Last updated on 2026-10-05 06:52:54 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)
Traceback:
6: 1: tryCatchOne(expr, names, parentenv, handlers[[1L]])cpp_horseshoe(X, Y, intercept, as.integer(nburn), as.integer(npost),
seed, verbose, as.integer(printevery), as.integer(chain_index)) 7:
tryCatchList(expr, classes, parentenv, handlers) 2:
horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn, 8: npost = npost, seed = seed_chain, verbose = output_verbose, tryCatch(eval(c.expr, envir = args, enclos = envir), error = function(e) e) printevery = printevery, chain_index = chain)
3: 9: eval(c.expr, envir = args, enclos = envir)FUN(X[[i]], ...)
4: 10: eval(c.expr, envir = args, enclos = envir)lapply(X = S, FUN = FUN, ...)
5:
doTryCatch(return(expr), name, parentenv, handler)11:
doTryCatch(return(expr), name, parentenv, handler) 6:
tryCatchOne(expr, names, parentenv, handlers[[1L]])
12: 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatchList(expr, classes, parentenv, handlers)
13:
tryCatchList(expr, classes, parentenv, handlers) 8:
tryCatch(eval(c.expr, envir = args, enclos = envir), error = function(e) e)14:
9: tryCatch(expr, error = function(e) {FUN(X[[i]], ...) call <- conditionCall(e)
10: if (!is.null(call)) {lapply(X = S, FUN = FUN, ...) if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L)
dcall <- deparse(call, nlines = 1L)11: prefix <- paste("Error in", dcall, ": ")doTryCatch(return(expr), name, parentenv, handler) LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]12: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 13: type = "b")tryCatchList(expr, classes, parentenv, handlers)
if (w > LONG) 14: prefix <- paste0(prefix, "\n ")tryCatch(expr, error = function(e) { } call <- conditionCall(e) else prefix <- "Error : " if (!is.null(call)) { msg <- paste0(prefix, conditionMessage(e), "\n") if (identical(call[[1L]], quote(doTryCatch))) .Internal(seterrmessage(msg[1L])) call <- sys.call(-4L) if (!silent && isTRUE(getOption("show.error.messages"))) { dcall <- deparse(call, nlines = 1L) cat(msg, file = outFile) .Internal(printDeferredWarnings()) prefix <- paste("Error in", dcall, ": ") } LONG <- 75L invisible(structure(msg, class = "try-error", condition = e)) sm <- strsplit(conditionMessage(e), "\n")[[1L]]})
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")15: if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], try(lapply(X = S, FUN = FUN, ...), silent = TRUE) type = "b")
if (w > LONG) 16: prefix <- paste0(prefix, "\n ")sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) }
else prefix <- "Error : "17: msg <- paste0(prefix, conditionMessage(e), "\n")FUN(X[[i]], ...) .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)18: .Internal(printDeferredWarnings()) }lapply(seq_len(cores), inner.do) invisible(structure(msg, class = "try-error", condition = e))
})19:
mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed, 15: mc.silent = silent, mc.cores = cores)try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
20: 16: e$fun(obj, substitute(ex), parent.frame(), e$data)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
21: 17: foreach::foreach(chain = 1:nchains, .combine = list, .multicombine = TRUE, FUN(X[[i]], ...) .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$h, mc.silent = silent, mc.cores = cores)
20: v = extra_parameters$v, nburn = nburn, npost = npost, e$fun(obj, substitute(ex), parent.frame(), e$data) seed = seed_chain, verbose = output_verbose, printevery = printevery,
chain_index = chain)21: }, Horseshoe = {foreach::foreach(chain = 1:nchains, .combine = list, .multicombine = TRUE, .maxcombine = ifelse(nchains >= 2, nchains, 2)) %dopar% { horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn, seed_chain = if (!is.null(seed)) npost = npost, seed = seed_chain, verbose = output_verbose, seed + chain printevery = printevery, chain_index = chain) else NULL }, ARD = { return(switch(model, Multi_Laplace = { ARD_mcmc(X, Y, intercept = !standardize, nburn = nburn, multi_laplace_mcmc(X, Y, intercept = !standardize, h = extra_parameters$h, npost = npost, seed = seed_chain, verbose = output_verbose, v = extra_parameters$v, nburn = nburn, npost = npost, printevery = printevery, chain_index = chain) seed = seed_chain, verbose = output_verbose, printevery = printevery, }, Spike_Laplace = { chain_index = chain) 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) }, ARD = { printevery = printevery, chain_index = chain) ARD_mcmc(X, Y, intercept = !standardize, nburn = nburn, })) 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, 22: npost = npost, seed = seed_chain, verbose = output_verbose, printevery = printevery, chain_index = chain) }))withCallingHandlers(expr, warning = function(w) if (inherits(w, } classes)) tryInvokeRestart("muffleWarning"))
