Last updated on 2026-09-26 09:51:21 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 | 18.00 | 62.00 | 80.00 | 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]], ...)
Traceback:
1: 10: cpp_horseshoe(X, Y, intercept, as.integer(nburn), as.integer(npost), lapply(X = S, FUN = FUN, ...) seed, verbose, as.integer(printevery), as.integer(chain_index))
11: 2: doTryCatch(return(expr), name, parentenv, handler)horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn,
npost = npost, seed = seed_chain, verbose = output_verbose, 12: printevery = printevery, chain_index = chain)tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: 13: eval(c.expr, envir = args, enclos = envir)tryCatchList(expr, classes, parentenv, handlers)
4: 14: eval(c.expr, envir = args, enclos = envir)
5: tryCatch(expr, error = function(e) {doTryCatch(return(expr), name, parentenv, handler)
call <- conditionCall(e) 6: if (!is.null(call)) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L) 7: dcall <- deparse(call, nlines = 1L)tryCatchList(expr, classes, parentenv, handlers) prefix <- paste("Error in", dcall, ": ")
LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") 8: if (is.na(w)) tryCatch(eval(c.expr, envir = args, enclos = envir), error = function(e) e) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b") 9: FUN(X[[i]], ...) if (w > LONG)
10: prefix <- paste0(prefix, "\n ")lapply(X = S, FUN = FUN, ...) }
11: else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n")doTryCatch(return(expr), name, parentenv, handler) .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)12: .Internal(printDeferredWarnings())tryCatchOne(expr, names, parentenv, handlers[[1L]]) }
invisible(structure(msg, class = "try-error", condition = e))13: })tryCatchList(expr, classes, parentenv, handlers)
15: 14: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)tryCatch(expr, error = function(e) {
16: call <- conditionCall(e)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch))) 17: call <- sys.call(-4L)FUN(X[[i]], ...) dcall <- deparse(call, nlines = 1L)
prefix <- paste("Error in", dcall, ": ")18: LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]]lapply(seq_len(cores), inner.do) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w)) 19: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed, mc.silent = silent, mc.cores = cores) type = "b")
if (w > LONG) 20: prefix <- paste0(prefix, "\n ")e$fun(obj, substitute(ex), parent.frame(), e$data) }
else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n")21: .Internal(seterrmessage(msg[1L]))foreach::foreach(chain = 1:nchains, .combine = list, .multicombine = TRUE, if (!silent && isTRUE(getOption("show.error.messages"))) { .maxcombine = ifelse(nchains >= 2, nchains, 2)) %dopar% { seed_chain = if (!is.null(seed)) cat(msg, file = outFile) seed + chain .Internal(printDeferredWarnings()) else NULL } return(switch(model, Multi_Laplace = { invisible(structure(msg, class = "try-error", condition = e)) 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, 15: chain_index = chain) }, Horseshoe = {try(lapply(X = S, FUN = FUN, ...), silent = TRUE) horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn,
npost = npost, seed = seed_chain, verbose = output_verbose, 16: printevery = printevery, chain_index = chain)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) }, ARD = {
ARD_mcmc(X, Y, intercept = !standardize, nburn = nburn, 17: npost = npost, seed = seed_chain, verbose = output_verbose, FUN(X[[i]], ...) printevery = printevery, chain_index = chain)
}, Spike_Laplace = {18: lapply(seq_len(cores), inner.do) spike_laplace_partially_mcmc(X, Y, intercept = !standardize,
a = extra_parameters$a, b = extra_parameters$b, nburn = nburn, 19: npost = npost, seed = seed_chain, verbose = output_verbose, mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed, mc.silent = silent, mc.cores = cores) printevery = printevery, chain_index = chain)
}))20: }e$fun(obj, substitute(ex), parent.frame(), e$data)
22: 21: withCallingHandlers(expr, warning = function(w) if (inherits(w, foreach::foreach(chain = 1:nchains, .combine = list, .multicombine = TRUE, classes)) tryInvokeRestart("muffleWarning")) .maxcombine = ifelse(nchains >= 2, nchains, 2)) %dopar% {
