Last updated on 2026-03-02 11:51:11 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.9.0 | 4.39 | 84.39 | 88.78 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.9.0 | 2.76 | 59.56 | 62.32 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.9.0 | 119.64 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.9.0 | 8.00 | 146.19 | 154.19 | OK | |
| r-devel-macos-arm64 | 0.9.0 | 1.00 | 26.00 | 27.00 | OK | |
| r-devel-windows-x86_64 | 0.9.0 | 7.00 | 111.00 | 118.00 | OK | |
| r-patched-linux-x86_64 | 0.9.0 | 6.51 | 74.58 | 81.09 | OK | |
| r-release-linux-x86_64 | 0.9.0 | 4.56 | 75.25 | 79.81 | OK | |
| r-release-macos-arm64 | 0.9.0 | 1.00 | 31.00 | 32.00 | OK | |
| r-release-macos-x86_64 | 0.9.0 | 3.00 | 106.00 | 109.00 | OK | |
| r-release-windows-x86_64 | 0.9.0 | 7.00 | 102.00 | 109.00 | OK | |
| r-oldrel-macos-arm64 | 0.9.0 | 1.00 | 39.00 | 40.00 | OK | |
| r-oldrel-macos-x86_64 | 0.9.0 | 12.00 | ERROR | |||
| r-oldrel-windows-x86_64 | 0.9.0 | 9.00 | 123.00 | 132.00 | OK |
Version: 0.9.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [12s/11s]
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)
Important: 'crs_column' and 'crs' arguments are deprecated and will be removed in the next version.
If possible, use the default values of these arguments to avoid future issues.
> 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
Reading layer `rivers' from data source
`/data/gannet/ripley/R/packages/tests-clang/duckspatial.Rcheck/duckspatial/spatial/rivers.geojson'
using driver `GeoJSON'
Simple feature collection with 100 features and 1 field
Geometry type: LINESTRING
Dimension: XY
Bounding box: xmin: 2766878 ymin: 2222357 xmax: 3578648 ymax: 2459939
Projected CRS: ETRS89-extended / LAEA Europe
Saving _problems/test-compatibility-5.R
Saving _problems/test-compatibility-47.R
Saving _problems/test-compatibility-76.R
Saving _problems/test-compatibility-104.R
[ FAIL 4 | WARN 0 | SKIP 17 | PASS 0 ]
══ Skipped tests (17) ══════════════════════════════════════════════════════════
• On CRAN (17): 'test-db_read.R:2:1', 'test-db_register.R:3:1',
'test-db_write.R:3:1', 'test-ddbs_area.R:3:1', 'test-ddbs_bbox.R:3:1',
'test-ddbs_combine.R:3:1', 'test-ddbs_concave_hull.R:3:1',
'test-ddbs_convex_hull.R:3:1', 'test-ddbs_distance.R:3:1',
'test-ddbs_envelope.R:3:1', 'test-ddbs_generate_points.R:5:1',
'test-ddbs_interpolate_aw.R:2:1', 'test-ddbs_join.R:3:1',
'test-ddbs_length.R:3:1', 'test-ddbs_transform.R:5:1',
'test-ddbs_union.R:3:1', 'test-utils.R:2:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-compatibility.R:5:5'): Compatibility: Arrow Views behave like Persistent Tables ──
Error in `duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)`: Invalid Error: Invalid Input Error: Initialization function "spatial_duckdb_cpp_init" from file "/data/gannet/ripley/.local/share/R/duckdb/extensions/v1.4.4/linux_amd64/spatial.duckdb_extension" threw an exception: "Attempted to dereference shared_ptr that is NULL!"
i Context: rapi_execute
i Error type: INVALID
Backtrace:
▆
1. ├─duckspatial::ddbs_create_conn("memory") at test-compatibility.R:5:5
2. │ └─duckspatial::ddbs_load(conn, quiet = TRUE)
3. │ ├─base::suppressMessages(DBI::dbExecute(conn, "LOAD spatial;"))
4. │ │ └─base::withCallingHandlers(...)
