Last updated on 2026-08-02 04:48:58 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.4 | 76.18 | 175.22 | 251.40 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.0.4 | 58.20 | 139.74 | 197.94 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 1.0.4 | 96.00 | 275.32 | 371.32 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.0.4 | 65.00 | 127.77 | 192.77 | OK | |
| r-devel-windows-x86_64 | 1.0.4 | 83.00 | 209.00 | 292.00 | OK | |
| r-patched-linux-x86_64 | 1.0.4 | 78.71 | 178.61 | 257.32 | OK | |
| r-release-linux-x86_64 | 1.0.4 | 74.89 | 178.35 | 253.24 | OK | |
| r-release-macos-arm64 | 1.0.4 | 16.00 | 47.00 | 63.00 | OK | |
| r-release-macos-x86_64 | 1.0.4 | 52.00 | 216.00 | 268.00 | OK | |
| r-release-windows-x86_64 | 1.0.4 | 85.00 | 208.00 | 293.00 | OK | |
| r-oldrel-macos-arm64 | 1.0.4 | 15.00 | 41.00 | 56.00 | ERROR | |
| r-oldrel-macos-x86_64 | 1.0.4 | 51.00 | 193.00 | 244.00 | OK | |
| r-oldrel-windows-x86_64 | 1.0.4 | 124.00 | 276.00 | 400.00 | OK |
Version: 1.0.4
Check: for new files in some other directories
Result: NOTE
Found the following files/directories:
‘~/tmp/scratch/Rtmp01Rf0v’ ‘~/tmp/scratch/Rtmp07esmI’
‘~/tmp/scratch/Rtmp0DQy4D’ ‘~/tmp/scratch/Rtmp0YEWxG’
‘~/tmp/scratch/Rtmp1dp3qU’ ‘~/tmp/scratch/Rtmp1vMlGe’
‘~/tmp/scratch/Rtmp1xEH1L’ ‘~/tmp/scratch/Rtmp1yC6Wb’
‘~/tmp/scratch/Rtmp2jJkPs’ ‘~/tmp/scratch/Rtmp3dXiQR’
‘~/tmp/scratch/Rtmp3yEd6B’ ‘~/tmp/scratch/Rtmp47GSz0’
‘~/tmp/scratch/Rtmp4ycvNe’ ‘~/tmp/scratch/Rtmp4z10kn’
‘~/tmp/scratch/Rtmp56By8S’ ‘~/tmp/scratch/Rtmp5Vd9q7’
‘~/tmp/scratch/Rtmp6FDati’ ‘~/tmp/scratch/Rtmp6uqej6’
‘~/tmp/scratch/Rtmp6xKbr9’ ‘~/tmp/scratch/Rtmp72aWHV’
‘~/tmp/scratch/Rtmp8v7PDD’ ‘~/tmp/scratch/RtmpAbSqxc’
‘~/tmp/scratch/RtmpAlOSPa’ ‘~/tmp/scratch/RtmpBFIOnJ’
‘~/tmp/scratch/RtmpBwFRNX’ ‘~/tmp/scratch/RtmpBxA58z’
‘~/tmp/scratch/RtmpC8io1V’ ‘~/tmp/scratch/RtmpCCqt40’
‘~/tmp/scratch/RtmpCJ94aV’ ‘~/tmp/scratch/RtmpCbfGxj’
‘~/tmp/scratch/RtmpD5ISgr’ ‘~/tmp/scratch/RtmpDtPA0a’
‘~/tmp/scratch/RtmpDyaQ8v’ ‘~/tmp/scratch/RtmpE5TF6h’
‘~/tmp/scratch/RtmpEXZ18U’ ‘~/tmp/scratch/RtmpEyHqvb’
‘~/tmp/scratch/RtmpFIv0u2’ ‘~/tmp/scratch/RtmpFchhbs’
‘~/tmp/scratch/RtmpFhttxC’ ‘~/tmp/scratch/RtmpFog4lM’
‘~/tmp/scratch/RtmpGm2Z9Q’ ‘~/tmp/scratch/RtmpHT0FaV’
‘~/tmp/scratch/RtmpHhahAs’ ‘~/tmp/scratch/RtmpHi9hNC’
