CRAN Package Check Results for Package ipeaplot

Last updated on 2026-05-21 08:50:45 CEST.

Check Details

Version: 0.5.2
Check: re-building of vignette outputs
Result: 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:2393684:0:2393684] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x14) ==== backtrace (tid:2393684) ==== 0 /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7fc790fb2df4] 1 /lib64/libucs.so.0(+0x17aed) [0x7fc790fb4aed] 2 /lib64/libucs.so.0(+0x17cbd) [0x7fc790fb4cbd] 3 /lib64/libc.so.6(+0x1a040) [0x7fc7a9429040] 4 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.5.2/linux_amd64/spatial.duckdb_extension(+0x1181e00) [0x7fc654f81e00] 5 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.5.2/linux_amd64/spatial.duckdb_extension(+0x1152a28) [0x7fc654f52a28] 6 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.5.2/linux_amd64/spatial.duckdb_extension(+0x75c104) [0x7fc65455c104] 7 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.5.2/linux_amd64/spatial.duckdb_extension(+0x75a499) [0x7fc65455a499] 8 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper29LoadExternalExtensionInternalERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEERNS_19ExtensionActiveLoadE+0x18f) [0x7fc6a5479e3f] 9 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper21LoadExternalExtensionERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEE+0x4a) [0x7fc6a5479bea] 10 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZNK6duckdb12PhysicalLoad15GetDataInternalERNS_16ExecutionContextERNS_9DataChunkERNS_19OperatorSourceInputE+0x151) [0x7fc6a625e831] 11 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor15FetchFromSourceERNS_9DataChunkE+0x9b) [0x7fc6a6a8d8eb] 12 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor7ExecuteEm+0x146) [0x7fc6a6a8a4c6] 13 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12PipelineTask11ExecuteTaskENS_17TaskExecutionModeE+0x112) [0x7fc6a6a8a0f2] 14 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12ExecutorTask7ExecuteENS_17TaskExecutionModeE+0xa0) [0x7fc6a6a83d90] 15 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb8Executor11ExecuteTaskEb+0x1c0) [0x7fc6a6a890f0] 16 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb13ClientContext19ExecuteTaskInternalERNS_17ClientContextLockERNS_15BaseQueryResultEb+0x40) [0x7fc6a68981f0] 17 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb18PendingQueryResult15ExecuteInternalERNS_17ClientContextLockE+0x7a) [0x7fc6a689a97a] 18 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb13ClientContext7ExecuteERKNSt3__112basic_stringIcNS1_11char_traitsIcEENS1_9allocatorIcEEEERNS_10shared_ptrINS_21PreparedStatementDataELb1EEERKNS_22PendingQueryParametersE+0xa0) [0x7fc6a689a6c0] 19 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb17PreparedStatement7ExecuteERNSt3__113unordered_mapINS1_12basic_stringIcNS1_11char_traitsIcEENS1_9allocatorIcEEEENS_18BoundParameterDataENS_33CaseInsensitiveStringHashFunctionENS_29CaseInsensitiveStringEqualityENS6_INS1_4pairIKS8_S9_EEEEEEb+0x1c3) [0x7fc6a68bd473] 20 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb17PreparedStatement7ExecuteERNS_6vectorINS_5ValueELb1ENSt3__19allocatorIS2_EEEEb+0x172) [0x7fc6a68bd712] 21 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_Z12rapi_executeN5cpp1116external_pointerIN6duckdb10RStatementEXadL_ZNS_15default_deleterIS2_EEvPT_EEEENS1_11ConvertOptsE+0x115) [0x7fc6a5107f75] 22 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_duckdb_rapi_execute+0x66) [0x7fc6a51704a6] 23 /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8f4d4) [0x559d351df4d4] 24 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdadb8) [0x559d3522adb8] 25 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc913c) [0x559d3521913c] 26 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x559d352188f5] 27 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9394) [0x559d35219394] 28 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x26e) [0x559d352189be] 29 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9394) [0x559d35219394] 30 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdcec0) [0x559d3522cec0] 31 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcd579) [0x559d3521d579] 32 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc913c) [0x559d3521913c] 33 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x559d352188f5] 34 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0a59) [0x559d35230a59] 35 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdff4b) [0x559d3522ff4b] 36 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9817) [0x559d35219817] 37 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f8) [0x559d35218d48] 38 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9394) [0x559d35219394] 39 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdcec0) [0x559d3522cec0] 40 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcd579) [0x559d3521d579] 41 