5. │ ├─DBI::dbExecute(conn, "LOAD spatial;")
6. │ └─DBI::dbExecute(conn, "LOAD spatial;")
7. │ ├─DBI::dbSendStatement(conn, statement, ...)
8. │ └─DBI::dbSendStatement(conn, statement, ...)
9. │ ├─DBI::dbSendQuery(conn, statement, ...)
10. │ └─duckdb::dbSendQuery(conn, statement, ...)
11. │ └─duckdb (local) .local(conn, statement, ...)
12. │ └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
13. │ └─duckdb:::duckdb_execute(res)
14. │ └─duckdb:::rethrow_rapi_execute(...)
15. │ ├─rlang::try_fetch(...)
16. │ │ ├─base::tryCatch(...)
17. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
18. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
19. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
20. │ │ └─base::withCallingHandlers(...)
21. │ └─duckdb:::rapi_execute(stmt, convert_opts)
22. ├─duckdb (local) `<fn>`(...)
23. │ └─rlang::abort(error_parts, class = "duckdb_error", !!!fields)
24. │ └─rlang:::signal_abort(cnd, .file)
25. │ └─base::signalCondition(cnd)
26. └─rlang (local) `<fn>`(`<dckdb_rr>`)
27. └─handlers[[1L]](cnd)
28. └─duckdb:::rethrow_error_from_rapi(e, call)
29. └─rlang::abort(msg, call = call)
── Error ('test-compatibility.R:47:5'): Round trip: write -> read for various geometry types ──
Error in `duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)`: Invalid Error: Invalid Input Error: Initialization function "spatial_duckdb_cpp_init" from file "/data/gannet/ripley/.local/share/R/duckdb/extensions/v1.4.4/linux_amd64/spatial.duckdb_extension" threw an exception: "Missing DB manager"
i Context: rapi_execute
i Error type: INVALID
Backtrace:
▆
1. ├─duckspatial::ddbs_create_conn("memory") at test-compatibility.R:47:5
2. │ └─duckspatial::ddbs_load(conn, quiet = TRUE)
3. │ ├─base::suppressMessages(DBI::dbExecute(conn, "LOAD spatial;"))
4. │ │ └─base::withCallingHandlers(...)
5. │ ├─DBI::dbExecute(conn, "LOAD spatial;")
6. │ └─DBI::dbExecute(conn, "LOAD spatial;")
7. │ ├─DBI::dbSendStatement(conn, statement, ...)
8. │ └─DBI::dbSendStatement(conn, statement, ...)
9. │ ├─DBI::dbSendQuery(conn, statement, ...)
10. │ └─duckdb::dbSendQuery(conn, statement, ...)
11. │ └─duckdb (local) .local(conn, statement, ...)
12. │ └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
13. │ └─duckdb:::duckdb_execute(res)
14. │ └─duckdb:::rethrow_rapi_execute(...)
15. │ ├─rlang::try_fetch(...)
16. │ │ ├─base::tryCatch(...)
17. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
18. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
19. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
20. │ │ └─base::withCallingHandlers(...)
21. │ └─duckdb:::rapi_execute(stmt, convert_opts)
22. ├─duckdb (local) `<fn>`(...)
23. │ └─rlang::abort(error_parts, class = "duckdb_error", !!!fields)
24. │ └─rlang:::signal_abort(cnd, .file)
25. │ └─base::signalCondition(cnd)
26. └─rlang (local) `<fn>`(`<dckdb_rr>`)
27. └─handlers[[1L]](cnd)
28. └─duckdb:::rethrow_error_from_rapi(e, call)
29. └─rlang::abort(msg, call = call)
── Error ('test-compatibility.R:76:5'): Round trip: register -> read for various geometry types ──
Error in `duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)`: Invalid Error: Invalid Input Error: Initialization function "spatial_duckdb_cpp_init" from file "/data/gannet/ripley/.local/share/R/duckdb/extensions/v1.4.4/linux_amd64/spatial.duckdb_extension" threw an exception: "Missing DB manager"
i Context: rapi_execute
i Error type: INVALID
Backtrace:
▆
1. ├─duckspatial::ddbs_create_conn("memory") at test-compatibility.R:76:5
2. │ └─duckspatial::ddbs_load(conn, quiet = TRUE)
3. │ ├─base::suppressMessages(DBI::dbExecute(conn, "LOAD spatial;"))
4. │ │ └─base::withCallingHandlers(...)