‘~/tmp/scratch/RtmpI5anBW’ ‘~/tmp/scratch/RtmpI7Cb7u’
‘~/tmp/scratch/RtmpIAvV9F’ ‘~/tmp/scratch/RtmpIiHYKe’
‘~/tmp/scratch/RtmpK1YOSG’ ‘~/tmp/scratch/RtmpKVMDwa’
‘~/tmp/scratch/RtmpKXp5qW’ ‘~/tmp/scratch/RtmpKqZ0GE’
‘~/tmp/scratch/RtmpLpvKXB’ ‘~/tmp/scratch/RtmpM5iuGn’
‘~/tmp/scratch/RtmpMGKmvM’ ‘~/tmp/scratch/RtmpMc6ebT’
‘~/tmp/scratch/RtmpMqKHnG’ ‘~/tmp/scratch/RtmpMqyVXy’
‘~/tmp/scratch/RtmpMsmrE1’ ‘~/tmp/scratch/RtmpNGjVun’
‘~/tmp/scratch/RtmpNkZQfj’ ‘~/tmp/scratch/RtmpNyF2VW’
‘~/tmp/scratch/RtmpO2XdzE’ ‘~/tmp/scratch/RtmpQJVCVr’
‘~/tmp/scratch/RtmpR7Hcyy’ ‘~/tmp/scratch/RtmpRWJkLT’
‘~/tmp/scratch/RtmpRqRW9m’ ‘~/tmp/scratch/RtmpSmSUZ8’
‘~/tmp/scratch/RtmpTfoZg4’ ‘~/tmp/scratch/RtmpTzuuRF’
‘~/tmp/scratch/RtmpUgAlmJ’ ‘~/tmp/scratch/RtmpUv45Ri’
‘~/tmp/scratch/RtmpV0te5B’ ‘~/tmp/scratch/RtmpV21PAG’
‘~/tmp/scratch/RtmpVb56Z2’ ‘~/tmp/scratch/RtmpW6lDwM’
‘~/tmp/scratch/RtmpWKzH5N’ ‘~/tmp/scratch/RtmpXrazdd’
‘~/tmp/scratch/RtmpYHX6Fg’ ‘~/tmp/scratch/RtmpYUziWE’
‘~/tmp/scratch/RtmpZ59KJ5’ ‘~/tmp/scratch/RtmpZS6Hrd’
‘~/tmp/scratch/RtmpZVdveo’ ‘~/tmp/scratch/RtmpZeQRLM’
‘~/tmp/scratch/RtmpaDWWux’ ‘~/tmp/scratch/RtmpaTdr1E’
‘~/tmp/scratch/RtmpaVBt8v’ ‘~/tmp/scratch/Rtmpaa4Qfq’
‘~/tmp/scratch/Rtmpan90pN’ ‘~/tmp/scratch/Rtmpb5MObm’
‘~/tmp/scratch/RtmpbQI9Ms’ ‘~/tmp/scratch/Rtmpbo8CDP’
‘~/tmp/scratch/Rtmpc3l1dU’ ‘~/tmp/scratch/Rtmpc4vu1D’
‘~/tmp/scratch/Rtmpcrrodh’ ‘~/tmp/scratch/Rtmpcy5tva’
‘~/tmp/scratch/RtmpcyfKZk’ ‘~/tmp/scratch/Rtmpd0Nr7x’
‘~/tmp/scratch/Rtmpe2VmfN’ ‘~/tmp/scratch/Rtmpe9Dhmy’
‘~/tmp/scratch/RtmpfVAp5X’ ‘~/tmp/scratch/RtmpfcalIy’
‘~/tmp/scratch/RtmpfivS7e’ ‘~/tmp/scratch/RtmpfseAJG’
‘~/tmp/scratch/Rtmph62Dfd’ ‘~/tmp/scratch/Rtmph9FyxD’
‘~/tmp/scratch/RtmphMQ6vK’ ‘~/tmp/scratch/RtmphfQQZ5’
‘~/tmp/scratch/Rtmphjt9ij’ ‘~/tmp/scratch/RtmphvmiCe’
‘~/tmp/scratch/Rtmpj7N6Tp’ ‘~/tmp/scratch/RtmpjK9K3Z’
‘~/tmp/scratch/RtmpjaCtUu’ ‘~/tmp/scratch/RtmpjfVSbp’
‘~/tmp/scratch/RtmpkCrROq’ ‘~/tmp/scratch/RtmpkcxB1N’
‘~/tmp/scratch/RtmpkkcWiN’ ‘~/tmp/scratch/RtmplWEjsj’
‘~/tmp/scratch/RtmplkRLRg’ ‘~/tmp/scratch/RtmpmDEoYG’
‘~/tmp/scratch/RtmpmOuEh2’ ‘~/tmp/scratch/Rtmpmjwxzw’
‘~/tmp/scratch/Rtmpo1sGYK’ ‘~/tmp/scratch/RtmpoHM5qh’
‘~/tmp/scratch/Rtmppwkxe0’ ‘~/tmp/scratch/Rtmpq4vKk8’
‘~/tmp/scratch/RtmpqA1eAF’ ‘~/tmp/scratch/RtmpqYnLDC’