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc913c) [0x559d3521913c] 42 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x559d352188f5] 43 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0a59) [0x559d35230a59] 44 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdff4b) [0x559d3522ff4b] 45 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9817) [0x559d35219817] 46 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f8) [0x559d35218d48] 47 /data/gannet/ripley/R/test-clang/rlang/libs/rlang.so(+0x4983) [0x7fc7a6eb7983] 48 /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8d623) [0x559d351dd623] 49 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcfb74) [0x559d3521fb74] 50 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc913c) [0x559d3521913c] 51 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x559d352188f5] 52 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0a59) [0x559d35230a59] 53 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdff4b) [0x559d3522ff4b] 54 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9817) [0x559d35219817] 55 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f8) [0x559d35218d48] 56 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe5db8) [0x559d35235db8] 57 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x559d35218b20] 58 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe50ab) [0x559d352350ab] 59 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x559d35218b20] 60 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0a59) [0x559d35230a59] 61 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdff4b) [0x559d3522ff4b] ================================= *** caught segfault *** address 0x4d200248654, 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$ref, duckdb_convert_opts_impl(res@connection@convert_opts, arrow = res@arrow)) 9: duckdb_execute(res) 10: duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow) 11: .local(conn, statement, ...) 12: dbSendQuery(conn, statement, ...) 13: dbSendQuery(conn, statement, ...) 14: dbSendStatement(conn, statement, ...) 15: dbSendStatement(conn, statement, ...) 16: DBI::dbExecute(conn, glue::glue("LOAD {extension};")) 17: DBI::dbExecute(conn, glue::glue("LOAD {extension};")) 18: withCallingHandlers(expr, message = function(c) if (inherits(c, classes)) tryInvokeRestart("muffleMessage")) 19: suppressMessages(DBI::dbExecute(conn, glue::glue("LOAD {extension};"))) 20: ddbs_load(conn, quiet = TRUE) 21: ddbs_create_conn(dbdir = "memory", ...) 22: ddbs_default_conn() 23: duckspatial::ddbs_open_dataset(filename) 24: doTryCatch(return(expr), name, parentenv, handler) 25: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 26: tryCatchList(expr, classes, parentenv, handlers) 27: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))}) 28: try(silent = TRUE, temp <- duckspatial::ddbs_open_dataset(filename)) 29: geobr_open_dataset(temp_full_file_path) 30: download_parquet(filename_to_download = temp_meta$file_name, showProgress, cache) 31: geobr::read_municipality(year = 2010) 32: eval(expr, envir) 33: eval(expr, envir) 34: withVisible(eval(expr, envir)) 35: 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)}) 36: eval(call) 37: eval(call) 38: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers) 39: doWithOneRestart(return(expr), restart) 40: withOneRestart(expr, restarts[[1L]]) 41: withRestartList(expr, restarts[-nr]) 42: doWithOneRestart(return(expr), restart) 43: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 44: withRestartList(expr, restarts) 45: withRestarts(with_handlers({ for (expr in tle$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) 46: evaluate::evaluate(...) 47: 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$render, options)) 48: in_dir(input_dir(), expr) 49: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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))) 50: eng_r(options) 51: block_exec(params) 52: call_block(x) 53: process_group(group) 54: 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) }) 55: 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())) 56: 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) 57: process_file(text, output) 58: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 59: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) 60: vweave_rmarkdown(...) 61: engine$weave(file, quiet = quiet, encoding = enc) 62: doTryCatch(return(expr), name, parentenv, handler) 63: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 64: tryCatchList(expr, classes, parentenv, handlers) 65: tryCatch({ engine$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)))}) 66: tools:::.buildOneVignette("intro_ipeaplot.Rmd", "/data/gannet/ripley/R/packages/tests-clang/ipeaplot.Rcheck/vign_test/ipeaplot", TRUE, FALSE, "intro_ipeaplot", "UTF-8", "/tmp/RtmpiMdqx8/working_dir/RtmpdvAP5C/file24836e34a8ad3b.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 Flavor: r-devel-linux-x86_64-fedora-clang