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Last updated on 2026-07-17 11:50:29 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.2.1 | 13.12 | 206.22 | 219.34 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.2.1 | 10.02 | 140.18 | 150.20 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.2.1 | 24.00 | 276.57 | 300.57 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 1.2.1 | 10.00 | 138.03 | 148.03 | OK | |
| r-devel-windows-x86_64 | 1.2.1 | 20.00 | 216.00 | 236.00 | OK | |
| r-patched-linux-x86_64 | 1.2.1 | 15.42 | 196.56 | 211.98 | OK | |
| r-release-linux-x86_64 | 1.2.1 | 14.16 | 186.34 | 200.50 | OK | |
| r-release-macos-arm64 | 1.2.1 | 3.00 | 38.00 | 41.00 | OK | |
| r-release-macos-x86_64 | 1.2.1 | 10.00 | 140.00 | 150.00 | OK | |
| r-release-windows-x86_64 | 1.2.1 | 21.00 | 213.00 | 234.00 | OK | |
| r-oldrel-macos-arm64 | 1.2.1 | 3.00 | 40.00 | 43.00 | OK | |
| r-oldrel-macos-x86_64 | 1.2.1 | 9.00 | 118.00 | 127.00 | OK | |
| r-oldrel-windows-x86_64 | 1.2.1 | 22.00 | 266.00 | 288.00 | OK |
Version: 1.2.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [9s/19s]
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 1.2.1 attached
* Compatible with DuckDB >= v1.5.4.2
Default output has changed on v1.0.0:
duckspatial now returns lazy `duckspatial_df` (dbplyr) objects
instead of `sf` objects.
To restore the previous behaviour:
ddbs_options(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
duckdb is keeping downloaded extensions in a temporary directory:
ℹ /tmp/RtmplhwcLW/working_dir/RtmpilM050/duckdb/extensions
This is removed when the R session ends, so extensions are re-downloaded each session.
ℹ To keep them, point `options(duckdb.extension_directory =)` or the `DUCKDB_EXTENSION_DIRECTORY` environment variable at a permanent path.
[gannet:1979338:0:1979338] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x449)
==== backtrace (tid:1979338) ====
0 /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7fbceddb7df4]
1 /lib64/libucs.so.0(+0x17aed) [0x7fbceddb9aed]
2 /lib64/libucs.so.0(+0x17cbd) [0x7fbceddb9cbd]
3 /lib64/libc.so.6(+0x1a040) [0x7fbd03728040]
4 /tmp/RtmplhwcLW/working_dir/RtmpilM050/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x1196b50) [0x7fbb60ccbb50]
5 /tmp/RtmplhwcLW/working_dir/RtmpilM050/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x1168728) [0x7fbb60c9d728]
6 /tmp/RtmplhwcLW/working_dir/RtmpilM050/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x773544) [0x7fbb602a8544]
7 /tmp/RtmplhwcLW/working_dir/RtmpilM050/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x7718d9) [0x7fbb602a68d9]
8 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper29LoadExternalExtensionInternalERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEERNS_19ExtensionActiveLoadE+0x18f) [0x7fbc26a7f85f]
9 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper21LoadExternalExtensionERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEE+0x4a) [0x7fbc26a7f60a]
10 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZNK6duckdb12PhysicalLoad15GetDataInternalERNS_16ExecutionContextERNS_9DataChunkERNS_19OperatorSourceInputE+0x151) [0x7fbc2786d401]
11 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor15FetchFromSourceERNS_9DataChunkE+0x98) [0x7fbc280a10c8]
12 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor7ExecuteEm+0x146) [0x7fbc2809dca6]
13 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12PipelineTask11ExecuteTaskENS_17TaskExecutionModeE+0x112) [0x7fbc2809d8d2]
14 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12ExecutorTask7ExecuteENS_17TaskExecutionModeE+0xa0) [0x7fbc28097570]
15 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb8Executor11ExecuteTaskEb+0x1c0) [0x7fbc2809c8d0]
16 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb13ClientContext19ExecuteTaskInternalERNS_17ClientContextLockERNS_15BaseQueryResultEb+0x40) [0x7fbc27ea8c60]
17 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb18PendingQueryResult15ExecuteInternalERNS_17ClientContextLockE+0x7a) [0x7fbc27eab3ba]
18 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb13ClientContext7ExecuteERKNSt3__112basic_stringIcNS1_11char_traitsIcEENS1_9allocatorIcEEEERNS_10shared_ptrINS_21PreparedStatementDataELb1EEERKNS_22PendingQueryParametersE+0xa0) [0x7fbc27eab100]
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) [0x7fbc27ece3a3]
20 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb17PreparedStatement7ExecuteERNS_6vectorINS_5ValueELb1ENSt3__19allocatorIS2_EEEEb+0x172) [0x7fbc27ece642]
21 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(+0x1087fc) [0x7fbc267087fc]
22 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_duckdb_rapi_execute+0x63) [0x7fbc26772f73]
23 /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8f5b4) [0x55e296e625b4]
