Last updated on 2026-04-14 18:52:46 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.0 | 11.72 | 162.01 | 173.73 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.0.0 | 7.40 | 119.59 | 126.99 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.0.0 | 21.00 | 253.86 | 274.86 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 1.0.0 | 21.00 | 294.82 | 315.82 | OK | |
| r-devel-macos-arm64 | 1.0.0 | 3.00 | 38.00 | 41.00 | OK | |
| r-devel-windows-x86_64 | 1.0.0 | 16.00 | 178.00 | 194.00 | OK | |
| r-patched-linux-x86_64 | 1.0.0 | 10.38 | 153.37 | 163.75 | OK | |
| r-release-linux-x86_64 | 1.0.0 | 7.28 | 149.64 | 156.92 | OK | |
| r-release-macos-arm64 | 1.0.0 | 3.00 | 38.00 | 41.00 | OK | |
| r-release-macos-x86_64 | 1.0.0 | 8.00 | 130.00 | 138.00 | OK | |
| r-release-windows-x86_64 | 1.0.0 | 13.00 | 174.00 | 187.00 | OK | |
| r-oldrel-macos-arm64 | 0.9.0 | 1.00 | 39.00 | 40.00 | OK | |
| r-oldrel-macos-x86_64 | 1.0.0 | 8.00 | 119.00 | 127.00 | OK | |
| r-oldrel-windows-x86_64 | 1.0.0 | 18.00 | 212.00 | 230.00 | OK |
Version: 1.0.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [7s/21s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(duckspatial)
duckspatial 1.0.0 attached
* Compatible with DuckDB v1.5.1
* This release introduces breaking changes
* See full release notes for migration guidance
Default output has changed:
duckspatial now returns lazy `duckspatial_df` (dbplyr) objects
instead of `sf` objects.
To restore the previous behaviour:
ddbs_options(duckspatial.mode = 'sf')
> library(duckdb)
Loading required package: DBI
>
> test_check("duckspatial")
Reading layer `countries' from data source
`/data/gannet/ripley/R/packages/tests-clang/duckspatial.Rcheck/duckspatial/spatial/countries.geojson'
using driver `GeoJSON'
Simple feature collection with 257 features and 6 fields
Geometry type: POLYGON
Dimension: XY
Bounding box: xmin: -178.9125 ymin: -89.9 xmax: 180 ymax: 83.65187
Geodetic CRS: WGS 84
Reading layer `argentina' from data source
`/data/gannet/ripley/R/packages/tests-clang/duckspatial.Rcheck/duckspatial/spatial/argentina.geojson'
using driver `GeoJSON'
Simple feature collection with 1 feature and 6 fields
Geometry type: POLYGON
Dimension: XY
Bounding box: xmin: -73.52455 ymin: -52.39755 xmax: -53.62409 ymax: -21.81793
Geodetic CRS: WGS 84
Error in `source_dir()`:
! Failed to evaluate './setup.R'.
Caused by error in `duckdb_result()`:
! Invalid Error: Invalid Input Error: Initialization function "spatial_duckdb_cpp_init" from file "/data/gannet/ripley/.local/share/R/duckdb/extensions/v1.5.2/linux_amd64/spatial.duckdb_extension" threw an exception: "Missing DB manager"
ℹ Context: rapi_execute
ℹ Error type: INVALID
Backtrace:
▆
1. ├─testthat::test_check("duckspatial")
2. │ └─testthat::test_dir(...)
3. │ └─testthat:::test_files(...)
4. │ └─testthat:::test_files_serial(...)
5. │ └─testthat:::test_files_setup_state(...)
6. │ └─testthat::source_test_setup(".", env)
7. │ └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)
8. │ └─base::lapply(...)
9. │ └─testthat (local) FUN(X[[i]], ...)
10. │ └─testthat::source_file(...)
11. │ ├─base::withCallingHandlers(...)
12. │ └─base::eval(exprs, env)
13. │ └─base::eval(exprs, env)
14. │ ├─duckspatial::as_duckspatial_df(argentina_sf) at ./setup.R:15:1
15. │ └─duckspatial:::as_duckspatial_df.sf(argentina_sf)
16. │ └─duckspatial:::ddbs_default_conn()
17. │ └─duckspatial::ddbs_create_conn(dbdir = "memory", ...)
