Last updated on 2026-10-07 09:51:55 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.9 | 73.11 | 188.62 | 261.73 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.0.9 | 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 | 1.0.10 | 66.00 | 121.75 | 187.75 | 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 | 18.00 | 57.00 | 75.00 | ERROR | |
| r-oldrel-macos-x86_64 | 1.0.10 | 52.00 | 208.00 | 260.00 | OK | |
| r-oldrel-windows-x86_64 | 1.0.9 | 115.00 | 303.00 | 418.00 | 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 = {
Traceback:
1: horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn, cpp_horseshoe(X, Y, intercept, as.integer(nburn), as.integer(npost), npost = npost, seed = seed_chain, verbose = output_verbose, seed, verbose, as.integer(printevery), as.integer(chain_index)) printevery = printevery, chain_index = chain)
2: }, ARD = {horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn, ARD_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)
}, Spike_Laplace = { 3: spike_laplace_partially_mcmc(X, Y, intercept = !standardize, eval(c.expr, envir = args, enclos = envir) a = extra_parameters$a, b = extra_parameters$b, nburn = nburn,
npost = npost, seed = seed_chain, verbose = output_verbose, 4: printevery = printevery, chain_index = chain)eval(c.expr, envir = args, enclos = envir) }))
} 5:
doTryCatch(return(expr), name, parentenv, handler)22: withCallingHandlers(expr, warning = function(w) if (inherits(w,
classes)) tryInvokeRestart("muffleWarning"))
6: 23: tryCatchOne(expr, names, parentenv, handlers[[1L]])suppressWarnings(foreach::foreach(chain = 1:nchains, .combine = list,
.multicombine = TRUE, .maxcombine = ifelse(nchains >= 2, 7: tryCatchList(expr, classes, parentenv, handlers) nchains, 2)) %dopar% {
seed_chain = if (!is.null(seed)) 8: seed + chaintryCatch(eval(c.expr, envir = args, enclos = envir), error = function(e) e) else NULL
return(switch(model, Multi_Laplace = { 9: multi_laplace_mcmc(X, Y, intercept = !standardize, h = extra_parameters$h, FUN(X[[i]], ...) v = extra_parameters$v, nburn = nburn, npost = npost,
seed = seed_chain, verbose = output_verbose, printevery = printevery, 10: chain_index = chain)lapply(X = S, FUN = FUN, ...) }, Horseshoe = {
horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn, 11: npost = npost, seed = seed_chain, verbose = output_verbose, doTryCatch(return(expr), name, parentenv, handler) printevery = printevery, chain_index = chain)
}, ARD = {12: ARD_mcmc(X, Y, intercept = !standardize, nburn = nburn, tryCatchOne(expr, names, parentenv, handlers[[1L]]) npost = npost, seed = seed_chain, verbose = output_verbose,
printevery = printevery, chain_index = chain)13: }, Spike_Laplace = {tryCatchList(expr, classes, parentenv, handlers) spike_laplace_partially_mcmc(X, Y, intercept = !standardize,
a = extra_parameters$a, b = extra_parameters$b, nburn = nburn, 14: npost = npost, seed = seed_chain, verbose = output_verbose, tryCatch(expr, error = function(e) { printevery = printevery, chain_index = chain) call <- conditionCall(e) })) if (!is.null(call)) {}) if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)24: dcall <- deparse(call, nlines = 1L)BMI_LASSO(data$data_MI$X, data$data_MI$Y, model = "Horseshoe", prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] nburn = 4000, npost = 4000, output_verbose = FALSE, nchains = 2, w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") ncores = 2, seed = seed)
if (is.na(w)) 25: eval(expr, envir)
26: eval(expr, envir) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b")
if (w > LONG) 27: prefix <- paste0(prefix, "\n ")withVisible(eval(expr, envir)) } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))28: if (!silent && isTRUE(getOption("show.error.messages"))) {withCallingHandlers(code, error = function (e) cat(msg, file = outFile)rlang::entrace(e), message = function (cnd) .Internal(printDeferredWarnings()) }{ watcher$capture_plot_and_output() invisible(structure(msg, class = "try-error", condition = e)) if (on_message$capture) {}) watcher$push(cnd)
}15: if (on_message$silence) {try(lapply(X = S, FUN = FUN, ...), silent = TRUE) invokeRestart("muffleMessage")
