Last updated on 2026-07-01 18:49:47 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.5.2 | 6.14 | 73.09 | 79.23 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.5.2 | 5.15 | 58.46 | 63.61 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.5.2 | 11.00 | 118.58 | 129.58 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 0.5.2 | 11.00 | 155.12 | 166.12 | OK | |
| r-devel-windows-x86_64 | 0.5.2 | 9.00 | 93.00 | 102.00 | OK | |
| r-patched-linux-x86_64 | 0.5.2 | 6.73 | 69.03 | 75.76 | ERROR | |
| r-release-linux-x86_64 | 0.5.2 | ERROR | ||||
| r-release-macos-arm64 | 0.5.2 | 2.00 | 43.00 | 45.00 | OK | |
| r-release-macos-x86_64 | 0.5.2 | 5.00 | 120.00 | 125.00 | OK | |
| r-release-windows-x86_64 | 0.5.2 | 9.00 | 98.00 | 107.00 | OK | |
| r-oldrel-macos-arm64 | 0.5.2 | 2.00 | 60.00 | 62.00 | OK | |
| r-oldrel-macos-x86_64 | 0.5.2 | 5.00 | 118.00 | 123.00 | OK | |
| r-oldrel-windows-x86_64 | 0.5.2 | 11.00 | 116.00 | 127.00 | 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
Quitting from intro_ipeaplot.Rmd:204-208 [unnamed-chunk-12]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `UseMethod()`:
! no applicable method for 'collect' applied to an object of class "NULL"
---
Backtrace:
▆
1. └─geobr::read_state(year = 2010)
2. └─geobr:::select_metadata(...)
3. └─geobr:::download_metadata2()
4. └─dplyr::collect(geobr_open_dataset(tempf))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'intro_ipeaplot.Rmd' failed with diagnostics:
no applicable method for 'collect' applied to an object of class "NULL"
--- failed re-building ‘intro_ipeaplot.Rmd’
SUMMARY: processing the following file failed:
‘intro_ipeaplot.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-patched-linux-x86_64
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
Downloading 26% ■■■■■■■■■ 3s
Downloading 44% ■■■■■■■■■■■■■■ 3s
Downloading 59% ■■■■■■■■■■■■■■■■■■■ 4s
Downloading 73% ■■■■■■■■■■■■■■■■■■■■■■■ 3s
Downloading 84% ■■■■■■■■■■■■■■■■■■■■■■■■■■ 2s
Downloading 95% ■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■ 1s
Downloading 100% ■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■ 0s
Quitting from intro_ipeaplot.Rmd:204-208 [unnamed-chunk-12]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `UseMethod()`:
! no applicable method for 'collect' applied to an object of class "NULL"
---
Backtrace:
▆
1. └─geobr::read_state(year = 2010)
2. └─geobr:::select_metadata(...)
3. └─geobr:::download_metadata2()
4. └─dplyr::collect(geobr_open_dataset(tempf))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'intro_ipeaplot.Rmd' failed with diagnostics:
no applicable method for 'collect' applied to an object of class "NULL"
--- failed re-building ‘intro_ipeaplot.Rmd’
SUMMARY: processing the following file failed:
‘intro_ipeaplot.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
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:912998:0:914462] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x449)
==== backtrace (tid: 914462) ====
0 /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7f22ae9b2df4]
1 /lib64/libucs.so.0(+0x17aed) [0x7f22ae9b4aed]
2 /lib64/libucs.so.0(+0x17cbd) [0x7f22ae9b4cbd]
3 /lib64/libc.so.6(+0x1a040) [0x7f22c6d28040]
4 /data/gannet/ripley/R/test-clang/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x1196b50) [0x7f2168b96b50]
5 /data/gannet/ripley/R/test-clang/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x1168728) [0x7f2168b68728]
6 /data/gannet/ripley/R/test-clang/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x773544) [0x7f2168173544]
7 /data/gannet/ripley/R/test-clang/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x7718d9) [0x7f21681718d9]
8 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper29LoadExternalExtensionInternalERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEERNS_19ExtensionActiveLoadE+0x18f) [0x7f21c147f85f]
9 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper21LoadExternalExtensionERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEE+0x4a) [0x7f21c147f60a]
10 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZNK6duckdb12PhysicalLoad15GetDataInternalERNS_16ExecutionContextERNS_9DataChunkERNS_19OperatorSourceInputE+0x151) [0x7f21c226d401]
11 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor15FetchFromSourceERNS_9DataChunkE+0x98) [0x7f21c2aa10c8]
12 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor7ExecuteEm+0x146) [0x7f21c2a9dca6]
13 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12PipelineTask11ExecuteTaskENS_17TaskExecutionModeE+0x154) [0x7f21c2a9d914]
14 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12ExecutorTask7ExecuteENS_17TaskExecutionModeE+0xa0) [0x7f21c2a97570]
15 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb13TaskScheduler14ExecuteForeverEPNSt3__16atomicIbEE+0x39a) [0x7f21c2aa432a]
16 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(+0x1aafe9c) [0x7f21c2aafe9c]
17 /lib64/libc.so.6(+0x71f14) [0x7f22c6d7ff14]
18 /lib64/libc.so.6(+0xf532c) [0x7f22c6e0332c]
=================================
*** caught segfault ***
address 0x4d2000dee66, 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)), domain = NA)})
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/RtmpTCojU4/working_dir/RtmpSyTiUh/filede86850e908f2.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
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
Downloading 19% ■■■■■■■ 4s
Downloading 33% ■■■■■■■■■■■ 7s
Downloading 51% ■■■■■■■■■■■■■■■■ 6s
Downloading 63% ■■■■■■■■■■■■■■■■■■■■ 6s
Downloading 78% ■■■■■■■■■■■■■■■■■■■■■■■■ 3s
Downloading 96% ■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■ 1s
Downloading 100% ■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■ 0s
Quitting from intro_ipeaplot.Rmd:204-208 [unnamed-chunk-12]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `UseMethod()`:
! no applicable method for 'collect' applied to an object of class "NULL"
---
Backtrace:
▆
1. └─geobr::read_state(year = 2010)
2. └─geobr:::select_metadata(...)
3. └─geobr:::download_metadata2()
4. └─dplyr::collect(geobr_open_dataset(tempf))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'intro_ipeaplot.Rmd' failed with diagnostics:
no applicable method for 'collect' applied to an object of class "NULL"
--- failed re-building ‘intro_ipeaplot.Rmd’
SUMMARY: processing the following file failed:
‘intro_ipeaplot.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-linux-x86_64