24 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdae98) [0x55e296eade98]
25 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc921c) [0x55e296e9c21c]
26 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55e296e9b9d5]
27 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9474) [0x55e296e9c474]
28 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x26e) [0x55e296e9ba9e]
29 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9474) [0x55e296e9c474]
30 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdcfa0) [0x55e296eaffa0]
31 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcd659) [0x55e296ea0659]
32 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc921c) [0x55e296e9c21c]
33 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55e296e9b9d5]
34 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0b39) [0x55e296eb3b39]
35 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe002b) [0x55e296eb302b]
36 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc98f7) [0x55e296e9c8f7]
37 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f8) [0x55e296e9be28]
38 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9474) [0x55e296e9c474]
39 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdcfa0) [0x55e296eaffa0]
40 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcd659) [0x55e296ea0659]
41 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc921c) [0x55e296e9c21c]
42 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55e296e9b9d5]
43 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0b39) [0x55e296eb3b39]
44 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe002b) [0x55e296eb302b]
45 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc98f7) [0x55e296e9c8f7]
46 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f8) [0x55e296e9be28]
47 /data/gannet/ripley/R/test-clang/rlang/libs/rlang.so(+0x4993) [0x7fbd00a34993]
48 /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8d703) [0x55e296e60703]
49 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcfc54) [0x55e296ea2c54]
50 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc921c) [0x55e296e9c21c]
51 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55e296e9b9d5]
52 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0b39) [0x55e296eb3b39]
53 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe002b) [0x55e296eb302b]
54 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc98f7) [0x55e296e9c8f7]
55 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f8) [0x55e296e9be28]
56 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe5e98) [0x55e296eb8e98]
57 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x55e296e9bc00]
58 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe518b) [0x55e296eb818b]
59 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x55e296e9bc00]
60 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0b39) [0x55e296eb3b39]
61 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe002b) [0x55e296eb302b]
=================================
*** caught segfault ***
address 0x4d2001e33ca, 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$ref, duckdb_convert_opts_impl(res@connection@convert_opts, arrow = res@arrow))
9: duckdb_execute(res)
10: duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
11: .local(conn, statement, ...)
12: dbSendQuery(conn, statement, ...)
13: dbSendQuery(conn, statement, ...)
14: dbSendStatement(conn, statement, ...)
15: dbSendStatement(conn, statement, ...)
16: DBI::dbExecute(conn, glue::glue("LOAD {extension};"))
17: DBI::dbExecute(conn, glue::glue("LOAD {extension};"))
18: withCallingHandlers(expr, message = function(c) if (inherits(c, classes)) tryInvokeRestart("muffleMessage"))
19: suppressMessages(DBI::dbExecute(conn, glue::glue("LOAD {extension};")))
20: doTryCatch(return(expr), name, parentenv, handler)
21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
22: tryCatchList(expr, classes, parentenv, handlers)
23: tryCatch({ suppressMessages(DBI::dbExecute(conn, glue::glue("LOAD {extension};")))}, error = function(e) { cli::cli_abort(c("Failed to load the {extension} extension.", x = conditionMessage(e), i = "The binary may be corrupt or incompatible with this platform/DuckDB version.", i = "Try reinstalling with {.code ddbs_install(extension = '{extension}', upgrade = TRUE)}"))})
24: ddbs_load(conn, quiet = TRUE)
25: ddbs_create_conn(dbdir = "memory", ...)
26: ddbs_default_conn()
27: as_duckspatial_df.sf(argentina_sf)
28: duckspatial::as_duckspatial_df(argentina_sf)
29: eval(exprs, env)
30: eval(exprs, env)
31: withCallingHandlers(invisible(eval(exprs, env)), error = function(err) { cli::cli_abort("Failed to evaluate {.path {path}}.", parent = err, call = error_call)})
32: source_file(path, env = env, chdir = chdir, wrap = wrap, shuffle = shuffle, error_call = error_call)
33: FUN(X[[i]], ...)
