Last updated on 2026-08-03 18:50:09 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 | 58.92 | 134.98 | 193.90 | 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 | 84.00 | 205.00 | 289.00 | OK | |
| r-oldrel-macos-arm64 | 1.0.4 | 14.00 | 40.00 | 54.00 | 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/Rtmp0apP4j’ ‘~/tmp/scratch/Rtmp0juL3N’
‘~/tmp/scratch/Rtmp2XPf2C’ ‘~/tmp/scratch/Rtmp3YAu4F’
‘~/tmp/scratch/Rtmp3wARPI’ ‘~/tmp/scratch/Rtmp5Nj9pM’
‘~/tmp/scratch/Rtmp5evoBo’ ‘~/tmp/scratch/Rtmp5lWtxk’
‘~/tmp/scratch/Rtmp5sV6yo’ ‘~/tmp/scratch/Rtmp5xoS8r’
‘~/tmp/scratch/Rtmp683M9x’ ‘~/tmp/scratch/Rtmp6vHNYy’
‘~/tmp/scratch/Rtmp7UZUA8’ ‘~/tmp/scratch/Rtmp8IzNbl’
‘~/tmp/scratch/Rtmp8RPESa’ ‘~/tmp/scratch/Rtmp8gOVEH’
‘~/tmp/scratch/Rtmp8iSDdp’ ‘~/tmp/scratch/Rtmp8l1t0f’
‘~/tmp/scratch/Rtmp92NHzT’ ‘~/tmp/scratch/RtmpAKwsg3’
‘~/tmp/scratch/RtmpBF0mQD’ ‘~/tmp/scratch/RtmpDEbkiK’
‘~/tmp/scratch/RtmpDKFkIb’ ‘~/tmp/scratch/RtmpDQwxeL’
‘~/tmp/scratch/RtmpErqK0e’ ‘~/tmp/scratch/RtmpF968z7’
‘~/tmp/scratch/RtmpFSOyfO’ ‘~/tmp/scratch/RtmpFahqt0’
‘~/tmp/scratch/RtmpFhEqaZ’ ‘~/tmp/scratch/RtmpGMaA9G’
‘~/tmp/scratch/RtmpGSZYxS’ ‘~/tmp/scratch/RtmpHVVCbC’
‘~/tmp/scratch/RtmpHgSDMj’ ‘~/tmp/scratch/RtmpHgyj4c’
‘~/tmp/scratch/RtmpHl82DT’ ‘~/tmp/scratch/RtmpIE2EKN’
‘~/tmp/scratch/RtmpIOxqGZ’ ‘~/tmp/scratch/RtmpIPKvMm’
‘~/tmp/scratch/RtmpIgWxLR’ ‘~/tmp/scratch/RtmpJ7sZjX’
‘~/tmp/scratch/RtmpJCSEmZ’ ‘~/tmp/scratch/RtmpJPRMlv’
‘~/tmp/scratch/RtmpL9s1QX’ ‘~/tmp/scratch/RtmpLjtGBW’
‘~/tmp/scratch/RtmpM4nczn’ ‘~/tmp/scratch/RtmpMolVa5’
‘~/tmp/scratch/RtmpNQO55n’ ‘~/tmp/scratch/RtmpNX9smD’
‘~/tmp/scratch/RtmpNdaHAe’ ‘~/tmp/scratch/RtmpNo7vZ7’
‘~/tmp/scratch/RtmpOwl3mz’ ‘~/tmp/scratch/RtmpPP7jBS’
‘~/tmp/scratch/RtmpPb7cgv’ ‘~/tmp/scratch/RtmpPbSwrP’
‘~/tmp/scratch/RtmpQ2SSFg’ ‘~/tmp/scratch/RtmpQJTjko’
‘~/tmp/scratch/RtmpQZvi2u’ ‘~/tmp/scratch/RtmpQll4sU’
‘~/tmp/scratch/RtmpRzZU4C’ ‘~/tmp/scratch/RtmpRzuWPI’
‘~/tmp/scratch/RtmpSefhpy’ ‘~/tmp/scratch/RtmpShTrgH’
‘~/tmp/scratch/RtmpT2E7lA’ ‘~/tmp/scratch/RtmpT2HegB’
‘~/tmp/scratch/RtmpTSNJDZ’ ‘~/tmp/scratch/RtmpTtOaiB’
‘~/tmp/scratch/RtmpUcBwfB’ ‘~/tmp/scratch/RtmpUki5eH’
‘~/tmp/scratch/RtmpUmq4ef’ ‘~/tmp/scratch/RtmpVDqCxP’
‘~/tmp/scratch/RtmpVI1SDq’ ‘~/tmp/scratch/RtmpVV4euU’
‘~/tmp/scratch/RtmpVfl2cD’ ‘~/tmp/scratch/RtmpVl0zQn’
‘~/tmp/scratch/RtmpW7hF0C’ ‘~/tmp/scratch/RtmpX3uhRt’
‘~/tmp/scratch/RtmpYCbgIx’ ‘~/tmp/scratch/RtmpYQYzXb’
‘~/tmp/scratch/RtmpYaBQKN’ ‘~/tmp/scratch/RtmpYvzzwd’
‘~/tmp/scratch/RtmpZX9WpY’ ‘~/tmp/scratch/RtmpZZf8nD’
‘~/tmp/scratch/RtmpZayGan’ ‘~/tmp/scratch/RtmpZs4g5k’
‘~/tmp/scratch/Rtmpa4jHuQ’ ‘~/tmp/scratch/RtmpaltxcQ’
‘~/tmp/scratch/RtmpbBGMF8’ ‘~/tmp/scratch/RtmpcKcKvM’
‘~/tmp/scratch/Rtmpd8ckkG’ ‘~/tmp/scratch/RtmpdKuLnd’
‘~/tmp/scratch/RtmpdN5feq’ ‘~/tmp/scratch/RtmpexGoiy’
‘~/tmp/scratch/RtmpeyVCbL’ ‘~/tmp/scratch/RtmpfalV71’