}16: }, warning = function (cnd) sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)){ if (getOption("warn") >= 2 || getOption("warn") < 0) { return()
}17: watcher$capture_plot_and_output()FUN(X[[i]], ...) if (on_warning$capture) { cnd <- sanitize_call(cnd)
watcher$push(cnd)18: }lapply(seq_len(cores), inner.do) if (on_warning$silence) {
invokeRestart("muffleWarning")19: }mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed, }, error = function (cnd) mc.silent = silent, mc.cores = cores){
watcher$capture_plot_and_output()20: cnd <- sanitize_call(cnd)e$fun(obj, substitute(ex), parent.frame(), e$data) watcher$push(cnd)
switch(on_error, continue = invokeRestart("eval_continue"), 21: stop = invokeRestart("eval_stop"), error = NULL)foreach::foreach(chain = 1:nchains, .combine = list, .multicombine = TRUE, }) .maxcombine = ifelse(nchains >= 2, nchains, 2)) %dopar% {
seed_chain = if (!is.null(seed)) 29: seed + chaineval(call) else NULL
return(switch(model, Multi_Laplace = {30: multi_laplace_mcmc(X, Y, intercept = !standardize, h = extra_parameters$h, eval(call) v = extra_parameters$v, nburn = nburn, npost = npost,
seed = seed_chain, verbose = output_verbose, printevery = printevery, 31: chain_index = chain)with_handlers({ }, Horseshoe = { for (expr in tle$exprs) { horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn, ev <- withVisible(eval(expr, envir)) npost = npost, seed = seed_chain, verbose = output_verbose, watcher$capture_plot_and_output() printevery = printevery, chain_index = chain) watcher$print_value(ev$value, ev$visible, envir) }, ARD = { } ARD_mcmc(X, Y, intercept = !standardize, nburn = nburn, TRUE npost = npost, seed = seed_chain, verbose = output_verbose, }, handlers) printevery = printevery, chain_index = chain)
}, Spike_Laplace = {32: doWithOneRestart(return(expr), restart) spike_laplace_partially_mcmc(X, Y, intercept = !standardize,
a = extra_parameters$a, b = extra_parameters$b, nburn = nburn, 33: npost = npost, seed = seed_chain, verbose = output_verbose, withOneRestart(expr, restarts[[1L]]) printevery = printevery, chain_index = chain)
}))}34:
withRestartList(expr, restarts[-nr])22:
withCallingHandlers(expr, warning = function(w) if (inherits(w, 35: classes)) tryInvokeRestart("muffleWarning"))doWithOneRestart(return(expr), restart)
23: 36: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])suppressWarnings(foreach::foreach(chain = 1:nchains, .combine = list,
.multicombine = TRUE, .maxcombine = ifelse(nchains >= 2, 37: nchains, 2)) %dopar% {withRestartList(expr, restarts) seed_chain = if (!is.null(seed))
seed + chain38: else NULLwithRestarts(with_handlers({ return(switch(model, Multi_Laplace = { for (expr in tle$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 = { TRUE horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn, npost = npost, seed = seed_chain, verbose = output_verbose, }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) printevery = printevery, chain_index = chain)
}, ARD = {39: ARD_mcmc(X, Y, intercept = !standardize, nburn = nburn, npost = npost, seed = seed_chain, verbose = output_verbose, evaluate::evaluate(...) printevery = printevery, chain_index = chain)
}, Spike_Laplace = {40: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, spike_laplace_partially_mcmc(X, Y, intercept = !standardize, keep_message = if (is.numeric(options$message)) TRUE else options$message, a = extra_parameters$a, b = extra_parameters$b, nburn = nburn, stop_on_error = if (is.numeric(options$error)) options$error else { npost = npost, seed = seed_chain, verbose = output_verbose, if (options$error && options$include) printevery = printevery, chain_index = chain) })) 0L}) else 2L
}, output_handler = knit_handlers(options$render, options))24:
BMI_LASSO(data$data_MI$X, data$data_MI$Y, model = "Horseshoe", 41: nburn = 4000, npost = 4000, output_verbose = FALSE, nchains = 2, in_dir(input_dir(), expr)
ncores = 2, seed = seed)42:
in_input_dir(evaluate(code, envir = env, new_device = FALSE, 25: keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, eval(expr, envir) keep_message = if (is.numeric(options$message)) TRUE else options$message,
stop_on_error = if (is.numeric(options$error)) options$error else {26: if (options$error && options$include) eval(expr, envir) 0L