22: 23: withCallingHandlers(expr, warning = function(w) if (inherits(w, suppressWarnings(foreach::foreach(chain = 1:nchains, .combine = list, classes)) tryInvokeRestart("muffleWarning"))
.multicombine = TRUE, .maxcombine = ifelse(nchains >= 2, 23: suppressWarnings(foreach::foreach(chain = 1:nchains, .combine = list, nchains, 2)) %dopar% { .multicombine = TRUE, .maxcombine = ifelse(nchains >= 2, nchains, 2)) %dopar% { seed_chain = if (!is.null(seed)) seed_chain = if (!is.null(seed)) seed + chain seed + chain else NULL else NULL return(switch(model, Multi_Laplace = { return(switch(model, Multi_Laplace = { multi_laplace_mcmc(X, Y, intercept = !standardize, h = extra_parameters$h, multi_laplace_mcmc(X, Y, intercept = !standardize, h = extra_parameters$h, v = extra_parameters$v, nburn = nburn, npost = npost, v = extra_parameters$v, nburn = nburn, npost = npost, seed = seed_chain, verbose = output_verbose, printevery = printevery, seed = seed_chain, verbose = output_verbose, printevery = printevery, chain_index = chain) chain_index = chain) }, Horseshoe = { }, Horseshoe = { horseshoe_mcmc(X, Y, intercept = !standardize, 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 = { ARD_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 = { }, Spike_Laplace = { spike_laplace_partially_mcmc(X, Y, intercept = !standardize, spike_laplace_partially_mcmc(X, Y, intercept = !standardize, a = extra_parameters$a, b = extra_parameters$b, nburn = nburn, a = extra_parameters$a, b = extra_parameters$b, 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) })) }))})})
24: 24: BMI_LASSO(data$data_MI$X, data$data_MI$Y, model = "Horseshoe", BMI_LASSO(data$data_MI$X, data$data_MI$Y, model = "Horseshoe", nburn = 4000, npost = 4000, output_verbose = FALSE, nchains = 2, nburn = 4000, npost = 4000, output_verbose = FALSE, nchains = 2, ncores = 2, seed = seed) ncores = 2, seed = seed)
25: 25: eval(expr, envir)eval(expr, envir)
26: 26: eval(expr, envir)
eval(expr, envir)27:
withVisible(eval(expr, envir))27:
withVisible(eval(expr, envir))28:
withCallingHandlers(code, error = function (e) 28: rlang::entrace(e), message = function (cnd) withCallingHandlers(code, error = function (e) {rlang::entrace(e), message = function (cnd) watcher$capture_plot_and_output(){ if (on_message$capture) { watcher$capture_plot_and_output() watcher$push(cnd) if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { } invokeRestart("muffleMessage") if (on_message$silence) { } invokeRestart("muffleMessage")}, warning = function (cnd) }{}, warning = function (cnd) if (getOption("warn") >= 2 || getOption("warn") < 0) {{ return() if (getOption("warn") >= 2 || getOption("warn") < 0) { } return() watcher$capture_plot_and_output() } if (on_warning$capture) { watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) cnd <- sanitize_call(cnd) watcher$push(cnd) watcher$push(cnd) } } if (on_warning$silence) { if (on_warning$silence) { invokeRestart("muffleWarning") invokeRestart("muffleWarning") } }}, error = function (cnd) }, error = function (cnd) {{ watcher$capture_plot_and_output() watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) cnd <- sanitize_call(cnd) watcher$push(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL) stop = invokeRestart("eval_stop"), error = NULL)})})
29: 29: eval(call)eval(call)
30: 30: eval(call)
eval(call)31:
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) TRUE
}, handlers)32:
doWithOneRestart(return(expr), restart)
32: 33: doWithOneRestart(return(expr), restart)withOneRestart(expr, restarts[[1L]])
34: 33: withRestartList(expr, restarts[-nr])withOneRestart(expr, restarts[[1L]])
35: 34: doWithOneRestart(return(expr), restart)withRestartList(expr, restarts[-nr])
36: 35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])doWithOneRestart(return(expr), restart)
37: withRestartList(expr, restarts)
36: 38: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])withRestarts(with_handlers({ for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir))37: watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir)withRestartList(expr, restarts)
} TRUE38: }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)withRestarts(with_handlers({
39: for (expr in tle$exprs) {evaluate::evaluate(...) ev <- withVisible(eval(expr, envir))
watcher$capture_plot_and_output()40: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, watcher$print_value(ev$value, ev$visible, envir) 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) TRUE 0L}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
else 2L39: }, output_handler = knit_handlers(options$render, options))evaluate::evaluate(...)