‘~/tmp/scratch/Rtmpr0KvuE’ ‘~/tmp/scratch/Rtmpr5AdVb’
‘~/tmp/scratch/RtmprEoT7r’ ‘~/tmp/scratch/RtmprLTTeJ’
‘~/tmp/scratch/RtmprUWL1g’ ‘~/tmp/scratch/RtmprqEWTz’
‘~/tmp/scratch/Rtmps3waGV’ ‘~/tmp/scratch/Rtmpt491Iy’
‘~/tmp/scratch/Rtmpt4bBC6’ ‘~/tmp/scratch/RtmptPipoG’
‘~/tmp/scratch/Rtmpu4x96m’ ‘~/tmp/scratch/RtmpuYXVxO’
‘~/tmp/scratch/Rtmpuf4q55’ ‘~/tmp/scratch/RtmpuiGiz8’
‘~/tmp/scratch/RtmpunH0hY’ ‘~/tmp/scratch/RtmpussMBb’
‘~/tmp/scratch/RtmpuziKp4’ ‘~/tmp/scratch/RtmpvGBLjY’
‘~/tmp/scratch/RtmpwJOIZ0’ ‘~/tmp/scratch/Rtmpwr9fLC’
‘~/tmp/scratch/Rtmpx9X2Lu’ ‘~/tmp/scratch/RtmpxGmp0l’
‘~/tmp/scratch/RtmpxKHOiW’ ‘~/tmp/scratch/RtmpxaIdGC’
‘~/tmp/scratch/RtmpydMsAC’ ‘~/tmp/scratch/Rtmpytjp2f’
‘~/tmp/scratch/Rtmpz1YCu6’ ‘~/tmp/scratch/Rtmpz9sEmb’
‘~/tmp/scratch/RtmpzBzfNW’ ‘~/tmp/scratch/RtmpzcvoqS’
‘~/tmp/scratch/Rtmpzhhn5l’ ‘~/tmp/scratch/xvfb-run.0WjWQK’
‘~/tmp/scratch/xvfb-run.0XQR5E’ ‘~/tmp/scratch/xvfb-run.11APaY’
‘~/tmp/scratch/xvfb-run.1Hv95m’ ‘~/tmp/scratch/xvfb-run.3jb05B’
‘~/tmp/scratch/xvfb-run.5D45ZM’ ‘~/tmp/scratch/xvfb-run.68rZzD’
‘~/tmp/scratch/xvfb-run.7Dn2gZ’ ‘~/tmp/scratch/xvfb-run.8pZhL6’
‘~/tmp/scratch/xvfb-run.8rt454’ ‘~/tmp/scratch/xvfb-run.9djELi’
‘~/tmp/scratch/xvfb-run.9lELR2’ ‘~/tmp/scratch/xvfb-run.A91ong’
‘~/tmp/scratch/xvfb-run.AXNPAX’ ‘~/tmp/scratch/xvfb-run.BXJVBC’
‘~/tmp/scratch/xvfb-run.C0e9lH’ ‘~/tmp/scratch/xvfb-run.CELTE3’
‘~/tmp/scratch/xvfb-run.CWSbln’ ‘~/tmp/scratch/xvfb-run.Fbv4w5’
‘~/tmp/scratch/xvfb-run.GrU3Cx’ ‘~/tmp/scratch/xvfb-run.H6fiVf’
‘~/tmp/scratch/xvfb-run.Hrylrw’ ‘~/tmp/scratch/xvfb-run.I21akc’
‘~/tmp/scratch/xvfb-run.IgBBQm’ ‘~/tmp/scratch/xvfb-run.IidtTW’
‘~/tmp/scratch/xvfb-run.IlbVxW’ ‘~/tmp/scratch/xvfb-run.KxzuDK’
‘~/tmp/scratch/xvfb-run.L0dzLL’ ‘~/tmp/scratch/xvfb-run.LCYHfu’
‘~/tmp/scratch/xvfb-run.Lbm7XV’ ‘~/tmp/scratch/xvfb-run.LdKLkR’
‘~/tmp/scratch/xvfb-run.LqGYNE’ ‘~/tmp/scratch/xvfb-run.MNOapE’
‘~/tmp/scratch/xvfb-run.MYOlJi’ ‘~/tmp/scratch/xvfb-run.O6gQWg’
‘~/tmp/scratch/xvfb-run.O97yb6’ ‘~/tmp/scratch/xvfb-run.ORJHjy’
‘~/tmp/scratch/xvfb-run.POjB7x’ ‘~/tmp/scratch/xvfb-run.PQ7c9i’
‘~/tmp/scratch/xvfb-run.QKpiuZ’ ‘~/tmp/scratch/xvfb-run.QaxXmN’
‘~/tmp/scratch/xvfb-run.Ru0Zuh’ ‘~/tmp/scratch/xvfb-run.UJ5Rwr’
‘~/tmp/scratch/xvfb-run.UkznpC’ ‘~/tmp/scratch/xvfb-run.XGShKZ’