5. │ ├─DBI::dbExecute(conn, "LOAD spatial;")
6. │ └─DBI::dbExecute(conn, "LOAD spatial;")
7. │ ├─DBI::dbSendStatement(conn, statement, ...)
8. │ └─DBI::dbSendStatement(conn, statement, ...)
9. │ ├─DBI::dbSendQuery(conn, statement, ...)
10. │ └─duckdb::dbSendQuery(conn, statement, ...)
11. │ └─duckdb (local) .local(conn, statement, ...)
12. │ └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
13. │ └─duckdb:::duckdb_execute(res)
14. │ └─duckdb:::rethrow_rapi_execute(...)
15. │ ├─rlang::try_fetch(...)
16. │ │ ├─base::tryCatch(...)
17. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
18. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
19. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
20. │ │ └─base::withCallingHandlers(...)
21. │ └─duckdb:::rapi_execute(stmt, convert_opts)
22. ├─duckdb (local) `<fn>`(...)
23. │ └─rlang::abort(error_parts, class = "duckdb_error", !!!fields)
24. │ └─rlang:::signal_abort(cnd, .file)
25. │ └─base::signalCondition(cnd)
26. └─rlang (local) `<fn>`(`<dckdb_rr>`)
27. └─handlers[[1L]](cnd)
28. └─duckdb:::rethrow_error_from_rapi(e, call)
29. └─rlang::abort(msg, call = call)
── Error ('test-compatibility.R:104:5'): Compatibility: Writing from file path and reading back ──
Error in `duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)`: Invalid Error: Invalid Input Error: Initialization function "spatial_duckdb_cpp_init" from file "/data/gannet/ripley/.local/share/R/duckdb/extensions/v1.4.4/linux_amd64/spatial.duckdb_extension" threw an exception: "Missing DB manager"
i Context: rapi_execute
i Error type: INVALID
Backtrace:
▆
1. ├─duckspatial::ddbs_create_conn("memory") at test-compatibility.R:104:5
2. │ └─duckspatial::ddbs_load(conn, quiet = TRUE)
3. │ ├─base::suppressMessages(DBI::dbExecute(conn, "LOAD spatial;"))
4. │ │ └─base::withCallingHandlers(...)
5. │ ├─DBI::dbExecute(conn, "LOAD spatial;")
6. │ └─DBI::dbExecute(conn, "LOAD spatial;")
7. │ ├─DBI::dbSendStatement(conn, statement, ...)
8. │ └─DBI::dbSendStatement(conn, statement, ...)
9. │ ├─DBI::dbSendQuery(conn, statement, ...)
10. │ └─duckdb::dbSendQuery(conn, statement, ...)
11. │ └─duckdb (local) .local(conn, statement, ...)
12. │ └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
13. │ └─duckdb:::duckdb_execute(res)
14. │ └─duckdb:::rethrow_rapi_execute(...)
15. │ ├─rlang::try_fetch(...)
16. │ │ ├─base::tryCatch(...)
17. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
18. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
19. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
20. │ │ └─base::withCallingHandlers(...)
21. │ └─duckdb:::rapi_execute(stmt, convert_opts)
22. ├─duckdb (local) `<fn>`(...)
