Last updated on 2026-05-21 02:58:00 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.5.1 | 6.15 | 69.55 | 75.70 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.5.1 | 4.47 | 56.96 | 61.43 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.5.2 | 12.00 | 123.46 | 135.46 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 0.5.2 | 12.00 | 155.00 | 167.00 | OK | |
| r-devel-windows-x86_64 | 0.5.1 | 9.00 | 105.00 | 114.00 | OK | |
| r-patched-linux-x86_64 | 0.5.1 | 6.54 | 75.56 | 82.10 | OK | |
| r-release-linux-x86_64 | 0.5.1 | 5.76 | 76.08 | 81.84 | OK | |
| r-release-macos-arm64 | 0.5.1 | 2.00 | 56.00 | 58.00 | OK | |
| r-release-macos-x86_64 | 0.5.1 | 5.00 | 121.00 | 126.00 | OK | |
| r-release-windows-x86_64 | 0.5.1 | 10.00 | 108.00 | 118.00 | OK | |
| r-oldrel-macos-arm64 | 0.5.1 | 2.00 | 50.00 | 52.00 | OK | |
| r-oldrel-macos-x86_64 | 0.5.1 | 5.00 | 163.00 | 168.00 | OK | |
| r-oldrel-windows-x86_64 | 0.5.1 | 12.00 | 128.00 | 140.00 | OK |
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