34: lapply(files, function(path) { source_file(path, env = env, chdir = chdir, wrap = wrap, shuffle = shuffle, error_call = error_call)})
35: source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)
36: source_test_setup(".", env)
37: test_files_setup_state(test_dir, test_package, load_helpers, env)
38: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call)
39: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle)
40: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
41: test_check("duckspatial")
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.2.1
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:1982266:0:1982266] Caught signal 11 (Segmentation fault: Sent by the kernel at address (nil))
<1b>[39m<1b>[31m==== backtrace (tid:1982266) ====
0 /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7fa217ce3df4]
1 /lib64/libucs.so.0(+0x17aed) [0x7fa217ce5aed]
2 /lib64/libucs.so.0(+0x17cbd) [0x7fa217ce5cbd]
3 /lib64/libc.so.6(+0x1a040) [0x7fa22e928040]
4 /tmp/RtmplhwcLW/working_dir/RtmpSUgDQG/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x1196b50) [0x7fa105ab4b50]
5 /tmp/RtmplhwcLW/working_dir/RtmpSUgDQG/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x1168728) [0x7fa105a86728]
6 /tmp/RtmplhwcLW/working_dir/RtmpSUgDQG/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x773544) [0x7fa105091544]
7 /tmp/RtmplhwcLW/working_dir/RtmpSUgDQG/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x7718d9) [0x7fa10508f8d9]
8 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper29LoadExternalExtensionInternalERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEERNS_19ExtensionActiveLoadE+0x18f) [0x7fa15107f85f]
9 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper21LoadExternalExtensionERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEE+0x4a) [0x7fa15107f60a]
10 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZNK6duckdb12PhysicalLoad15GetDataInternalERNS_16ExecutionContextERNS_9DataChunkERNS_19OperatorSourceInputE+0x151) [0x7fa151e6d401]
11 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor15FetchFromSourceERNS_9DataChunkE+0x98) [0x7fa1526a10c8]
12 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor7ExecuteEm+0x146) [0x7fa15269dca6]
13 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12PipelineTask11ExecuteTaskENS_17TaskExecutionModeE+0x112) [0x7fa15269d8d2]
14 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12ExecutorTask7ExecuteENS_17TaskExecutionModeE+0xa0) [0x7fa152697570]
15 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb8Executor11ExecuteTaskEb+0x1c0) [0x7fa15269c8d0]
16 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb13ClientContext19ExecuteTaskInternalERNS_17ClientContextLockERNS_15BaseQueryResultEb+0x40) [0x7fa1524a8c60]
17 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb18PendingQueryResult15ExecuteInternalERNS_17ClientContextLockE+0x7a) [0x7fa1524ab3ba]
18 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb13ClientContext7ExecuteERKNSt3__112basic_stringIcNS1_11char_traitsIcEENS1_9allocatorIcEEEERNS_10shared_ptrINS_21PreparedStatementDataELb1EEERKNS_22PendingQueryParametersE+0xa0) [0x7fa1524ab100]
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) [0x7fa1524ce3a3]
20 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb17PreparedStatement7ExecuteERNS_6vectorINS_5ValueELb1ENSt3__19allocatorIS2_EEEEb+0x172) [0x7fa1524ce642]
21 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(+0x1087fc) [0x7fa150d087fc]
22 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_duckdb_rapi_execute+0x63) [0x7fa150d72f73]
23 /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8f5b4) [0x55642a5695b4]
24 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdae98) [0x55642a5b4e98]
25 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc921c) [0x55642a5a321c]
26 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55642a5a29d5]
27 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9474) [0x55642a5a3474]
28 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x26e) [0x55642a5a2a9e]
29 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9474) [0x55642a5a3474]
30 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdcfa0) [0x55642a5b6fa0]
31 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcd659) [0x55642a5a7659]
32 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc921c) [0x55642a5a321c]
33 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55642a5a29d5]
34 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0b39) [0x55642a5bab39]
35 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe002b) [0x55642a5ba02b]
36 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc98f7) [0x55642a5a38f7]
37 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f8) [0x55642a5a2e28]
38 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9474) [0x55642a5a3474]
39 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdcfa0) [0x55642a5b6fa0]
40 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcd659) [0x55642a5a7659]
41 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc921c) [0x55642a5a321c]
42 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55642a5a29d5]
43 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0b39) [0x55642a5bab39]
44 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe002b) [0x55642a5ba02b]
45 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc98f7) [0x55642a5a38f7]
46 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f8) [0x55642a5a2e28]
47 /data/gannet/ripley/R/test-clang/rlang/libs/rlang.so(+0x4993) [0x7fa22c2f2993]
48 /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8d703) [0x55642a567703]
49 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcfc54) [0x55642a5a9c54]
50 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc921c) [0x55642a5a321c]
51 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55642a5a29d5]
52 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0b39) [0x55642a5bab39]
53 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe002b) [0x55642a5ba02b]
54 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc98f7) [0x55642a5a38f7]
55 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f8) [0x55642a5a2e28]
56 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe5e98) [0x55642a5bfe98]
57 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x55642a5a2c00]
58 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe518b) [0x55642a5bf18b]
59 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x55642a5a2c00]
60 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0b39) [0x55642a5bab39]
61 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe002b) [0x55642a5ba02b]
=================================
*** caught segfault ***
address 0x4d2001e3f3a, 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$ref, duckdb_convert_opts_impl(res@connection@convert_opts, arrow = res@arrow))
9: duckdb_execute(res)
10: duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
11: .local(conn, statement, ...)
12: dbSendQuery(conn, statement, ...)
13: dbSendQuery(conn, statement, ...)
14: dbSendStatement(conn, statement, ...)
15: dbSendStatement(conn, statement, ...)
16: DBI::dbExecute(conn, glue::glue("LOAD {extension};"))
17: DBI::dbExecute(conn, glue::glue("LOAD {extension};"))
18: withCallingHandlers(expr, message = function(c) if (inherits(c, classes)) tryInvokeRestart("muffleMessage"))
19: suppressMessages(DBI::dbExecute(conn, glue::glue("LOAD {extension};")))
20: doTryCatch(return(expr), name, parentenv, handler)
21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
22: tryCatchList(expr, classes, parentenv, handlers)
23: tryCatch({ suppressMessages(DBI::dbExecute(conn, glue::glue("LOAD {extension};")))}, error = function(e) { cli::cli_abort(c("Failed to load the {extension} extension.", x = conditionMessage(e), i = "The binary may be corrupt or incompatible with this platform/DuckDB version.", i = "Try reinstalling with {.code ddbs_install(extension = '{extension}', upgrade = TRUE)}"))})
24: ddbs_load(conn, quiet = TRUE)
25: ddbs_create_conn(dbdir = "memory", ...)
26: ddbs_default_conn()
27: resolve_spatial_connections(target, source, conn, quiet = quiet)
28: ddbs_interpolate_aw(target = grid, source = nc, tid = "target_id", sid = "source_id", extensive = "BIR74", weight = "total", mode = "sf")
29: eval(expr, envir)
30: eval(expr, envir)
31: withVisible(eval(expr, envir))
32: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$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$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
33: eval(call)
34: eval(call)
35: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
36: doWithOneRestart(return(expr), restart)
37: withOneRestart(expr, restarts[[1L]])
38: withRestartList(expr, restarts[-nr])
39: doWithOneRestart(return(expr), restart)
40: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
41: withRestartList(expr, restarts)
42: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
43: evaluate::evaluate(...)
44: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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))
45: in_dir(input_dir(), expr)
46: 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$render, options)))
47: eng_r(options)
48: block_exec(params)
49: call_block(x)
50: process_group(group)
51: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
52: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
53: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
54: process_file(text, output)
55: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
56: rmarkdown::render(input = input, output_format = output_format, knit_root_dir = knit_root_dir, params = params, run_pandoc = FALSE, envir = env)
57: execute(params$input, params$format, params$tempDir, params$libDir, params$dependencies, params$cwd, params$params, params$resourceDir, params$handledLanguages, params$markdown)
58: .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>[31mError in `value[[3L]]()`:
! Failed to load the spatial extension.
✖ Invalid Error: Invalid Input Error: Initialization functio<1b>[39m<1b>[31mn
"spatial_duckdb_cpp_init" from file
"/tmp/RtmplhwcLW/working_dir/Rtmpeh5GLW/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension"
threw an exception: "Missing DB manager" ℹ Context: rapi_execute ℹ Error
type: INVALID
ℹ The binary may be corrupt or incompatible with this platform/DuckDB version.
ℹ Try reinstalling with `ddbs_install(extension = 'spatial', upgrade = TRUE)`
Backtrace:
▆
1. └─duckspatial::ddbs_open_dataset(...)
2. └─duckspatial:::ddbs_default_conn()
3. └─duckspatial::ddbs_create_conn(dbdir = "memory", ...)
4. └─duckspatial::ddbs_load(conn, quiet = TRUE)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. └─value[[3L]](cond)
9. └─cli::cli_abort(...)
10. └─rlang::abort(...)
<1b>[39m<1b>[31m
Quitting from duckspatial.qmd:78-87 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `value[[3L]]()`:
! Failed to load the spatial extension.
✖ Invalid Error: Invalid Input Error: Initialization function
"spatial_duckdb_cpp_init" from file
"/tmp/RtmplhwcLW/working_dir/Rtmpeh5GLW/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension"
threw an exception: "Missing DB manager" ℹ Context: rapi_execute ℹ Error
type: INVALID
ℹ The binary may be corrupt or incompatible with this platform/DuckDB version.
ℹ Try reinstalling with `ddbs_install(extension = 'spatial', upgrade = TRUE)`
---
Backtrace:
▆
1. └─duckspatial::ddbs_open_dataset(...)
2. └─duckspatial:::ddbs_default_conn()
3. └─duckspatial::ddbs_create_conn(dbdir = "memory", ...)
4. └─duckspatial::ddbs_load(conn, quiet = TRUE)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<1b>[39m<1b>[31mExecution halted
<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 in `quarto_render()`:
✖ Error returned by quarto CLI.
-----------------------------
processing file: duckspatial.qmd
<1b>[31mError in `value[[3L]]()`:<1b>[39m
! Failed to load the spatial extension.
✖ Invalid Error: Invalid Input Error: Initialization functio<1b>[31mn<1b>[39m
"spatial_duckdb_cpp_init" from file
"/tmp/RtmplhwcLW/working_dir/Rtmpeh5GLW/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension"
threw an exception: "Missing DB manager" ℹ Context: rapi_execute ℹ Error
type: INVALID
ℹ The binary may be corrupt or incompatible with this platform/DuckDB
version.
ℹ Try reinstalling with `ddbs_install(extension = 'spatial', upgrade = TRUE)`
Backtrace:
▆
1. └─duckspatial::ddbs_open_dataset(...)
2. └─duckspatial:::ddbs_default_conn()
3. └─duckspatial::ddbs_create_conn(dbdir = "memory", ...)
4. └─duckspatial::ddbs_load(conn, quiet = TRUE)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. └─value[[3L]](cond)
9. └─cli::cli_abort(...)
10. └─rlang::abort(...)
Quitting from duckspatial.qmd:78-87 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `value[[3L]]()`:
! Failed to load the spatial extension.
✖ Invalid Error: Invalid Input Error: Initialization function
"spatial_duckdb_cpp_init" from file
"/tmp/RtmplhwcLW/working_dir/Rtmpeh5GLW/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension"
threw an exception: "Missing DB manager" ℹ Context: rapi_execute ℹ Error
type: INVALID
ℹ The binary may be corrupt or incompatible with this platform/DuckDB
version.
ℹ Try reinstalling with `ddbs_install(extension = 'spatial', upgrade = TRUE)`
---
Backtrace:
▆
1. └─duckspatial::ddbs_open_dataset(...)
2. └─duckspatial:::ddbs_default_conn()
3. └─duckspatial::ddbs_create_conn(dbdir = "memory", ...)
4. └─duckspatial::ddbs_load(conn, quiet = TRUE)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<1b>[31mExecution halted<1b>[39m
<1b>[33mWARN: Error encountered when rendering files<1b>[39m
Caused by error in `processx::run()`:
! System command 'quarto' failed
--- failed re-building ‘duckspatial.qmd’
--- re-building ‘spatial_joins.qmd’ using html
<1b>[31m
processing file: spatial_joins.qmd
<1b>[39m<1b>[31m[gannet:1988211:0:1988603] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x6d3662)
<1b>[39m<1b>[31m==== backtrace (tid:1988603) ====
0 /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7f09519e4df4]
1 /lib64/libucs.so.0(+0x17aed) [0x7f09519e6aed]
2 /lib64/libucs.so.0(+0x17cbd) [0x7f09519e6cbd]
3 /lib64/libc.so.6(+0x1a040) [0x7f0968029040]
4 /tmp/RtmplhwcLW/working_dir/RtmpLGNJRH/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0xc3af88) [0x7f083076ff88]
5 /tmp/RtmplhwcLW/working_dir/RtmpLGNJRH/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0xc3e647) [0x7f0830773647]
6 /tmp/RtmplhwcLW/working_dir/RtmpLGNJRH/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0xc3e7c4) [0x7f08307737c4]
7 /tmp/RtmplhwcLW/working_dir/RtmpLGNJRH/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x116876a) [0x7f0830c9d76a]
8 /tmp/RtmplhwcLW/working_dir/RtmpLGNJRH/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x773544) [0x7f08302a8544]
9 /tmp/RtmplhwcLW/working_dir/RtmpLGNJRH/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x7718d9) [0x7f08302a68d9]
10 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper29LoadExternalExtensionInternalERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEERNS_19ExtensionActiveLoadE+0x18f) [0x7f088a67f85f]
11 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper21LoadExternalExtensionERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEE+0x4a) [0x7f088a67f60a]
12 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZNK6duckdb12PhysicalLoad15GetDataInternalERNS_16ExecutionContextERNS_9DataChunkERNS_19OperatorSourceInputE+0x151) [0x7f088b46d401]
13 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor15FetchFromSourceERNS_9DataChunkE+0x98) [0x7f088bca10c8]
14 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor7ExecuteEm+0x146) [0x7f088bc9dca6]
15 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12PipelineTask11ExecuteTaskENS_17TaskExecutionModeE+0x154) [0x7f088bc9d914]
16 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12ExecutorTask7ExecuteENS_17TaskExecutionModeE+0xa0) [0x7f088bc97570]
17 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb13TaskScheduler14ExecuteForeverEPNSt3__16atomicIbEE+0x39a) [0x7f088bca432a]
18 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(+0x1aafe9c) [0x7f088bcafe9c]
19 /lib64/libc.so.6(+0x71f14) [0x7f0968080f14]
20 /lib64/libc.so.6(+0xf532c) [0x7f096810432c]
=================================
*** caught segfault ***
address 0x4d2001e5673, 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: doTryCatch(return(expr), name, parentenv, handler)
21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
22: tryCatchList(expr, classes, parentenv, handlers)
23: tryCatch({ suppressMessages(DBI::dbExecute(conn, glue::glue("LOAD {extension};")))}, error = function(e) { cli::cli_abort(c("Failed to load the {extension} extension.", x = conditionMessage(e), i = "The binary may be corrupt or incompatible with this platform/DuckDB version.", i = "Try reinstalling with {.code ddbs_install(extension = '{extension}', upgrade = TRUE)}"))})
24: ddbs_load(conn, quiet = TRUE)
25: ddbs_create_conn(dbdir = "memory", ...)
26: ddbs_default_conn()
27: resolve_spatial_connections(x, y, conn, conn_x, conn_y, quiet = quiet)
28: ddbs_join(x = points_sf, y = countries_sf, join = "within")
29: eval(expr, envir)
30: eval(expr, envir)
31: withVisible(eval(expr, envir))
32: 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)})
33: eval(call)
34: eval(call)
35: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
36: doWithOneRestart(return(expr), restart)
37: withOneRestart(expr, restarts[[1L]])
38: withRestartList(expr, restarts[-nr])
39: doWithOneRestart(return(expr), restart)
40: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
41: withRestartList(expr, restarts)
42: withRestarts(with_handlers({ for (expr in tle$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)
43: evaluate::evaluate(...)
44: 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$render, options))
45: in_dir(input_dir(), expr)
46: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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)))
47: eng_r(options)
48: block_exec(params)
49: call_block(x)
50: process_group(group)
51: 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) })
52: 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()))
53: 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)
54: process_file(text, output)
55: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
56: rmarkdown::render(input = input, output_format = output_format, knit_root_dir = knit_root_dir, params = params, run_pandoc = FALSE, envir = env)
57: execute(params$input, params$format, params$tempDir, params$libDir, params$dependencies, params$cwd, params$params, params$resourceDir, params$handledLanguages, params$markdown)
58: .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
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