Check results for 'BMIselect'

using R Under development (unstable) (2026-02-12 r89409)
using platform: aarch64-apple-darwin23
R was compiled by Apple clang version 17.0.0 (clang-1700.3.19.1) GNU Fortran (GCC) 14.2.0
running under: macOS Sequoia 15.7.1
using session charset: UTF-8 * current time: 2026-02-13 02:25:48 UTC
checking for file ‘BMIselect/DESCRIPTION’ ... OK
this is package ‘BMIselect’ version ‘1.0.3’
package encoding: UTF-8
checking package namespace information ... OK
checking package dependencies ... OK
checking if this is a source package ... OK
checking if there is a namespace ... OK
checking for executable files ... OK
checking for hidden files and directories ... OK
checking for portable file names ... OK
checking for sufficient/correct file permissions ... OK
checking whether package ‘BMIselect’ can be installed ... [1s/1s] OK See the install log for details.
checking installed package size ... OK
checking package directory ... OK
checking ‘build’ directory ... OK
checking DESCRIPTION meta-information ... OK
checking top-level files ... OK
checking for left-over files ... OK
checking index information ... OK
checking package subdirectories ... OK
checking code files for non-ASCII characters ... OK
checking R files for syntax errors ... OK
checking whether the package can be loaded ... [0s/0s] OK
checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
checking whether the package can be unloaded cleanly ... [0s/0s] OK
checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
checking loading without being on the library search path ... [0s/0s] OK
checking dependencies in R code ... OK
checking S3 generic/method consistency ... OK
checking replacement functions ... OK
checking foreign function calls ... OK
checking R code for possible problems ... [2s/2s] OK
checking Rd files ... [0s/0s] OK
checking Rd metadata ... OK
checking Rd cross-references ... OK
checking for missing documentation entries ... OK
checking for code/documentation mismatches ... OK
checking Rd \usage sections ... OK
checking Rd contents ... OK
checking for unstated dependencies in examples ... OK
checking installed files from ‘inst/doc’ ... OK
checking files in ‘vignettes’ ... OK
checking examples ... [11s/6s] OK
checking for unstated dependencies in vignettes ... OK
checking package vignettes ... OK
checking re-building of vignette outputs ... [95s/35s] 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: H_update_beta(X, Y, XtX, alpha, lambda2, tau2, sigma2) 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: H_update_beta(X, Y, XtX, alpha, lambda2, tau2, sigma2) 2: horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn, npost = npost, seed = seed_chain, verbose = output_verbose, printevery = printevery, chain_index = chain) 3: 10: lapply(X = S, FUN = FUN, ...) 11: doTryCatch(return(expr), name, parentenv, handler) 12: eval(c.expr, envir = args, enclos = envir) 4: 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: 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: 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)tryCatchOne(expr, names, parentenv, handlers[[1L]]) 13: tryCatchList(expr, classes, parentenv, handlers) }, Horseshoe = { horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn, npost = npost, seed = seed_chain, verbose = output_verbose, printevery = printevery, chain_index = chain) 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 ") }, ARD = { ARD_mcmc(X, Y, intercept = !standardize, nburn = nburn, npost = npost, seed = seed_chain, verbose = output_verbose, printevery = printevery, chain_index = chain) } 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) }, Spike_Laplace = { spike_laplace_partially_mcmc(X, Y, intercept = !standardize, a = extra_parameters$a, b = extra_parameters$b, nburn = nburn, 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) npost = npost, seed = seed_chain, verbose = output_verbose, printevery = printevery, chain_index = chain) })) 21: foreach::foreach(chain = 1:nchains, .combine = list, .multicombine = TRUE, } 22: .maxcombine = ifelse(nchains >= 2, nchains, 2)) %dopar% { seed_chain = if (!is.null(seed)) seed + chainwithCallingHandlers(expr, warning = function(w) if (inherits(w, classes)) tryInvokeRestart("muffleWarning")) else NULL return(switch(model, Multi_Laplace = { multi_laplace_mcmc(X, Y, intercept = !standardize, h = extra_parameters$h, 23: suppressWarnings(foreach::foreach(chain = 1:nchains, .combine = list, .multicombine = TRUE, .maxcombine = ifelse(nchains >= 2, v = extra_parameters$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 = { nchains, 2)) %dopar% { seed_chain = if (!is.null(seed)) seed + chain 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) }))} else NULL return(switch(model, Multi_Laplace = { multi_laplace_mcmc(X, Y, intercept = !standardize, h = extra_parameters$h, 22: withCallingHandlers(expr, warning = function(w) if (inherits(w, v = extra_parameters$v, nburn = nburn, npost = npost, seed = seed_chain, verbose = output_verbose, printevery = printevery, chain_index = chain) classes)) tryInvokeRestart("muffleWarning")) 23: }, Horseshoe = { horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn, npost = npost, seed = seed_chain, verbose = output_verbose, 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, 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) }, 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, 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) 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)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$capture_plot_and_output()27: withVisible(eval(expr, envir)) if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd)28: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) } if (on_warning$silence) { invokeRestart("muffleWarning"){ watcher$capture_plot_and_output() if (on_message$capture) { }}, error = function (cnd) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)}) } watcher$capture_plot_and_output() if (on_warning$capture) { 29: eval(call) 30: eval(call) cnd <- sanitize_call(cnd) watcher$push(cnd) } 31: with_handlers({ if (on_warning$silence) { invokeRestart("muffleWarning") } for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers) 32: }, error = function (cnd) { watcher$capture_plot_and_output()doWithOneRestart(return(expr), restart) 33: withOneRestart(expr, restarts[[1L]]) 34: withRestartList(expr, restarts[-nr]) 35: cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), doWithOneRestart(return(expr), restart) 36: stop = invokeRestart("eval_stop"), error = NULL)}) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 37: 29: eval(call) 30: eval(call) withRestartList(expr, restarts) 38: withRestarts(with_handlers({ for (expr in tle$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: 31: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers) 32: doWithOneRestart(return(expr), restart) 33: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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: withOneRestart(expr, restarts[[1L]]) 34: withRestartList(expr, restarts[-nr]) 35: doWithOneRestart(return(expr), restart) 36: 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, withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 37: stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))) withRestartList(expr, restarts) 38: 43: eng_r(options) withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) }44: block_exec(params) 45: call_block(x) TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) 46: process_group(group) 47: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {39: evaluate::evaluate(...) if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }) 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$render, options)) 48: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {41: in_dir(input_dir(), expr) if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) 42: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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$include) error <<- format(e) }), list(rlang_trace_top_env = knit_global())) 0L else 2L }, output_handler = knit_handlers(options$render, options)))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()) 43: eng_r(options) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) 44: block_exec(params) 45: call_block(x) 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(...) 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: 54: engine$weave(file, quiet = quiet, encoding = enc) 55: doTryCatch(return(expr), name, parentenv, handler)with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) 56: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 57: tryCatchList(expr, classes, parentenv, handlers) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) 58: tryCatch({ }), list(rlang_trace_top_env = knit_global())) 49: engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine)xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) engine = engine) } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))}) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) 59: tools::buildVignettes(dir = "/Volumes/Builds/packages/sonoma-arm64/results/4.6/BMIselect.Rcheck/vign_test/BMIselect", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpGsvQRC/file92b255d98505.rds") An irrecoverable exception occurred. R is aborting now ... 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/sonoma-arm64/results/4.6/BMIselect.Rcheck/vign_test/BMIselect", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpGsvQRC/file92b255d98505.rds") An irrecoverable exception occurred. R is aborting now ... Quitting from Introduction.Rmd:164-171 [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
checking PDF version of manual ... [2s/2s] OK
DONE Status: 1 ERROR
using check arguments '--no-clean-on-error '