Created
October 11, 2024 10:56
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hard to trigger error first seen in ubuntu 24.04, now similar on intel mac
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| ############################################################################## | |
| ############################################################################## | |
| ### | |
| ### Running command: | |
| ### | |
| ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data BiocFileCache | |
| ### | |
| ############################################################################## | |
| ############################################################################## | |
| * checking for file ‘BiocFileCache/DESCRIPTION’ ... OK | |
| * preparing ‘BiocFileCache’: | |
| * checking DESCRIPTION meta-information ... OK | |
| * installing the package to build vignettes | |
| * creating vignettes ...sh: line 1: 22366 Segmentation fault: 11 '/Library/Frameworks/R.framework/Resources/bin/Rscript' --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)" > '/tmp/RtmpiFiMqj/xshell55f3109b71b0' 2>&1 | |
| ERROR | |
| --- re-building ‘BiocFileCache.Rmd’ using rmarkdown | |
| --- finished re-building ‘BiocFileCache.Rmd’ | |
| --- re-building ‘BiocFileCache_Troubleshooting.Rmd’ using rmarkdown | |
| --- finished re-building ‘BiocFileCache_Troubleshooting.Rmd’ | |
| --- re-building ‘BiocFileCache_UseCases.Rmd’ using rmarkdown | |
| *** caught segfault *** | |
| address 0x0, cause 'unknown' | |
| Traceback: | |
| 1: curl::curl_fetch_disk(url, x$path, handle = handle) | |
| 2: request_fetch.write_disk(req$output, req$url, handle) | |
| 3: request_fetch(req$output, req$url, handle) | |
| 4: request_perform(req, hu$handle$handle) | |
| 5: GET(websource, write_disk(localfile, overwrite = TRUE), proxy, config = config, ...) | |
| 6: withCallingHandlers(expr, warning = function(w) if (inherits(w, classes)) tryInvokeRestart("muffleWarning")) | |
| 7: suppressWarnings({ GET(websource, write_disk(localfile, overwrite = TRUE), proxy, config = config, ...)}) | |
| 8: doTryCatch(return(expr), name, parentenv, handler) | |
| 9: tryCatchOne(expr, names, parentenv, handlers[[1L]]) | |
| 10: tryCatchList(expr, classes, parentenv, handlers) | |
| 11: tryCatch({ if (!is(proxy, "request")) { if (proxy == "") { proxy = NULL } else { proxy = use_proxy(proxy) } } if (!all(file.exists(dirname(localfile)))) dir.create(dirname(localfile), recursive = TRUE) if (interactive() && (packageVersion("httr") > "1.0.0")) { response <- suppressWarnings({ GET(websource, progress(con = stderr()), config = config, write_disk(localfile, overwrite = TRUE), proxy, ...) }) cat("\n") } else { response <- suppressWarnings({ GET(websource, write_disk(localfile, overwrite = TRUE), proxy, config = config, ...) }) } if (length(status_code(response))) { if (status_code(response) != 302L) stop_for_status(response) } TRUE}, error = function(err) { warning("download failed", "\n web resource path: ", sQuote(websource), "\n local file path: ", sQuote(localfile), "\n reason: ", conditionMessage(err), call. = FALSE) FALSE}) | |
| 12: (function (websource, localfile, proxy, config, ...) { tryCatch({ if (!is(proxy, "request")) { if (proxy == "") { proxy = NULL } else { proxy = use_proxy(proxy) } } if (!all(file.exists(dirname(localfile)))) dir.create(dirname(localfile), recursive = TRUE) if (interactive() && (packageVersion("httr") > "1.0.0")) { response <- suppressWarnings({ GET(websource, progress(con = stderr()), config = config, write_disk(localfile, overwrite = TRUE), proxy, ...) }) cat("\n") } else { response <- suppressWarnings({ GET(websource, write_disk(localfile, overwrite = TRUE), proxy, config = config, ...) }) } if (length(status_code(response))) { if (status_code(response) != 302L) stop_for_status(response) } TRUE }, error = function(err) { warning("download failed", "\n web resource path: ", sQuote(websource), "\n local file path: ", sQuote(localfile), "\n reason: ", conditionMessage(err), call. = FALSE) FALSE })})(dots[[1L]][[1L]], dots[[2L]][[1L]], proxy = "", config = list()) | |
| 13: mapply(FUN = f, ..., SIMPLIFY = FALSE) | |
| 14: Map(.httr_download, fpath, rpath, MoreArgs = list(proxy = proxy, config = config, ...)) | |
| 15: .util_download(x, rid[i], proxy, config, "bfcadd()", ...) | |
| 16: bfcadd(x, rname, ...) | |
| 17: bfcadd(x, rname, ...) | |
| 18: doTryCatch(return(expr), name, parentenv, handler) | |
| 19: tryCatchOne(expr, names, parentenv, handlers[[1L]]) | |
| 20: tryCatchList(expr, classes, parentenv, handlers) | |
| 21: tryCatch({ res <- bfcrid(bfcquery(x, rname, field = "rname", exact = exact)) if (length(res) == 0L) { message("adding rname '", rname, "'") names(bfcadd(x, rname, ...)) } else { names(update_time_and_path(x, res)) }}, error = function(e) { warning("\ntrying to add rname '", rname, "' produced error:", "\n ", conditionMessage(e)) NA_character_}, finally = function() { .unlock2(locfile_path)}) | |
| 22: FUN(X[[i]], ...) | |
| 23: vapply(rnames, add_or_return_rname, character(1), x = x, ..., exact = exact) | |
| 24: bfcrpath(bfc, c(url, url2)) | |
| 25: bfcrpath(bfc, c(url, url2)) | |
| 26: eval(expr, envir) | |
| 27: eval(expr, envir) | |
| 28: withVisible(eval(expr, envir)) | |
| 29: withCallingHandlers(code, 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$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = invokeRestart("eval_error", cnd))}) | |
| 30: eval(call) | |
| 31: eval(call) | |
| 32: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers) | |
| 33: doWithOneRestart(return(expr), restart) | |
| 34: withOneRestart(expr, restarts[[1L]]) | |
| 35: withRestartList(expr, restarts[-nr]) | |
| 36: doWithOneRestart(return(expr), restart) | |
| 37: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) | |
| 38: withRestartList(expr, restarts[-nr]) | |
| 39: doWithOneRestart(return(expr), restart) | |
| 40: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) | |
| 41: withRestartList(expr, restarts) | |
| 42: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE, eval_error = function(cnd) signalCondition(cnd)) | |
| 43: evaluate::evaluate(...) | |
| 44: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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)) | |
| 45: in_dir(input_dir(), expr) | |
| 46: 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$render, options))) | |
| 47: eng_r(options) | |
| 48: block_exec(params) | |
| 49: call_block(x) | |
| 50: process_group(group) | |
| 51: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)) | |
| 52: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from lines ", loc) }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) | |
| 53: process_file(text, output) | |
| 54: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) | |
| 55: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) | |
| 56: vweave_rmarkdown(...) | |
| 57: engine$weave(file, quiet = quiet, encoding = enc) | |
| 58: doTryCatch(return(expr), name, parentenv, handler) | |
| 59: tryCatchOne(expr, names, parentenv, handlers[[1L]]) | |
| 60: tryCatchList(expr, classes, parentenv, handlers) | |
| 61: 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)))}) | |
| 62: tools::buildVignettes(dir = ".", tangle = TRUE) | |
| An irrecoverable exception occurred. R is aborting now ... |
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