18. │ └─duckspatial::ddbs_load(conn, quiet = TRUE)
19. │ ├─base::suppressMessages(DBI::dbExecute(conn, glue::glue("LOAD {extension};")))
20. │ │ └─base::withCallingHandlers(...)
21. │ ├─DBI::dbExecute(conn, glue::glue("LOAD {extension};"))
22. │ └─DBI::dbExecute(conn, glue::glue("LOAD {extension};"))
23. │ ├─DBI::dbSendStatement(conn, statement, ...)
24. │ └─DBI::dbSendStatement(conn, statement, ...)
25. │ ├─DBI::dbSendQuery(conn, statement, ...)
26. │ └─duckdb::dbSendQuery(conn, statement, ...)
27. │ └─duckdb (local) .local(conn, statement, ...)
28. │ └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
29. │ └─duckdb:::duckdb_execute(res)
30. │ └─duckdb:::rethrow_rapi_execute(...)
31. │ ├─rlang::try_fetch(...)
32. │ │ ├─base::tryCatch(...)
33. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
34. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
35. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
36. │ │ └─base::withCallingHandlers(...)
37. │ └─duckdb:::rapi_execute(stmt, convert_opts)
38. ├─duckdb (local) `<fn>`(...)
39. │ └─rlang::abort(error_parts, class = "duckdb_error", !!!fields)
40. │ └─rlang:::signal_abort(cnd, .file)
41. │ └─base::signalCondition(cnd)
42. └─rlang (local) `<fn>`(`<dckdb_rr>`)
43. └─handlers[[1L]](cnd)
44. └─duckdb:::rethrow_error_from_rapi(e, call)
45. └─rlang::abort(msg, call = call)
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.0.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘aw_interpolation.qmd’ using html
<1b>[31m
processing file: aw_interpolation.qmd
<1b>[39m<1b>[31m[gannet:950693:0:950693] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x14)
<1b>[39m<1b>[31m==== backtrace (tid: 950693) ====
0 /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7f39317b7df4]
1 /lib64/libucs.so.0(+0x17aed) [0x7f39317b9aed]
2 /lib64/libucs.so.0(+0x17cbd) [0x7f39317b9cbd]
3 /lib64/libc.so.6(+0x1a040) [0x7f3947d28040]
4 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.5.2/linux_amd64/spatial.duckdb_extension(+0x1181e00) [0x7f3808d81e00]
5 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.5.2/linux_amd64/spatial.duckdb_extension(+0x1152a28) [0x7f3808d52a28]
6 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.5.2/linux_amd64/spatial.duckdb_extension(+0x75c104) [0x7f380835c104]
7 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.5.2/linux_amd64/spatial.duckdb_extension(+0x75a499) [0x7f380835a499]
8 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper29LoadExternalExtensionInternalERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEERNS_19ExtensionActiveLoadE+0x18f) [0x7f386a479e3f]
9 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper21LoadExternalExtensionERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEE+0x4a) [0x7f386a479bea]
10 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZNK6duckdb12PhysicalLoad15GetDataInternalERNS_16ExecutionContextERNS_9DataChunkERNS_19OperatorSourceInputE+0x151) [0x7f386b25e831]
11 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor15FetchFromSourceERNS_9DataChunkE+0x9b) [0x7f386ba8d8eb]
12 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor7ExecuteEm+0x146) [0x7f386ba8a4c6]
13 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12PipelineTask11ExecuteTaskENS_17TaskExecutionModeE+0x112) [0x7f386ba8a0f2]
14 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12ExecutorTask7ExecuteENS_17TaskExecutionModeE+0xa0) [0x7f386ba83d90]
15 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb8Executor11ExecuteTaskEb+0x1c0) [0x7f386ba890f0]
16 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb13ClientContext19ExecuteTaskInternalERNS_17ClientContextLockERNS_15BaseQueryResultEb+0x40) [0x7f386b8981f0]
17 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb18PendingQueryResult15ExecuteInternalERNS_17ClientContextLockE+0x7a) [0x7f386b89a97a]
18 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb13ClientContext7ExecuteERKNSt3__112basic_stringIcNS1_11char_traitsIcEENS1_9allocatorIcEEEERNS_10shared_ptrINS_21PreparedStatementDataELb1EEERKNS_22PendingQueryParametersE+0xa0) [0x7f386b89a6c0]
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) [0x7f386b8bd473]
20 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb17PreparedStatement7ExecuteERNS_6vectorINS_5ValueELb1ENSt3__19allocatorIS2_EEEEb+0x172) [0x7f386b8bd712]
21 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_Z12rapi_executeN5cpp1116external_pointerIN6duckdb10RStatementEXadL_ZNS_15default_deleterIS2_EEvPT_EEEENS1_11ConvertOptsE+0x115) [0x7f386a107f75]
22 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_duckdb_rapi_execute+0x66) [0x7f386a1704a6]
23 /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8f384) [0x55a5d8d3b384]
24 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdab18) [0x55a5d8d86b18]
