updated on 2026-09-24 08:51:23 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 | 58.06 | 140.67 | 198.73 | 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 | 313.00 | 401.00 | 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 | 20.00 | 59.00 | 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 | 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) 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))
Traceback:
17: 1: FUN(X[[i]], ...)cpp_horseshoe(X, Y, intercept, as.integer(nburn), as.integer(npost),
seed, verbose, as.integer(printevery), as.integer(chain_index))18:
lapply(seq_len(cores), inner.do) 2:
horseshoe_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)
3: 20: eval(c.expr, envir = args, enclos = envir)e$fun(obj, substitute(ex), parent.frame(), e$data)
4: 21: eval(c.expr, envir = args, enclos = envir)foreach::foreach(chain = 1:nchains, .combine = list, .multicombine = TRUE,
.maxcombine = ifelse(nchains >= 2, nchains, 2)) %dopar% { 5: seed_chain = if (!is.null(seed)) doTryCatch(return(expr), name, parentenv, handler) seed + chain
else NULL 6: return(switch(model, Multi_Laplace = {tryCatchOne(expr, names, parentenv, handlers[[1L]]) multi_laplace_mcmc(X, Y, intercept = !standardize, h = extra_parameters$h,
v = extra_parameters$v, nburn = nburn, npost = npost, 7: seed = seed_chain, verbose = output_verbose, printevery = printevery, tryCatchList(expr, classes, parentenv, handlers) chain_index = chain)
}, Horseshoe = { 8: horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn, tryCatch(eval(c.expr, envir = args, enclos = envir), error = function(e) e) npost = npost, seed = seed_chain, verbose = output_verbose,
printevery = printevery, chain_index = chain) 9: }, ARD = {FUN(X[[i]], ...) ARD_mcmc(X, Y, intercept = !standardize, nburn = nburn,
npost = npost, seed = seed_chain, verbose = output_verbose, 10: printevery = printevery, chain_index = chain)lapply(X = S, FUN = FUN, ...) }, Spike_Laplace = {
spike_laplace_partially_mcmc(X, Y, intercept = !standardize, 11: a = extra_parameters$a, b = extra_parameters$b, nburn = nburn, doTryCatch(return(expr), name, parentenv, handler) npost = npost, seed = seed_chain, verbose = output_verbose,
printevery = printevery, chain_index = chain)12: }))tryCatchOne(expr, names, parentenv, handlers[[1L]])}
13: 22: tryCatchList(expr, classes, parentenv, handlers)withCallingHandlers(expr, warning = function(w) if (inherits(w,
classes)) tryInvokeRestart("muffleWarning"))14:
tryCatch(expr, error = function(e) {23: call <- conditionCall(e)suppressWarnings(foreach::foreach(chain = 1:nchains, .combine = list, if (!is.null(call)) { .multicombine = TRUE, .maxcombine = ifelse(nchains >= 2, if (identical(call[[1L]], quote(doTryCatch))) nchains, 2)) %dopar% { call <- sys.call(-4L) seed_chain = if (!is.null(seed)) dcall <- deparse(call, nlines = 1L) seed + chain prefix <- paste("Error in", dcall, ": ") LONG <- 75L else NULL sm <- strsplit(conditionMessage(e), "\n")[[1L]] return(switch(model, Multi_Laplace = { w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") multi_laplace_mcmc(X, Y, intercept = !standardize, h = extra_parameters$h, if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], v = extra_parameters$v, nburn = nburn, npost = npost, type = "b") if (w > LONG) seed = seed_chain, verbose = output_verbose, printevery = printevery, prefix <- paste0(prefix, "\n ") chain_index = chain) } }, Horseshoe = { else prefix <- "Error : " horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn, msg <- paste0(prefix, conditionMessage(e), "\n") npost = npost, seed = seed_chain, verbose = output_verbose, .Internal(seterrmessage(msg[1L])) printevery = printevery, chain_index = chain) if (!silent && isTRUE(getOption("show.error.messages"))) { }, ARD = { cat(msg, file = outFile) ARD_mcmc(X, Y, intercept = !standardize, 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)) }, Spike_Laplace = {}) spike_laplace_partially_mcmc(X, Y, intercept = !standardize,
a = extra_parameters$a, b = extra_parameters$b, nburn = nburn, 15: npost = npost, seed = seed_chain, verbose = output_verbose, try(lapply(X = S, FUN = FUN, ...), silent = TRUE) printevery = printevery, chain_index = chain)
}))16: })sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
24: 17: BMI_LASSO(data$data_MI$X, data$data_MI$Y, model = "Horseshoe", FUN(X[[i]], ...) nburn = 4000, npost = 4000, output_verbose = FALSE, nchains = 2,
ncores = 2, seed = seed)18:
lapply(seq_len(cores), inner.do)25:
eval(expr, envir)19:
mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed, 26: mc.silent = silent, mc.cores = cores)eval(expr, envir)
20: 27: e$fun(obj, substitute(ex), parent.frame(), e$data)withVisible(eval(expr, envir))
28: 21: withCallingHandlers(code, error = function (e) foreach::foreach(chain = 1:nchains, .combine = list, .multicombine = TRUE, rlang::entrace(e), message = function (cnd) .maxcombine = ifelse(nchains >= 2, nchains, 2)) %dopar% {{ watcher$capture_plot_and_output() seed_chain = if (!is.null(seed)) if (on_message$capture) { seed + chain watcher$push(cnd) else NULL } if (on_message$silence) { return(switch(model, Multi_Laplace = { invokeRestart("muffleMessage") multi_laplace_mcmc(X, Y, intercept = !standardize, h = extra_parameters$h, } v = extra_parameters$v, nburn = nburn, npost = npost, }, warning = function (cnd) seed = seed_chain, verbose = output_verbose, printevery = printevery, 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$capture_plot_and_output() }, ARD = { if (on_warning$capture) { ARD_mcmc(X, Y, intercept = !standardize, nburn = nburn, cnd <- sanitize_call(cnd) watcher$push(cnd) npost = npost, seed = seed_chain, verbose = output_verbose, printevery = printevery, chain_index = chain) } }, Spike_Laplace = { if (on_warning$silence) { spike_laplace_partially_mcmc(X, Y, intercept = !standardize, invokeRestart("muffleWarning") a = extra_parameters$a, b = extra_parameters$b, nburn = nburn, } npost = npost, seed = seed_chain, verbose = output_verbose, }, error = function (cnd) printevery = printevery, chain_index = chain){ })) watcher$capture_plot_and_output()} cnd <- sanitize_call(cnd)
watcher$push(cnd)22: switch(on_error, continue = invokeRestart("eval_continue"), withCallingHandlers(expr, warning = function(w) if (inherits(w, stop = invokeRestart("eval_stop"), error = NULL) classes)) tryInvokeRestart("muffleWarning"))})
29: 23: eval(call)suppressWarnings(foreach::foreach(chain = 1:nchains, .combine = list,
.multicombine = TRUE, .maxcombine = ifelse(nchains >= 2, 30: nchains, 2)) %dopar% {eval(call) seed_chain = if (!is.null(seed))
seed + chain31: else NULLwith_handlers({ return(switch(model, Multi_Laplace = { for (expr in tle$exprs) { multi_laplace_mcmc(X, Y, intercept = !standardize, h = extra_parameters$h, ev <- withVisible(eval(expr, envir)) v = extra_parameters$v, nburn = nburn, npost = npost, watcher$capture_plot_and_output() seed = seed_chain, verbose = output_verbose, printevery = printevery, watcher$print_value(ev$value, ev$visible, envir) chain_index = chain) } }, Horseshoe = { horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn, TRUE npost = npost, seed = seed_chain, verbose = output_verbose, }, handlers) printevery = printevery, chain_index = chain)
}, ARD = {32: ARD_mcmc(X, Y, intercept = !standardize, nburn = nburn, doWithOneRestart(return(expr), restart) npost = npost, seed = seed_chain, verbose = output_verbose, printevery = printevery, chain_index = chain)
}, Spike_Laplace = {33: spike_laplace_partially_mcmc(X, Y, intercept = !standardize, withOneRestart(expr, restarts[[1L]]) a = extra_parameters$a, b = extra_parameters$b, nburn = nburn,
npost = npost, seed = seed_chain, verbose = output_verbose, 34: printevery = printevery, chain_index = chain)withRestartList(expr, restarts[-nr]) }))
})
35: 24: doWithOneRestart(return(expr), restart)BMI_LASSO(data$data_MI$X, data$data_MI$Y, model = "Horseshoe", nburn = 4000, npost = 4000, output_verbose = FALSE, nchains = 2,
ncores = 2, seed = seed)
36: 25: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
eval(expr, envir)
37: 26: withRestartList(expr, restarts)eval(expr, envir)
38:
withRestarts(with_handlers({27: for (expr in tle$exprs) {withVisible(eval(expr, envir)) ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output()
watcher$print_value(ev$value, ev$visible, envir)28: }withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) TRUE{}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) watcher$capture_plot_and_output()
if (on_message$capture) {39: watcher$push(cnd)evaluate::evaluate(...) }
if (on_message$silence) {40: invokeRestart("muffleMessage")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, }, warning = function (cnd) stop_on_error = if (is.numeric(options$error)) options$error else {{ if (getOption("warn") >= 2 || getOption("warn") < 0) { if (options$error && options$include) return() 0L } else 2L watcher$capture_plot_and_output() }, output_handler = knit_handlers(options$render, options)) if (on_warning$capture) {