‘~/tmp/scratch/RtmpfjB7Er’ ‘~/tmp/scratch/Rtmpfm4idN’
‘~/tmp/scratch/Rtmpg4U262’ ‘~/tmp/scratch/RtmpgBNkLT’
‘~/tmp/scratch/RtmpgH4Rso’ ‘~/tmp/scratch/Rtmpi235bB’
‘~/tmp/scratch/RtmpiDSeYp’ ‘~/tmp/scratch/RtmpidpJgc’
‘~/tmp/scratch/Rtmpj3zskb’ ‘~/tmp/scratch/RtmpjiVhgk’
‘~/tmp/scratch/RtmpkB8aOR’ ‘~/tmp/scratch/RtmpkmRqd5’
‘~/tmp/scratch/Rtmpknj5yc’ ‘~/tmp/scratch/Rtmpl5ipQf’
‘~/tmp/scratch/Rtmpl8PyDh’ ‘~/tmp/scratch/RtmplOjMoG’
‘~/tmp/scratch/RtmplkQd9l’ ‘~/tmp/scratch/RtmpmPSbiq’
‘~/tmp/scratch/RtmpmdbtMM’ ‘~/tmp/scratch/RtmpmlBiEK’
‘~/tmp/scratch/Rtmpn4wcVI’ ‘~/tmp/scratch/RtmpnsIDFq’
‘~/tmp/scratch/Rtmpnzsiko’ ‘~/tmp/scratch/RtmpoZLyP7’
‘~/tmp/scratch/Rtmpp0dxbi’ ‘~/tmp/scratch/RtmppoTbjj’
‘~/tmp/scratch/Rtmpq7k0cm’ ‘~/tmp/scratch/RtmpqcVfRw’
‘~/tmp/scratch/RtmprMlEgK’ ‘~/tmp/scratch/RtmprgsefV’
‘~/tmp/scratch/RtmpsEWwIl’ ‘~/tmp/scratch/RtmpsNm1NC’
‘~/tmp/scratch/RtmptMSb5D’ ‘~/tmp/scratch/RtmptUZAjc’
‘~/tmp/scratch/RtmptoSI3i’ ‘~/tmp/scratch/Rtmpu6gGvW’
‘~/tmp/scratch/RtmpuJRDQt’ ‘~/tmp/scratch/RtmpuK1d2q’
‘~/tmp/scratch/RtmpuMSCgy’ ‘~/tmp/scratch/Rtmpuacak3’
‘~/tmp/scratch/RtmpurRfze’ ‘~/tmp/scratch/RtmpuyLq6M’
‘~/tmp/scratch/RtmpvFE8rp’ ‘~/tmp/scratch/RtmpvspshZ’
‘~/tmp/scratch/RtmpxHoeXB’ ‘~/tmp/scratch/Rtmpy7QZDR’
‘~/tmp/scratch/RtmpyNHybL’ ‘~/tmp/scratch/RtmpyP5k8J’
‘~/tmp/scratch/RtmpzMV9PQ’ ‘~/tmp/scratch/RtmpzU2CsF’
‘~/tmp/scratch/RtmpzWgyiM’ ‘~/tmp/scratch/RtmpzptrWf’
‘~/tmp/scratch/xvfb-run.11JBIN’ ‘~/tmp/scratch/xvfb-run.1gyDeq’
‘~/tmp/scratch/xvfb-run.26K1us’ ‘~/tmp/scratch/xvfb-run.26Qpkp’
‘~/tmp/scratch/xvfb-run.3tPQiQ’ ‘~/tmp/scratch/xvfb-run.7ioxXm’
‘~/tmp/scratch/xvfb-run.9fKnq0’ ‘~/tmp/scratch/xvfb-run.BT8bZ8’
‘~/tmp/scratch/xvfb-run.BssbBe’ ‘~/tmp/scratch/xvfb-run.BwQbAD’
‘~/tmp/scratch/xvfb-run.CZu9xc’ ‘~/tmp/scratch/xvfb-run.CwlH6d’
‘~/tmp/scratch/xvfb-run.DntMur’ ‘~/tmp/scratch/xvfb-run.DsWF0t’
‘~/tmp/scratch/xvfb-run.Ezq3Yz’ ‘~/tmp/scratch/xvfb-run.F50Kue’
‘~/tmp/scratch/xvfb-run.FZVYQY’ ‘~/tmp/scratch/xvfb-run.FdoVZg’
‘~/tmp/scratch/xvfb-run.GO3Qym’ ‘~/tmp/scratch/xvfb-run.GXCpwm’
‘~/tmp/scratch/xvfb-run.IfdNuV’ ‘~/tmp/scratch/xvfb-run.Jxlnf5’
‘~/tmp/scratch/xvfb-run.Khce4Y’ ‘~/tmp/scratch/xvfb-run.LEa0dT’
‘~/tmp/scratch/xvfb-run.Lx7p9z’ ‘~/tmp/scratch/xvfb-run.MIYnVZ’
‘~/tmp/scratch/xvfb-run.ODPAaT’ ‘~/tmp/scratch/xvfb-run.OTYByw’
‘~/tmp/scratch/xvfb-run.OylF5n’ ‘~/tmp/scratch/xvfb-run.QIdYnh’
‘~/tmp/scratch/xvfb-run.QPljzG’ ‘~/tmp/scratch/xvfb-run.SkMnef’
‘~/tmp/scratch/xvfb-run.TEaigK’ ‘~/tmp/scratch/xvfb-run.VxPjDo’
‘~/tmp/scratch/xvfb-run.XB5ClR’ ‘~/tmp/scratch/xvfb-run.XRmeaJ’
‘~/tmp/scratch/xvfb-run.XnE0DN’ ‘~/tmp/scratch/xvfb-run.YH5aDk’
‘~/tmp/scratch/xvfb-run.YlfZnH’ ‘~/tmp/scratch/xvfb-run.YoQJ8P’
‘~/tmp/scratch/xvfb-run.Z761Ei’ ‘~/tmp/scratch/xvfb-run.bCuUBj’
‘~/tmp/scratch/xvfb-run.bK2MTq’ ‘~/tmp/scratch/xvfb-run.bPalxJ’