25 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c6c) [0x55a5d8d74c6c]
26 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55a5d8d743f5]
27 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8ec4) [0x55a5d8d74ec4]
28 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x26e) [0x55a5d8d744be]
29 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8ec4) [0x55a5d8d74ec4]
30 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdcc20) [0x55a5d8d88c20]
31 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcd2f9) [0x55a5d8d792f9]
32 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c6c) [0x55a5d8d74c6c]
33 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55a5d8d743f5]
34 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0489) [0x55a5d8d8c489]
35 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf98c) [0x55a5d8d8b98c]
36 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x55a5d8d74846]
37 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8ec4) [0x55a5d8d74ec4]
38 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdcc20) [0x55a5d8d88c20]
39 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcd2f9) [0x55a5d8d792f9]
40 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c6c) [0x55a5d8d74c6c]
41 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55a5d8d743f5]
42 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0489) [0x55a5d8d8c489]
43 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf98c) [0x55a5d8d8b98c]
44 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x55a5d8d74846]
45 /data/gannet/ripley/R/test-clang/rlang/libs/rlang.so(+0x4983) [0x7f39456b8983]
46 /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8d4d3) [0x55a5d8d394d3]
47 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcf8e4) [0x55a5d8d7b8e4]
48 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c6c) [0x55a5d8d74c6c]
49 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55a5d8d743f5]
50 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0489) [0x55a5d8d8c489]
51 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf98c) [0x55a5d8d8b98c]
52 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x55a5d8d74846]
53 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe59b8) [0x55a5d8d919b8]
54 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x55a5d8d74620]
55 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe4afb) [0x55a5d8d90afb]
56 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x55a5d8d74620]
57 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0489) [0x55a5d8d8c489]
58 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf98c) [0x55a5d8d8b98c]
59 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcf173) [0x55a5d8d7b173]
60 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c6c) [0x55a5d8d74c6c]
61 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55a5d8d743f5]
=================================
*** caught segfault ***
address 0x4d2000e81a5, 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: resolve_spatial_connections(target, source, conn, quiet = quiet)
24: ddbs_interpolate_aw(target = grid, source = nc, tid = "target_id", sid = "source_id", extensive = "BIR74", weight = "total", mode = "sf")
25: eval(expr, envir)
26: eval(expr, envir)
27: withVisible(eval(expr, envir))
28: 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)})
29: eval(call)
30: eval(call)
31: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
32: doWithOneRestart(return(expr), restart)
33: withOneRestart(expr, restarts[[1L]])
34: withRestartList(expr, restarts[-nr])
35: doWithOneRestart(return(expr), restart)
36: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
37: withRestartList(expr, restarts)
38: withRestarts(with_handlers({ for (expr in tle$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)
39: evaluate::evaluate(...)
40: 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$render, options))
41: in_dir(input_dir(), expr)
42: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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)))
43: eng_r(options)
44: block_exec(params)
45: call_block(x)
46: process_group(group)
47: 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) })
48: 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()))
49: 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)
50: process_file(text, output)
51: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
52: rmarkdown::render(input = input, output_format = output_format, knit_root_dir = knit_root_dir, params = params, run_pandoc = FALSE, envir = env)
53: execute(params$input, params$format, params$tempDir, params$libDir, params$dependencies, params$cwd, params$params, params$resourceDir, params$handledLanguages, params$markdown)
54: .main()
An irrecoverable exception occurred. R is aborting now ...