cnd <- sanitize_call(cnd)41: watcher$push(cnd)in_dir(input_dir(), expr) }
if (on_warning$silence) {42: invokeRestart("muffleWarning") }in_input_dir(evaluate(code, envir = env, new_device = FALSE, }, error = function (cnd) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, { keep_message = if (is.numeric(options$message)) TRUE else options$message, watcher$capture_plot_and_output() stop_on_error = if (is.numeric(options$error)) options$error else { cnd <- sanitize_call(cnd) if (options$error && options$include) watcher$push(cnd) 0L switch(on_error, continue = invokeRestart("eval_continue"), else 2L stop = invokeRestart("eval_stop"), error = NULL) }, output_handler = knit_handlers(options$render, options)))})
43: 29: eng_r(options)eval(call)
44: 30: block_exec(params)eval(call)
31: 45: with_handlers({call_block(x)
for (expr in tle$exprs) {46: ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output()process_group(group) watcher$print_value(ev$value, ev$visible, envir)
}47: TRUE}, handlers)withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {32: if (progress && is.function(pb$interrupt)) pb$interrupt()doWithOneRestart(return(expr), restart) if (is_R_CMD_build() || is_R_CMD_check())
33: error <<- format(e)withOneRestart(expr, restarts[[1L]]) })
34: 48: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), withRestartList(expr, restarts[-nr])
error = function(e) {35: if (progress && is.function(pb$interrupt)) doWithOneRestart(return(expr), restart) pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) 36: error <<- format(e)withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) }), list(rlang_trace_top_env = knit_global()))
37: 49: withRestartList(expr, restarts)
xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 38: error = function(e) {withRestarts(with_handlers({ if (progress && is.function(pb$interrupt)) for (expr in tle$exprs) { pb$interrupt() ev <- withVisible(eval(expr, envir)) if (is_R_CMD_build() || is_R_CMD_check()) watcher$capture_plot_and_output() error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { watcher$print_value(ev$value, ev$visible, envir) setwd(wd) } write_utf8(res, output %n% stdout()) TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
paste0("\nQuitting from ", loc, if (!is.null(error)) 39: paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)evaluate::evaluate(...)
50: 40: process_file(text, output)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 {51: if (options$error && options$include) knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 0L
else 2L52: }, output_handler = knit_handlers(options$render, options))
rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 41: output_dir = getwd(), ...)in_dir(input_dir(), expr)
53: 42: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, vweave_rmarkdown(...)
stop_on_error = if (is.numeric(options$error)) options$error else {54: if (options$error && options$include) engine$weave(file, quiet = quiet, encoding = enc) 0L
else 2L55: }, output_handler = knit_handlers(options$render, options)))doTryCatch(return(expr), name, parentenv, handler)
43:
eng_r(options)56:
tryCatchOne(expr, names, parentenv, handlers[[1L]])44:
block_exec(params)57: tryCatchList(expr, classes, parentenv, handlers)
58: 45: tryCatch({call_block(x) engine$weave(file, quiet = quiet, encoding = enc)
setwd(startdir)46: output <- find_vignette_product(name, by = "weave", engine = engine)process_group(group) if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet)47: output <- find_vignette_product(name, by = "texi2pdf", withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { engine = engine) if (progress && is.function(pb$interrupt)) } pb$interrupt() outputs <- c(outputs, output) if (is_R_CMD_build() || is_R_CMD_check()) }, error = function(e) { error <<- format(e) thisOK <<- FALSE }) fails <<- c(fails, file)
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", 48: file, conditionMessage(e)))with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), }) error = function(e) {
if (progress && is.function(pb$interrupt)) 59: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/BMIselect.Rcheck/vign_test/BMIselect", pb$interrupt() skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmpt7ealW/file1238b32d7719a.rds") if (is_R_CMD_build() || is_R_CMD_check())
error <<- format(e)An irrecoverable exception occurred. R is aborting now ...
}), 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/Rtmpt7ealW/file1238b32d7719a.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