‘~/tmp/scratch/xvfb-run.g0IqgU’ ‘~/tmp/scratch/xvfb-run.hSc82j’
‘~/tmp/scratch/xvfb-run.iSEDRK’ ‘~/tmp/scratch/xvfb-run.icARkX’
‘~/tmp/scratch/xvfb-run.j2pAYr’ ‘~/tmp/scratch/xvfb-run.jOSrOD’
‘~/tmp/scratch/xvfb-run.jUptnP’ ‘~/tmp/scratch/xvfb-run.jkoucd’
‘~/tmp/scratch/xvfb-run.jvP84a’ ‘~/tmp/scratch/xvfb-run.l329S1’
‘~/tmp/scratch/xvfb-run.nKfX2v’ ‘~/tmp/scratch/xvfb-run.q5cmWX’
‘~/tmp/scratch/xvfb-run.qf20tj’ ‘~/tmp/scratch/xvfb-run.qqlKgU’
‘~/tmp/scratch/xvfb-run.rLQciZ’ ‘~/tmp/scratch/xvfb-run.s1if1J’
‘~/tmp/scratch/xvfb-run.uikOUE’ ‘~/tmp/scratch/xvfb-run.vtSwOE’
‘~/tmp/scratch/xvfb-run.wuJSeH’ ‘~/tmp/scratch/xvfb-run.yaSwN6’
‘~/tmp/scratch/xvfb-run.yq5hTo’ ‘~/tmp/scratch/xvfb-run.zFvS7R’
‘~/tmp/scratch/xvfb-run.zf8NNp’ ‘~/tmp/scratch/xvfb-run.zwWzRF’
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$h,
Traceback:
1: cpp_horseshoe(X, Y, intercept, as.integer(nburn), as.integer(npost), seed, verbose, as.integer(printevery), as.integer(chain_index))
2: horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn, npost = npost, seed = seed_chain, verbose = output_verbose, printevery = printevery, chain_index = chain)
3: eval(c.expr, envir = args, enclos = envir) v = extra_parameters$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,
4: eval(c.expr, envir = args, enclos = envir)
5: doTryCatch(return(expr), name, parentenv, handler)
6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
7: 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 = {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, ...)
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, 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) 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 = { 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 ") } 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) 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))
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)
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, { 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) 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, })
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$visible, envir) } TRUE .multicombine = TRUE, .maxcombine = ifelse(nchains >= 2, nchains, 2)) %dopar% { seed_chain = if (!is.null(seed)) seed + chain else NULL return(switch(model, Multi_Laplace = { multi_laplace_mcmc(X, Y, intercept = !standardize, h = extra_parameters$h, v = extra_parameters$v, nburn = nburn, npost = npost, seed = seed_chain, verbose = output_verbose, printevery = printevery, chain_index = chain) }, Horseshoe = { horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn, npost = npost, seed = seed_chain, verbose = output_verbose, printevery = printevery, chain_index = chain) }, ARD = {}, handlers)
32: doWithOneRestart(return(expr), restart)