‘~/tmp/scratch/xvfb-run.ZW1FGG’ ‘~/tmp/scratch/xvfb-run.aoFnOi’
‘~/tmp/scratch/xvfb-run.auaM8V’ ‘~/tmp/scratch/xvfb-run.bqmoiK’
‘~/tmp/scratch/xvfb-run.cCbpVc’ ‘~/tmp/scratch/xvfb-run.cTt7x0’
‘~/tmp/scratch/xvfb-run.d2Zv6D’ ‘~/tmp/scratch/xvfb-run.dzOCYY’
‘~/tmp/scratch/xvfb-run.e3T8iB’ ‘~/tmp/scratch/xvfb-run.ekQ6t9’
‘~/tmp/scratch/xvfb-run.eqmzts’ ‘~/tmp/scratch/xvfb-run.hFLQv7’
‘~/tmp/scratch/xvfb-run.itEvm8’ ‘~/tmp/scratch/xvfb-run.jA1KBC’
‘~/tmp/scratch/xvfb-run.jX6dOk’ ‘~/tmp/scratch/xvfb-run.lzm0g8’
‘~/tmp/scratch/xvfb-run.oIgyTf’ ‘~/tmp/scratch/xvfb-run.ox65gz’
‘~/tmp/scratch/xvfb-run.p8be9G’ ‘~/tmp/scratch/xvfb-run.r9YJhp’
‘~/tmp/scratch/xvfb-run.sKpFbl’ ‘~/tmp/scratch/xvfb-run.ssI6Xk’
‘~/tmp/scratch/xvfb-run.tIzL3a’ ‘~/tmp/scratch/xvfb-run.tx2WIE’
‘~/tmp/scratch/xvfb-run.xKvrvt’
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0.4
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 = { horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn, npost = npost, seed = seed_chain, verbose = output_verbose, 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, npost = npost, seed = seed_chain, verbose = output_verbose, printevery = printevery, chain_index = chain) }))}
22: withCallingHandlers(expr, warning = function(w) if (inherits(w, classes)) tryInvokeRestart("muffleWarning"))
23: suppressWarnings(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 = { horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn, npost = npost, seed = seed_chain, verbose = output_verbose, 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, npost = npost, seed = seed_chain, verbose = output_verbose, printevery = printevery, chain_index = chain) }))})
24: 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)
25: eval(expr, envir)
26: eval(expr, envir)
27: withVisible(eval(expr, envir))
28: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
29: eval(call)
30:
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: eval(call)
31: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
32: doWithOneRestart(return(expr), restart)
33: withOneRestart(expr, restarts[[1L]])
tryCatchOne(expr, names, parentenv, handlers[[1L]])
7: tryCatchList(expr, classes, parentenv, handlers)
8: tryCatch(eval(c.expr, envir = args, enclos = envir), error = function(e) e)
9: FUN(X[[i]], ...)