<1b>[39m<1b>[33mWARN: Error encountered when rendering files<1b>[39m
Error: processing vignette 'aw_interpolation.qmd' failed with diagnostics:
! Error running quarto CLI from R.
Caused by error:
! Could not parse cli `{}` expression: ` { .__han…`.
Caused by error:
! <text>:1:49: unexpected symbol
1: { .__handler_frame__. <- TRUE .__setup_frame__.
^
--- failed re-building ‘aw_interpolation.qmd’
--- re-building ‘benchmark.qmd’ using html
<1b>[31m
processing file: benchmark.qmd
<1b>[39m<1b>[31moutput file: benchmark.knit.md
<1b>[39m<1b>[1mpandoc <1b>[22m
to: html
output-file: benchmark.html
standalone: true
embed-resources: true
wrap: none
default-image-extension: png
css:
- >-
/data/gannet/ripley/R/test-clang/quarto/rmarkdown/template/quarto_vignette/resources/vignette.css
variables: {}
<1b>[1mmetadata<1b>[22m
document-css: false
lang: en
engines:
- path: /data/gannet/ripley/Sources/quarto-1.9.36/share/extension-subtrees/julia-engine/_extensions/julia-engine/julia-engine.js
minimal: true
theme: none
title: Benchmark
date: '`r Sys.Date()`'
code-annotations: hover
urlcolor: blue
vignette: |
%\VignetteIndexEntry{Benchmark} %\VignetteEngine{quarto::html} %\VignetteEncoding{UTF-8}
knitr:
opts_chunk:
collapse: true
comment: '#>'
out.width: 100%
Output created: benchmark.html
--- finished re-building ‘benchmark.qmd’
--- re-building ‘duckspatial.qmd’ using html
<1b>[31m
processing file: duckspatial.qmd
<1b>[39m<1b>[31m[gannet:972312:0:972312] Caught signal 11 (Segmentation fault: Sent by the kernel at address (nil))
<1b>[39m<1b>[31m==== backtrace (tid: 972312) ====
0 /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7f6ede2e3df4]
1 /lib64/libucs.so.0(+0x17aed) [0x7f6ede2e5aed]
2 /lib64/libucs.so.0(+0x17cbd) [0x7f6ede2e5cbd]
3 /lib64/libc.so.6(+0x1a040) [0x7f6ef7e29040]
4 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.5.2/linux_amd64/spatial.duckdb_extension(+0x1181e00) [0x7f6dcf181e00]
5 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.5.2/linux_amd64/spatial.duckdb_extension(+0x1152a28) [0x7f6dcf152a28]
6 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.5.2/linux_amd64/spatial.duckdb_extension(+0x75c104) [0x7f6dce75c104]
7 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.5.2/linux_amd64/spatial.duckdb_extension(+0x75a499) [0x7f6dce75a499]
8 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper29LoadExternalExtensionInternalERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEERNS_19ExtensionActiveLoadE+0x18f) [0x7f6ee3079e3f]
9 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper21LoadExternalExtensionERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEE+0x4a) [0x7f6ee3079bea]
10 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZNK6duckdb12PhysicalLoad15GetDataInternalERNS_16ExecutionContextERNS_9DataChunkERNS_19OperatorSourceInputE+0x151) [0x7f6ee3e5e831]
11 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor15FetchFromSourceERNS_9DataChunkE+0x9b) [0x7f6ee468d8eb]
12 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor7ExecuteEm+0x146) [0x7f6ee468a4c6]
13 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12PipelineTask11ExecuteTaskENS_17TaskExecutionModeE+0x112) [0x7f6ee468a0f2]
14 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12ExecutorTask7ExecuteENS_17TaskExecutionModeE+0xa0) [0x7f6ee4683d90]
15 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb8Executor11ExecuteTaskEb+0x1c0) [0x7f6ee46890f0]
16 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb13ClientContext19ExecuteTaskInternalERNS_17ClientContextLockERNS_15BaseQueryResultEb+0x40) [0x7f6ee44981f0]
17 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb18PendingQueryResult15ExecuteInternalERNS_17ClientContextLockE+0x7a) [0x7f6ee449a97a]
18 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb13ClientContext7ExecuteERKNSt3__112basic_stringIcNS1_11char_traitsIcEENS1_9allocatorIcEEEERNS_10shared_ptrINS_21PreparedStatementDataELb1EEERKNS_22PendingQueryParametersE+0xa0) [0x7f6ee449a6c0]
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) [0x7f6ee44bd473]
20 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb17PreparedStatement7ExecuteERNS_6vectorINS_5ValueELb1ENSt3__19allocatorIS2_EEEEb+0x172) [0x7f6ee44bd712]
21 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_Z12rapi_executeN5cpp1116external_pointerIN6duckdb10RStatementEXadL_ZNS_15default_deleterIS2_EEvPT_EEEENS1_11ConvertOptsE+0x115) [0x7f6ee2d07f75]