33: withOneRestart(expr, restarts[[1L]])
34: withRestartList(expr, restarts[-nr])
35: doWithOneRestart(return(expr), restart)
ARD_mcmc(X, Y, intercept = !standardize, nburn = nburn, npost = npost, seed = seed_chain, verbose = output_verbose, printevery = printevery, chain_index = chain) }, Spike_Laplace = { spike_laplace_partially_mcmc(X, Y, intercept = !standardize, a = extra_parameters$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$Y, model = "Horseshoe", nburn = 4000, npost = 4000, output_verbose = FALSE, nchains = 2, 36: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
37: withRestartList(expr, restarts)
38: withRestarts(with_handlers({ for (expr in tle$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) 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")
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$render, options))
41: }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
29: eval(call)in_dir(input_dir(), expr)
42: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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)))
30: eval(call)
31: with_handlers({
43: eng_r(options)
44: block_exec(params)
45: call_block(x)
46: for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
32: doWithOneRestart(return(expr), restart)
33: withOneRestart(expr, restarts[[1L]])
process_group(group)
47: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
34: withRestartList(expr, restarts[-nr])
35: doWithOneRestart(return(expr), restart)
36: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
37: withRestartList(expr, restarts)
38: withRestarts(with_handlers({ for (expr in tle$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)
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)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$render, options)) }), list(rlang_trace_top_env = knit_global()))
49: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
41: in_dir(input_dir(), expr)
42: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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)
50: process_file(text, output)
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: 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$weave(file, quiet = quiet, encoding = enc)
55: doTryCatch(return(expr), name, parentenv, handler)
56: process_file(text, output)
51: tryCatchOne(expr, names, parentenv, handlers[[1L]])
57: tryCatchList(expr, classes, parentenv, handlers)
58: tryCatch({ engine$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", 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(...)
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/RtmpEigOR8/filee65a317f521b.rds")
An irrecoverable exception occurred. R is aborting now ...
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/RtmpEigOR8/filee65a317f521b.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