10: 34: withRestartList(expr, restarts[-nr])
35: doWithOneRestart(return(expr), restart)
36: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])lapply(X = S, FUN = FUN, ...)
11: doTryCatch(return(expr), name, parentenv, handler)
12:
37: withRestartList(expr, restarts)
38: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir)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))) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
39: evaluate::evaluate(...) 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))
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, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
41: in_dir(input_dir(), expr)
42: in_input_dir(evaluate(code, envir = env, new_device = FALSE, w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " keep_warning = if (is.numeric(options$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: msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) }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: invisible(structure(msg, class = "try-error", condition = e))})
15: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), try(lapply(X = S, FUN = FUN, ...), silent = TRUE) 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) {
16: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
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)
17: 52: FUN(X[[i]], ...)rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
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 = { horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn, npost = npost, seed = seed_chain, verbose = output_verbose, 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, output_dir = getwd(), ...)
53: vweave_rmarkdown(...)
54: engine$weave(file, quiet = quiet, encoding = enc) a = extra_parameters$a, b = extra_parameters$b, nburn = nburn, npost = npost, seed = seed_chain, verbose = output_verbose, printevery = printevery, chain_index = chain) }))
55: doTryCatch(return(expr), name, parentenv, handler)
56: tryCatchOne(expr, names, parentenv, handlers[[1L]])
}
22: withCallingHandlers(expr, warning = function(w) if (inherits(w, classes)) tryInvokeRestart("muffleWarning"))
23: suppressWarnings(foreach::foreach(chain = 1:nchains, .combine = list, .multicombine = TRUE, .maxcombine = ifelse(nchains >= 2, nchains, 2)) %dopar% { seed_chain = if (!is.null(seed)) seed + chain else NULL return(switch(model, Multi_Laplace = { multi_laplace_mcmc(X, Y, intercept = !standardize, h = extra_parameters$h, 57: tryCatchList(expr, classes, parentenv, handlers)
58: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
59: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/BMIselect.Rcheck/vign_test/BMIselect", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpXR0Qmx/fileab314d280a8c.rds")
An irrecoverable exception occurred. R is aborting now ...
v = extra_parameters$v, nburn = nburn, npost = npost, seed = seed_chain, verbose = output_verbose, printevery = printevery, chain_index = chain) }, Horseshoe = { horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn, npost = npost, seed = seed_chain, verbose = output_verbose, 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, npost = npost, seed = seed_chain, verbose = output_verbose, printevery = printevery, chain_index = chain) }))})
24: 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)
25: eval(expr, envir)
26: eval(expr, envir)
27: withVisible(eval(expr, envir))
28: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
29: eval(call)
30: eval(call)
31: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
32: doWithOneRestart(return(expr), restart)
33: withOneRestart(expr, restarts[[1L]])
34: withRestartList(expr, restarts[-nr])
35: doWithOneRestart(return(expr), restart)
36: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
37: withRestartList(expr, restarts)
38: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
39: evaluate::evaluate(...)
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, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
41: in_dir(input_dir(), expr)
42: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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/RtmpXR0Qmx/fileab314d280a8c.rds")
An irrecoverable exception occurred. R is aborting now ...
Quitting from Introduction.Rmd:164-179 [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::apply(c$post_pool_beta, 2, function(x) mean(abs(x) <= sqrt(stats::var(x))))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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