41:
in_dir(input_dir(), expr)40:
evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, 42: stop_on_error = if (is.numeric(options$error)) options$error else {in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, if (options$error && options$include) keep_message = if (is.numeric(options$message)) TRUE else options$message, 0L else 2L stop_on_error = if (is.numeric(options$error)) options$error else { }, output_handler = knit_handlers(options$render, options)) if (options$error && options$include)
0L else 2L41: in_dir(input_dir(), expr) }, output_handler = knit_handlers(options$render, options)))
43: 42: eng_r(options)in_input_dir(evaluate(code, envir = env, new_device = FALSE,
keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 44: keep_message = if (is.numeric(options$message)) TRUE else options$message, block_exec(params) stop_on_error = if (is.numeric(options$error)) options$error else {
if (options$error && options$include) 45: 0L else 2Lcall_block(x) }, output_handler = knit_handlers(options$render, options)))
46: 43: process_group(group)eng_r(options)
47: 44: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), block_exec(params) error = function(e) { if (progress && is.function(pb$interrupt))
pb$interrupt()45: if (is_R_CMD_build() || is_R_CMD_check()) call_block(x) error <<- format(e)
})46:
process_group(group)48:
with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 47: error = function(e) {withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), if (progress && is.function(pb$interrupt)) error = function(e) { pb$interrupt() if (progress && is.function(pb$interrupt)) if (is_R_CMD_build() || is_R_CMD_check()) pb$interrupt() error <<- format(e) if (is_R_CMD_build() || is_R_CMD_check()) }), list(rlang_trace_top_env = knit_global())) error <<- format(e)
49: })xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {48: if (progress && is.function(pb$interrupt)) with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) error <<- format(e) }), list(rlang_trace_top_env = knit_global())) }), 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)) 49: paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {50: if (progress && is.function(pb$interrupt)) process_file(text, output) pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) 51: error <<- format(e)knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) }), list(rlang_trace_top_env = knit_global())), function(loc) {
52: setwd(wd)rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), write_utf8(res, output %n% stdout()) output_dir = getwd(), ...) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))
}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)53:
vweave_rmarkdown(...)50:
process_file(text, output)54:
engine$weave(file, quiet = quiet, encoding = enc)51:
knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)55:
doTryCatch(return(expr), name, parentenv, handler)52:
rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 56: output_dir = getwd(), ...)tryCatchOne(expr, names, parentenv, handlers[[1L]])
53: 57: vweave_rmarkdown(...)tryCatchList(expr, classes, parentenv, handlers)
54: 58: engine$weave(file, quiet = quiet, encoding = enc)tryCatch({
engine$weave(file, quiet = quiet, encoding = enc)55: setwd(startdir)doTryCatch(return(expr), name, parentenv, handler) output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) {56: texi2pdf(file = output, clean = FALSE, quiet = quiet)tryCatchOne(expr, names, parentenv, handlers[[1L]]) output <- find_vignette_product(name, by = "texi2pdf",
engine = engine)57: }tryCatchList(expr, classes, parentenv, handlers) outputs <- c(outputs, output)
}, error = function(e) {58: thisOK <<- FALSEtryCatch({ fails <<- c(fails, file) engine$weave(file, quiet = quiet, encoding = enc) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", setwd(startdir) file, conditionMessage(e))) output <- find_vignette_product(name, by = "weave", engine = engine)})
if (!have.makefile && vignette_is_tex(output)) {59: texi2pdf(file = output, clean = FALSE, quiet = quiet)tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/BMIselect.Rcheck/vign_test/BMIselect", output <- find_vignette_product(name, by = "texi2pdf", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp8ininO/file16cc2a667fc8.rds") engine = engine)
}An irrecoverable exception occurred. R is aborting now ...
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/Rtmp8ininO/file16cc2a667fc8.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