22 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_duckdb_rapi_execute+0x66) [0x7f6ee2d704a6]
23 /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8f384) [0x5626cd181384]
24 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdab18) [0x5626cd1ccb18]
25 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c6c) [0x5626cd1bac6c]
26 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x5626cd1ba3f5]
27 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8ec4) [0x5626cd1baec4]
28 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x26e) [0x5626cd1ba4be]
29 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8ec4) [0x5626cd1baec4]
30 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdcc20) [0x5626cd1cec20]
31 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcd2f9) [0x5626cd1bf2f9]
32 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c6c) [0x5626cd1bac6c]
33 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x5626cd1ba3f5]
34 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0489) [0x5626cd1d2489]
35 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf98c) [0x5626cd1d198c]
36 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x5626cd1ba846]
37 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8ec4) [0x5626cd1baec4]
38 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdcc20) [0x5626cd1cec20]
39 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcd2f9) [0x5626cd1bf2f9]
40 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c6c) [0x5626cd1bac6c]
41 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x5626cd1ba3f5]
42 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0489) [0x5626cd1d2489]
43 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf98c) [0x5626cd1d198c]
44 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x5626cd1ba846]
45 /data/gannet/ripley/R/test-clang/rlang/libs/rlang.so(+0x4983) [0x7f6eee4eb983]
46 /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8d4d3) [0x5626cd17f4d3]
47 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcf8e4) [0x5626cd1c18e4]
48 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c6c) [0x5626cd1bac6c]
49 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x5626cd1ba3f5]
50 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0489) [0x5626cd1d2489]
51 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf98c) [0x5626cd1d198c]
52 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x5626cd1ba846]
53 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe59b8) [0x5626cd1d79b8]
54 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x5626cd1ba620]
55 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe4afb) [0x5626cd1d6afb]
56 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x5626cd1ba620]
57 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0489) [0x5626cd1d2489]
58 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf98c) [0x5626cd1d198c]
59 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcf173) [0x5626cd1c1173]
60 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c6c) [0x5626cd1bac6c]
61 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x5626cd1ba3f5]
=================================
*** caught segfault ***
address 0x4d2000ed618, 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$ref, duckdb_convert_opts_impl(res@connection@convert_opts, arrow = res@arrow))
9: duckdb_execute(res)
10: duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
11: .local(conn, statement, ...)
12: dbSendQuery(conn, statement, ...)
13: dbSendQuery(conn, statement, ...)
14: dbSendStatement(conn, statement, ...)
15: dbSendStatement(conn, statement, ...)
16: DBI::dbExecute(conn, glue::glue("LOAD {extension};"))
17: DBI::dbExecute(conn, glue::glue("LOAD {extension};"))
18: withCallingHandlers(expr, message = function(c) if (inherits(c, classes)) tryInvokeRestart("muffleMessage"))
19: suppressMessages(DBI::dbExecute(conn, glue::glue("LOAD {extension};")))
20: ddbs_load(conn, quiet = TRUE)
21: ddbs_create_conn(dbdir = "memory", ...)
22: ddbs_default_conn()
23: ddbs_open_dataset(system.file("spatial/countries.geojson", package = "duckspatial"))
24: eval(expr, envir)
25: eval(expr, envir)
26: withVisible(eval(expr, envir))
27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$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$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
28: eval(call)
29: eval(call)
30: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: evaluate::evaluate(...)