seed_chain = if (!is.null(seed)) seed + chain23: else NULLsuppressWarnings(foreach::foreach(chain = 1:nchains, .combine = list, return(switch(model, Multi_Laplace = { multi_laplace_mcmc(X, Y, intercept = !standardize, h = extra_parameters$h, .multicombine = TRUE, .maxcombine = ifelse(nchains >= 2, v = extra_parameters$v, nburn = nburn, npost = npost, nchains, 2)) %dopar% { seed = seed_chain, verbose = output_verbose, printevery = printevery, seed_chain = if (!is.null(seed)) seed + chain chain_index = chain) }, Horseshoe = { else NULL horseshoe_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$h, v = extra_parameters$v, nburn = nburn, npost = npost, printevery = printevery, chain_index = chain) }, ARD = { seed = seed_chain, verbose = output_verbose, printevery = printevery, ARD_mcmc(X, Y, intercept = !standardize, nburn = nburn, npost = npost, seed = seed_chain, verbose = output_verbose, chain_index = chain) printevery = printevery, chain_index = chain) }, Spike_Laplace = { }, Horseshoe = { spike_laplace_partially_mcmc(X, Y, intercept = !standardize, horseshoe_mcmc(X, Y, intercept = !standardize, 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) }, ARD = { 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"))})
23: suppressWarnings(foreach::foreach(chain = 1:nchains, .combine = list, 24: .multicombine = TRUE, .maxcombine = ifelse(nchains >= 2, BMI_LASSO(data$data_MI$X, data$data_MI$Y, model = "Horseshoe", nchains, 2)) %dopar% { nburn = 4000, npost = 4000, output_verbose = FALSE, nchains = 2, seed_chain = if (!is.null(seed)) ncores = 2, seed = seed) seed + chain else NULL
return(switch(model, Multi_Laplace = {25: multi_laplace_mcmc(X, Y, intercept = !standardize, h = extra_parameters$h, eval(expr, envir) v = extra_parameters$v, nburn = nburn, npost = npost,
seed = seed_chain, verbose = output_verbose, printevery = printevery, chain_index = chain)26: }, Horseshoe = {eval(expr, envir) horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn,
npost = npost, seed = seed_chain, verbose = output_verbose, 27: printevery = printevery, chain_index = chain) }, ARD = {withVisible(eval(expr, envir)) ARD_mcmc(X, Y, intercept = !standardize, nburn = nburn,
npost = npost, seed = seed_chain, verbose = output_verbose, 28: printevery = printevery, chain_index = chain)withCallingHandlers(code, error = function (e) }, Spike_Laplace = {rlang::entrace(e), message = function (cnd) spike_laplace_partially_mcmc(X, Y, intercept = !standardize, { a = extra_parameters$a, b = extra_parameters$b, nburn = nburn, watcher$capture_plot_and_output() npost = npost, seed = seed_chain, verbose = output_verbose, printevery = printevery, chain_index = chain) if (on_message$capture) { })) watcher$push(cnd)}) } if (on_message$silence) {
invokeRestart("muffleMessage")24: }BMI_LASSO(data$data_MI$X, data$data_MI$Y, model = "Horseshoe", }, warning = function (cnd) nburn = 4000, npost = 4000, output_verbose = FALSE, nchains = 2, { ncores = 2, seed = seed) if (getOption("warn") >= 2 || getOption("warn") < 0) {
return()25: } watcher$capture_plot_and_output()eval(expr, envir) if (on_warning$capture) {
cnd <- sanitize_call(cnd) watcher$push(cnd)26: } if (on_warning$silence) {eval(expr, envir) invokeRestart("muffleWarning")
}27: }, error = function (cnd) withVisible(eval(expr, envir)){
watcher$capture_plot_and_output() cnd <- sanitize_call(cnd)28: watcher$push(cnd)withCallingHandlers(code, error = function (e) switch(on_error, continue = invokeRestart("eval_continue"), rlang::entrace(e), message = function (cnd) stop = invokeRestart("eval_stop"), error = NULL){}) watcher$capture_plot_and_output()
29: if (on_message$capture) {eval(call)
watcher$push(cnd)30: }eval(call) if (on_message$silence) {
invokeRestart("muffleMessage")31: }with_handlers({}, warning = function (cnd) for (expr in tle$exprs) {{ ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) if (getOption("warn") >= 2 || getOption("warn") < 0) { } return() TRUE }}, handlers) watcher$capture_plot_and_output()
if (on_warning$capture) { cnd <- sanitize_call(cnd)32: watcher$push(cnd) }doWithOneRestart(return(expr), restart) if (on_warning$silence) { invokeRestart("muffleWarning")
}33: }, error = function (cnd) withOneRestart(expr, restarts[[1L]]){
watcher$capture_plot_and_output()34: withRestartList(expr, restarts[-nr]) cnd <- sanitize_call(cnd)
watcher$push(cnd)35: doWithOneRestart(return(expr), restart) switch(on_error, continue = invokeRestart("eval_continue"),
36: stop = invokeRestart("eval_stop"), error = NULL)})withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
29: 37: eval(call)withRestartList(expr, restarts)
30: 38: eval(call)withRestarts(with_handlers({
for (expr in tle$exprs) {31: ev <- withVisible(eval(expr, envir))with_handlers({ watcher$capture_plot_and_output() for (expr in tle$exprs) { watcher$print_value(ev$value, ev$visible, envir) ev <- withVisible(eval(expr, envir)) } watcher$capture_plot_and_output() TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) watcher$print_value(ev$value, ev$visible, envir)