else 2L27: }, output_handler = knit_handlers(options$render, options)))withVisible(eval(expr, envir))
43: 28: eng_r(options)withCallingHandlers(code, error = function (e)
rlang::entrace(e), message = function (cnd) 44: {block_exec(params)
watcher$capture_plot_and_output()45: if (on_message$capture) {call_block(x) watcher$push(cnd)
}46: if (on_message$silence) {process_group(group) invokeRestart("muffleMessage")
}47: }, warning = function (cnd) withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), { error = function(e) { if (getOption("warn") >= 2 || getOption("warn") < 0) { if (progress && is.function(pb$interrupt)) return() pb$interrupt() } if (is_R_CMD_build() || is_R_CMD_check()) watcher$capture_plot_and_output() error <<- format(e) if (on_warning$capture) { }) cnd <- sanitize_call(cnd)
watcher$push(cnd)48: }with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), if (on_warning$silence) { error = function(e) { invokeRestart("muffleWarning") if (progress && is.function(pb$interrupt)) } pb$interrupt()}, error = function (cnd) if (is_R_CMD_build() || is_R_CMD_check()) { error <<- format(e) watcher$capture_plot_and_output() }), list(rlang_trace_top_env = knit_global())) cnd <- sanitize_call(cnd)
watcher$push(cnd)49: switch(on_error, continue = invokeRestart("eval_continue"), xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), stop = invokeRestart("eval_stop"), error = NULL) error = function(e) {}) if (progress && is.function(pb$interrupt))
pb$interrupt()29: if (is_R_CMD_build() || is_R_CMD_check()) eval(call) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) {
setwd(wd) write_utf8(res, output %n% stdout())30: paste0("\nQuitting from ", loc, if (!is.null(error)) eval(call) paste0("\n", rule(), error, "\n", rule()))
}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)31:
with_handlers({50: for (expr in tle$exprs) {process_file(text, output) ev <- withVisible(eval(expr, envir))
watcher$capture_plot_and_output()51: watcher$print_value(ev$value, ev$visible, envir)knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) }
TRUE52: }, handlers)rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
output_dir = getwd(), ...)32:
doWithOneRestart(return(expr), restart)53:
vweave_rmarkdown(...)33:
withOneRestart(expr, restarts[[1L]])54:
engine$weave(file, quiet = quiet, encoding = enc)34:
withRestartList(expr, restarts[-nr])55:
doTryCatch(return(expr), name, parentenv, handler)35:
doWithOneRestart(return(expr), restart)56:
tryCatchOne(expr, names, parentenv, handlers[[1L]])36:
withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])57:
37: tryCatchList(expr, classes, parentenv, handlers)withRestartList(expr, restarts)
58: 38: tryCatch({withRestarts(with_handlers({ engine$weave(file, quiet = quiet, encoding = enc) for (expr in tle$exprs) { setwd(startdir) ev <- withVisible(eval(expr, envir)) output <- find_vignette_product(name, by = "weave", engine = engine) watcher$capture_plot_and_output() if (!have.makefile && vignette_is_tex(output)) { watcher$print_value(ev$value, ev$visible, envir) texi2pdf(file = output, clean = FALSE, quiet = quiet) } output <- find_vignette_product(name, by = "texi2pdf", TRUE engine = engine)}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) }
outputs <- c(outputs, output)39: }, error = function(e) {evaluate::evaluate(...) thisOK <<- FALSE
fails <<- c(fails, file)40: message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, file, conditionMessage(e))) keep_message = if (is.numeric(options$message)) TRUE else options$message, }) stop_on_error = if (is.numeric(options$error)) options$error else {
59: if (options$error && options$include) tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/BMIselect.Rcheck/vign_test/BMIselect", 0L skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpWz4eoW/file16f3928cb3c87.rds") else 2L
}, output_handler = knit_handlers(options$render, options))An irrecoverable exception occurred. R is aborting now ...
41: in_dir(input_dir(), expr)
42: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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/RtmpWz4eoW/file16f3928cb3c87.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