39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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))
40: in_dir(input_dir(), expr)
41: 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$render, options)))
42: eng_r(options)
43: block_exec(params)
44: call_block(x)
45: process_group(group)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
49: process_file(text, output)
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51: rmarkdown::render(input = input, output_format = output_format, knit_root_dir = knit_root_dir, params = params, run_pandoc = FALSE, envir = env)
52: execute(params$input, params$format, params$tempDir, params$libDir, params$dependencies, params$cwd, params$params, params$resourceDir, params$handledLanguages, params$markdown)
53: .main()
An irrecoverable exception occurred. R is aborting now ...
<1b>[39m<1b>[33mWARN: Error encountered when rendering files<1b>[39m
Error: processing vignette 'duckspatial.qmd' failed with diagnostics:
! Error running quarto CLI from R.
Caused by error:
! Could not parse cli `{}` expression: ` { .__han…`.
Caused by error:
! <text>:1:49: unexpected symbol
1: { .__handler_frame__. <- TRUE .__setup_frame__.
^
--- failed re-building ‘duckspatial.qmd’
--- re-building ‘spatial_joins.qmd’ using html
<1b>[31m
processing file: spatial_joins.qmd
<1b>[39m<1b>[31m[gannet:977666:0:977666] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x6d3662)
<1b>[39m<1b>[31m==== backtrace (tid: 977666) ====
0 /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7f909d5e4df4]
1 /lib64/libucs.so.0(+0x17aed) [0x7f909d5e6aed]
2 /lib64/libucs.so.0(+0x17cbd) [0x7f909d5e6cbd]
3 /lib64/libc.so.6(+0x1a040) [0x7f90b3c29040]
4 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.5.2/linux_amd64/spatial.duckdb_extension(+0xc26268) [0x7f8f84826268]
5 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.5.2/linux_amd64/spatial.duckdb_extension(+0xc29927) [0x7f8f84829927]
6 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.5.2/linux_amd64/spatial.duckdb_extension(+0xc29aa4) [0x7f8f84829aa4]
7 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.5.2/linux_amd64/spatial.duckdb_extension(+0x1152a6a) [0x7f8f84d52a6a]
8 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.5.2/linux_amd64/spatial.duckdb_extension(+0x75c104) [0x7f8f8435c104]
9 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.5.2/linux_amd64/spatial.duckdb_extension(+0x75a499) [0x7f8f8435a499]
10 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper29LoadExternalExtensionInternalERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEERNS_19ExtensionActiveLoadE+0x18f) [0x7f8fd6279e3f]
11 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper21LoadExternalExtensionERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEE+0x4a) [0x7f8fd6279bea]
12 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZNK6duckdb12PhysicalLoad15GetDataInternalERNS_16ExecutionContextERNS_9DataChunkERNS_19OperatorSourceInputE+0x151) [0x7f8fd705e831]
13 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor15FetchFromSourceERNS_9DataChunkE+0x9b) [0x7f8fd788d8eb]
14 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor7ExecuteEm+0x146) [0x7f8fd788a4c6]
15 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12PipelineTask11ExecuteTaskENS_17TaskExecutionModeE+0x112) [0x7f8fd788a0f2]
16 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12ExecutorTask7ExecuteENS_17TaskExecutionModeE+0xa0) [0x7f8fd7883d90]
17 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb8Executor11ExecuteTaskEb+0x1c0) [0x7f8fd78890f0]
18 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb13ClientContext19ExecuteTaskInternalERNS_17ClientContextLockERNS_15BaseQueryResultEb+0x40) [0x7f8fd76981f0]
19 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb18PendingQueryResult15ExecuteInternalERNS_17ClientContextLockE+0x7a) [0x7f8fd769a97a]
20 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb13ClientContext7ExecuteERKNSt3__112basic_stringIcNS1_11char_traitsIcEENS1_9allocatorIcEEEERNS_10shared_ptrINS_21PreparedStatementDataELb1EEERKNS_22PendingQueryParametersE+0xa0) [0x7f8fd769a6c0]
21 /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) [0x7f8fd76bd473]
22 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb17PreparedStatement7ExecuteERNS_6vectorINS_5ValueELb1ENSt3__19allocatorIS2_EEEEb+0x172) [0x7f8fd76bd712]
23 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_Z12rapi_executeN5cpp1116external_pointerIN6duckdb10RStatementEXadL_ZNS_15default_deleterIS2_EEvPT_EEEENS1_11ConvertOptsE+0x115) [0x7f8fd5f07f75]
24 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_duckdb_rapi_execute+0x66) [0x7f8fd5f704a6]
25 /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8f384) [0x561dbd5ca384]
26 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdab18) [0x561dbd615b18]
27 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c6c) [0x561dbd603c6c]
28 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x561dbd6033f5]