} TRUE39: evaluate::evaluate(...)}, handlers)
40: 32: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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$error else {
33: if (options$error && options$include) withOneRestart(expr, restarts[[1L]]) 0L
else 2L }, output_handler = knit_handlers(options$render, options))34:
withRestartList(expr, restarts[-nr])41:
35: in_dir(input_dir(), expr)doWithOneRestart(return(expr), restart)
36: 42: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])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,
37: stop_on_error = if (is.numeric(options$error)) options$error else {withRestartList(expr, restarts) if (options$error && options$include) 0L
else 2L }, output_handler = knit_handlers(options$render, options)))38:
withRestarts(with_handlers({43: for (expr in tle$exprs) {eng_r(options) ev <- withVisible(eval(expr, envir))
watcher$capture_plot_and_output()44: watcher$print_value(ev$value, ev$visible, envir)block_exec(params) }
TRUE45: }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
call_block(x)39: evaluate::evaluate(...)
46: 40: 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, 47: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), stop_on_error = if (is.numeric(options$error)) options$error else { error = function(e) { if (options$error && options$include) if (progress && is.function(pb$interrupt)) 0L pb$interrupt() else 2L if (is_R_CMD_build() || is_R_CMD_check()) }, output_handler = knit_handlers(options$render, options)) error <<- format(e)
})41: in_dir(input_dir(), expr)
48: 42: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {in_input_dir(evaluate(code, envir = env, new_device = FALSE, if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, error <<- format(e) keep_message = if (is.numeric(options$message)) TRUE else options$message, }), list(rlang_trace_top_env = knit_global())) stop_on_error = if (is.numeric(options$error)) options$error else {
49: if (options$error && options$include) xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { 0L if (progress && is.function(pb$interrupt)) else 2L pb$interrupt() }, output_handler = knit_handlers(options$render, options))) if (is_R_CMD_build() || is_R_CMD_check())
error <<- format(e)43: }), list(rlang_trace_top_env = knit_global())), function(loc) {eng_r(options)
setwd(wd)44: write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) block_exec(params) paste0("\n", rule(), error, "\n", rule()))
}, 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:
52: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
error = function(e) {53: if (progress && is.function(pb$interrupt)) pb$interrupt()vweave_rmarkdown(...) if (is_R_CMD_build() || is_R_CMD_check())
error <<- format(e)54: })engine$weave(file, quiet = quiet, encoding = enc)
48: 55: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), doTryCatch(return(expr), name, parentenv, handler)
error = function(e) {56: if (progress && is.function(pb$interrupt)) tryCatchOne(expr, names, parentenv, handlers[[1L]]) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check())
error <<- format(e)57: }), list(rlang_trace_top_env = knit_global()))tryCatchList(expr, classes, parentenv, handlers)
49: 58: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), tryCatch({ error = function(e) { engine$weave(file, quiet = quiet, encoding = enc) if (progress && is.function(pb$interrupt)) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) pb$interrupt() if (!have.makefile && vignette_is_tex(output)) { if (is_R_CMD_build() || is_R_CMD_check()) texi2pdf(file = output, clean = FALSE, quiet = quiet) error <<- format(e) output <- find_vignette_product(name, by = "texi2pdf", }), list(rlang_trace_top_env = knit_global())), function(loc) { engine = engine) } setwd(wd) outputs <- c(outputs, output) write_utf8(res, output %n% stdout())}, error = function(e) { paste0("\nQuitting from ", loc, if (!is.null(error)) thisOK <<- FALSE paste0("\n", rule(), error, "\n", rule())) fails <<- c(fails, file)}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))
})50:
process_file(text, output)
59: 51: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/BMIselect.Rcheck/vign_test/BMIselect", knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpMQ4gRO/file11d003df3f181.rds")52:
rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), An irrecoverable exception occurred. R is aborting now ...
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/RtmpMQ4gRO/file11d003df3f181.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