23. │ └─rlang::abort(error_parts, class = "duckdb_error", !!!fields)
24. │ └─rlang:::signal_abort(cnd, .file)
25. │ └─base::signalCondition(cnd)
26. └─rlang (local) `<fn>`(`<dckdb_rr>`)
27. └─handlers[[1L]](cnd)
28. └─duckdb:::rethrow_error_from_rapi(e, call)
29. └─rlang::abort(msg, call = call)
[ FAIL 4 | WARN 0 | SKIP 17 | PASS 0 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.9.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘aw_interpolation.Rmd’ using rmarkdown
[gannet:698037:0:698037] Caught signal 11 (Segmentation fault: address not mapped to object at address 0xf)
==== backtrace (tid: 698037) ====
0 /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7f98dfb7ddf4]
1 /lib64/libucs.so.0(+0x17aed) [0x7f98dfb7faed]
2 /lib64/libucs.so.0(+0x17cbd) [0x7f98dfb7fcbd]
3 /lib64/libc.so.6(+0x19c30) [0x7f98f6326c30]
4 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.4.4/linux_amd64/spatial.duckdb_extension(+0x10ecf30) [0x7f97bc4ecf30]
5 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.4.4/linux_amd64/spatial.duckdb_extension(+0x10cbeb8) [0x7f97bc4cbeb8]
6 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.4.4/linux_amd64/spatial.duckdb_extension(+0x7d8bb4) [0x7f97bbbd8bb4]
7 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.4.4/linux_amd64/spatial.duckdb_extension(+0x7d7159) [0x7f97bbbd7159]
8 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper29LoadExternalExtensionInternalERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEERNS_19ExtensionActiveLoadE+0x1b4) [0x7f98189734a4]
9 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper21LoadExternalExtensionERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEE+0x4a) [0x7f981897322a]
10 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZNK6duckdb12PhysicalLoad7GetDataERNS_16ExecutionContextERNS_9DataChunkERNS_19OperatorSourceInputE+0x151) [0x7f98197a9511]
11 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor15FetchFromSourceERNS_9DataChunkE+0x9f) [0x7f9819f5e6cf]
12 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor7ExecuteEm+0x133) [0x7f9819f5b163]
13 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12PipelineTask11ExecuteTaskENS_17TaskExecutionModeE+0x119) [0x7f9819f5ad99]
14 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12ExecutorTask7ExecuteENS_17TaskExecutionModeE+0xa0) [0x7f9819f546b0]
15 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb8Executor11ExecuteTaskEb+0x24a) [0x7f9819f59c7a]
16 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb13ClientContext19ExecuteTaskInternalERNS_17ClientContextLockERNS_15BaseQueryResultEb+0x40) [0x7f9819d96b00]
17 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb18PendingQueryResult15ExecuteInternalERNS_17ClientContextLockE+0x7a) [0x7f9819d9903a]
18 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb17PreparedStatement7ExecuteERNS_6vectorINS_5ValueELb1EEEb+0x5a) [0x7f9819db9b6a]
19 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_Z12rapi_executeN5cpp1116external_pointerIN6duckdb10RStatementEXadL_ZNS_15default_deleterIS2_EEvPT_EEEENS1_11ConvertOptsE+0x115) [0x7f9818701d95]
20 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_duckdb_rapi_execute+0x63) [0x7f981876b723]
21 /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8f2c4) [0x5555a96682c4]
22 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xd8ed8) [0x5555a96b1ed8]
23 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc702c) [0x5555a96a002c]
24 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x5555a969f7b5]
25 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc7284) [0x5555a96a0284]
26 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x26e) [0x5555a969f87e]
27 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc7284) [0x5555a96a0284]
28 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdafe0) [0x5555a96b3fe0]
29 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcb6b9) [0x5555a96a46b9]
30 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc702c) [0x5555a96a002c]
31 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x5555a969f7b5]
32 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xde849) [0x5555a96b7849]
33 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xddd4c) [0x5555a96b6d4c]
34 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x5555a969fc06]
35 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc7284) [0x5555a96a0284]
36 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdafe0) [0x5555a96b3fe0]
37 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcb6b9) [0x5555a96a46b9]
38 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc702c) [0x5555a96a002c]
39 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x5555a969f7b5]
40 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xde849) [0x5555a96b7849]
41 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xddd4c) [0x5555a96b6d4c]
42 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x5555a969fc06]
43 /data/gannet/ripley/R/test-clang/rlang/libs/rlang.so(+0x47d3) [0x7f98f36777d3]
44 /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8d413) [0x5555a9666413]
45 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcdca4) [0x5555a96a6ca4]
46 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc702c) [0x5555a96a002c]
47 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x5555a969f7b5]
48 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xde849) [0x5555a96b7849]
49 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xddd4c) [0x5555a96b6d4c]
50 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x5555a969fc06]
51 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe3d78) [0x5555a96bcd78]
52 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x5555a969f9e0]
53 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe2ebb) [0x5555a96bbebb]
54 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x5555a969f9e0]
55 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xde849) [0x5555a96b7849]
56 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xddd4c) [0x5555a96b6d4c]
57 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcd533) [0x5555a96a6533]
58 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc702c) [0x5555a96a002c]
59 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x5555a969f7b5]
60 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xde849) [0x5555a96b7849]
61 /data/gannet/ripley/R/R-clang/bin/exec/R(R_execMethod+0x2cb) [0x5555a96ba65b]
=================================
*** caught segfault ***
address 0x4d2000aa6b5, 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$ref, duckdb_convert_opts_impl(res@connection@convert_opts, arrow = res@arrow))
9: duckdb_execute(res)
10: duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
11: .local(conn, statement, ...)
12: dbSendQuery(conn, statement, ...)
13: dbSendQuery(conn, statement, ...)
14: dbSendStatement(conn, statement, ...)
15: dbSendStatement(conn, statement, ...)
16: DBI::dbExecute(conn, "LOAD spatial;")
17: DBI::dbExecute(conn, "LOAD spatial;")
18: withCallingHandlers(expr, message = function(c) if (inherits(c, classes)) tryInvokeRestart("muffleMessage"))
19: suppressMessages(DBI::dbExecute(conn, "LOAD spatial;"))
20: duckspatial::ddbs_load(conn, quiet = TRUE)
21: ddbs_create_conn()
22: ddbs_interpolate_aw(target = grid, source = nc, tid = "target_id", sid = "source_id", extensive = "BIR74", weight = "total", output = "sf")
23: eval(expr, envir)
24: eval(expr, envir)
25: withVisible(eval(expr, envir))
26: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$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$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
27: eval(call)
28: eval(call)
29: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
30: doWithOneRestart(return(expr), restart)
31: withOneRestart(expr, restarts[[1L]])
32: withRestartList(expr, restarts[-nr])
33: doWithOneRestart(return(expr), restart)
34: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
35: withRestartList(expr, restarts)
36: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
37: evaluate::evaluate(...)
38: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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))
39: in_dir(input_dir(), expr)
40: 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$render, options)))
41: eng_r(options)
42: block_exec(params)
43: call_block(x)
44: process_group(group)
45: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
46: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
47: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
48: process_file(text, output)
49: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
50: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
51: vweave_rmarkdown(...)
52: engine$weave(file, quiet = quiet, encoding = enc)
53: doTryCatch(return(expr), name, parentenv, handler)
54: tryCatchOne(expr, names, parentenv, handlers[[1L]])
55: tryCatchList(expr, classes, parentenv, handlers)
56: 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)))})
57: tools:::.buildOneVignette("aw_interpolation.Rmd", "/data/gannet/ripley/R/packages/tests-clang/duckspatial.Rcheck/vign_test/duckspatial", TRUE, FALSE, "aw_interpolation", "UTF-8", "/tmp/RtmptaCfjB/working_dir/Rtmp0tGucL/fileaa5e06995adbe.rds")
An irrecoverable exception occurred. R is aborting now ...
--- re-building ‘benchmark.Rmd’ using rmarkdown
--- finished re-building ‘benchmark.Rmd’
--- re-building ‘duckspatial.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘duckspatial.Rmd’
--- re-building ‘spatial_joins.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘spatial_joins.Rmd’
SUMMARY: processing the following file failed:
‘aw_interpolation.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.9.0
Check: package dependencies
Result: ERROR
Package required but not available: ‘arrow’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-oldrel-macos-x86_64