29 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8ec4) [0x561dbd603ec4]
30 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x26e) [0x561dbd6034be]
31 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8ec4) [0x561dbd603ec4]
32 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdcc20) [0x561dbd617c20]
33 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcd2f9) [0x561dbd6082f9]
34 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c6c) [0x561dbd603c6c]
35 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x561dbd6033f5]
36 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0489) [0x561dbd61b489]
37 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf98c) [0x561dbd61a98c]
38 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x561dbd603846]
39 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8ec4) [0x561dbd603ec4]
40 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdcc20) [0x561dbd617c20]
41 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcd2f9) [0x561dbd6082f9]
42 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c6c) [0x561dbd603c6c]
43 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x561dbd6033f5]
44 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0489) [0x561dbd61b489]
45 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf98c) [0x561dbd61a98c]
46 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x561dbd603846]
47 /data/gannet/ripley/R/test-clang/rlang/libs/rlang.so(+0x4983) [0x7f90b16b8983]
48 /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8d4d3) [0x561dbd5c84d3]
49 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcf8e4) [0x561dbd60a8e4]
50 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc8c6c) [0x561dbd603c6c]
51 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x561dbd6033f5]
52 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0489) [0x561dbd61b489]
53 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf98c) [0x561dbd61a98c]
54 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x561dbd603846]
55 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe59b8) [0x561dbd6209b8]
56 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x561dbd603620]
57 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe4afb) [0x561dbd61fafb]
58 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x561dbd603620]
59 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0489) [0x561dbd61b489]
60 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf98c) [0x561dbd61a98c]
61 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcf173) [0x561dbd60a173]
=================================
*** caught segfault ***
address 0x4d2000eeb02, 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: resolve_spatial_connections(x, y, conn, conn_x, conn_y, quiet = quiet)
24: ddbs_join(x = points_sf, y = countries_sf, join = "within")
25: eval(expr, envir)
26: eval(expr, envir)
27: withVisible(eval(expr, envir))
28: 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)})
29: eval(call)
30: eval(call)
31: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
32: doWithOneRestart(return(expr), restart)
33: withOneRestart(expr, restarts[[1L]])
34: withRestartList(expr, restarts[-nr])
35: doWithOneRestart(return(expr), restart)
36: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
37: withRestartList(expr, restarts)
38: withRestarts(with_handlers({ for (expr in tle$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)
39: evaluate::evaluate(...)
40: 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$render, options))
41: in_dir(input_dir(), expr)
42: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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)))
43: eng_r(options)
44: block_exec(params)
45: call_block(x)
46: process_group(group)
47: 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) })
48: 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()))
49: 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)
50: process_file(text, output)
51: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
52: rmarkdown::render(input = input, output_format = output_format, knit_root_dir = knit_root_dir, params = params, run_pandoc = FALSE, envir = env)
53: execute(params$input, params$format, params$tempDir, params$libDir, params$dependencies, params$cwd, params$params, params$resourceDir, params$handledLanguages, params$markdown)
54: .main()
An irrecoverable exception occurred. R is aborting now ...
<1b>[39m<1b>[33mWARN: Error encountered when rendering files<1b>[39m
Error: processing vignette 'spatial_joins.qmd' failed with diagnostics:
! Error running quarto CLI from R.
Caused by error:
! Could not parse cli `{}` expression: ` { .__han…`.
Caused by error:
! <text>:1:49: unexpected symbol
1: { .__handler_frame__. <- TRUE .__setup_frame__.
^
--- failed re-building ‘spatial_joins.qmd’
SUMMARY: processing the following files failed:
‘aw_interpolation.qmd’ ‘duckspatial.qmd’ ‘spatial_joins.qmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang