• using R Under development (unstable) (2026-06-29 r90199)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     clang version 22.1.8 (https://github.com/llvm/llvm-project ca7933e47d3a3451d81e72ac174dcb5aa28b59d1)     flang version 22.1.8 (https://github.com/llvm/llvm-project ca7933e47d3a3451d81e72ac174dcb5aa28b59d1)
• running under: Fedora Linux 42 (Workstation Edition)
• using session charset: UTF-8 * current time: 2026-06-29 16:37:46 UTC
• using option ‘--no-stop-on-test-error’
• checking for file ‘ipeaplot/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘ipeaplot’ version ‘0.5.2’
• 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 ‘ipeaplot’ can be installed ... [13s/36s] 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 ... [3s/12s] OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... [4s/10s] OK
• checking loading without being on the library search path ... [3s/12s] OK
• checking use of S3 registration ... 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 ... [19s/50s] OK
• checking Rd files ... OK
• checking Rd metadata ... OK
• checking Rd line widths ... 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 ... [4s/12s] OK
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [28s/71s] ERROR Error(s) in re-building vignettes: --- re-building ‘cookbook.Rmd’ using rmarkdown --- finished re-building ‘cookbook.Rmd’ --- re-building ‘intro_ipeaplot.Rmd’ using rmarkdown [gannet:3327956:0:3330647] Caught signal 11 (Segmentation fault: Sent by the kernel at address (nil)) ==== backtrace (tid:3330647) ====  0 /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7efe4b1b2df4]  1 /lib64/libucs.so.0(+0x17aed) [0x7efe4b1b4aed]  2 /lib64/libucs.so.0(+0x17cbd) [0x7efe4b1b4cbd]  3 /lib64/libc.so.6(+0x1a040) [0x7efe63629040]  4 /data/gannet/ripley/R/test-clang/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x1196b50) [0x7efce4b96b50]  5 /data/gannet/ripley/R/test-clang/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x1168728) [0x7efce4b68728]  6 /data/gannet/ripley/R/test-clang/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x773544) [0x7efce4173544]  7 /data/gannet/ripley/R/test-clang/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x7718d9) [0x7efce41718d9]  8 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper29LoadExternalExtensionInternalERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEERNS_19ExtensionActiveLoadE+0x18f) [0x7efd6627f85f]  9 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper21LoadExternalExtensionERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEE+0x4a) [0x7efd6627f60a] 10 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZNK6duckdb12PhysicalLoad15GetDataInternalERNS_16ExecutionContextERNS_9DataChunkERNS_19OperatorSourceInputE+0x151) [0x7efd6706d401] 11 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor15FetchFromSourceERNS_9DataChunkE+0x98) [0x7efd678a10c8] 12 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor7ExecuteEm+0x146) [0x7efd6789dca6] 13 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12PipelineTask11ExecuteTaskENS_17TaskExecutionModeE+0x154) [0x7efd6789d914] 14 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12ExecutorTask7ExecuteENS_17TaskExecutionModeE+0xa0) [0x7efd67897570] 15 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb13TaskScheduler14ExecuteForeverEPNSt3__16atomicIbEE+0x39a) [0x7efd678a432a] 16 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(+0x1aafe9c) [0x7efd678afe9c] 17 /lib64/libc.so.6(+0x71f14) [0x7efe63680f14] 18 /lib64/libc.so.6(+0xf532c) [0x7efe6370432c] =================================  *** caught segfault *** address 0x4d20032c7d4, cause 'unknown' Traceback:  1: rapi_execute(stmt, convert_opts)  2: withCallingHandlers(expr, condition = function(cnd) { { .__handler_frame__. <- TRUE .__setup_frame__. <- frame if (inherits(cnd, "message")) { except <- c("warning", "error") } else if (inherits(cnd, "warning")) { except <- "error" } else { except <- "" } } while (!is_null(cnd)) { if (inherits(cnd, "error")) { out <- handlers[[1L]](cnd) if (!inherits(out, "rlang_zap")) throw(out) } inherit <- .subset2(.subset2(cnd, "rlang"), "inherit") if (is_false(inherit)) { return() } cnd <- .subset2(cnd, "parent") }})  3: doTryCatch(return(expr), name, parentenv, handler)  4: tryCatchOne(expr, names, parentenv, handlers[[1L]])  5: tryCatchList(expr, classes, parentenv, handlers)  6: tryCatch(withCallingHandlers(expr, condition = function(cnd) { { .__handler_frame__. <- TRUE .__setup_frame__. <- frame if (inherits(cnd, "message")) { except <- c("warning", "error") } else if (inherits(cnd, "warning")) { except <- "error" } else { except <- "" } } while (!is_null(cnd)) { if (inherits(cnd, "error")) { out <- handlers[[1L]](cnd) if (!inherits(out, "rlang_zap")) throw(out) } inherit <- .subset2(.subset2(cnd, "rlang"), "inherit") if (is_false(inherit)) { return() } cnd <- .subset2(cnd, "parent") }}), stackOverflowError = handlers[[1L]])  7: rlang::try_fetch(rapi_execute(stmt, convert_opts), error = function(e) { rethrow_error_from_rapi(e, call)})  8: rethrow_rapi_execute(res@stmt_lst$ref, duckdb_convert_opts_impl(res@connection@convert_opts, arrow = res@arrow))  9: duckdb_execute(res) 10: duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow) 11: .local(conn, statement, ...) 12: dbSendQuery(conn, statement, ...) 13: dbSendQuery(conn, statement, ...) 14: dbSendStatement(conn, statement, ...) 15: dbSendStatement(conn, statement, ...) 16: DBI::dbExecute(conn, glue::glue("LOAD {extension};")) 17: DBI::dbExecute(conn, glue::glue("LOAD {extension};")) 18: withCallingHandlers(expr, message = function(c) if (inherits(c, classes)) tryInvokeRestart("muffleMessage")) 19: suppressMessages(DBI::dbExecute(conn, glue::glue("LOAD {extension};"))) 20: ddbs_load(conn, quiet = TRUE) 21: ddbs_create_conn(dbdir = "memory", ...) 22: ddbs_default_conn() 23: duckspatial::ddbs_open_dataset(filename) 24: doTryCatch(return(expr), name, parentenv, handler) 25: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 26: tryCatchList(expr, classes, parentenv, handlers) 27: 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))}) 28: try(silent = TRUE, temp <- duckspatial::ddbs_open_dataset(filename)) 29: geobr_open_dataset(tempf) 30: dplyr::collect(geobr_open_dataset(tempf)) 31: download_metadata2() 32: select_metadata(geography = "states", year = year, simplified = simplified, verbose = verbose) 33: geobr::read_state(year = 2010) 34: eval(expr, envir) 35: eval(expr, envir) 36: withVisible(eval(expr, envir)) 37: 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$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)}) 38: eval(call) 39: eval(call) 40: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers) 41: doWithOneRestart(return(expr), restart) 42: withOneRestart(expr, restarts[[1L]]) 43: withRestartList(expr, restarts[-nr]) 44: doWithOneRestart(return(expr), restart) 45: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 46: withRestartList(expr, restarts) 47: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) 48: evaluate::evaluate(...) 49: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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)) 50: in_dir(input_dir(), expr) 51: 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$render, options))) 52: eng_r(options) 53: block_exec(params) 54: call_block(x) 55: process_group(group) 56: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }) 57: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())) 58: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) 59: process_file(text, output) 60: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 61: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) 62: vweave_rmarkdown(...) 63: engine$weave(file, quiet = quiet, encoding = enc) 64: doTryCatch(return(expr), name, parentenv, handler) 65: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 66: tryCatchList(expr, classes, parentenv, handlers) 67: 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) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)), domain = NA)}) 68: tools:::.buildOneVignette("intro_ipeaplot.Rmd", "/data/gannet/ripley/R/packages/tests-clang/ipeaplot.Rcheck/vign_test/ipeaplot", TRUE, FALSE, "intro_ipeaplot", "UTF-8", "/tmp/RtmpM3InWN/working_dir/RtmpXOhbSg/file32bef23effd25e.rds") An irrecoverable exception occurred. R is aborting now ... SUMMARY: processing the following file failed:   ‘intro_ipeaplot.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [7s/18s] OK
• checking HTML version of manual ... OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 1 ERROR