Last updated on 2026-06-20 22:55:56 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.1 | 33.28 | 320.54 | 353.82 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.1.1 | 21.78 | 209.58 | 231.36 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.1.1 | 66.00 | 471.78 | 537.78 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 0.1.1 | 62.00 | 583.80 | 645.80 | OK | |
| r-devel-windows-x86_64 | 0.1.1 | 33.00 | 269.00 | 302.00 | OK | |
| r-patched-linux-x86_64 | 0.1.1 | 32.59 | 302.36 | 334.95 | OK | |
| r-release-linux-x86_64 | 0.1.1 | 29.55 | 303.08 | 332.63 | OK | |
| r-release-macos-arm64 | 0.1.1 | 8.00 | 73.00 | 81.00 | OK | |
| r-release-macos-x86_64 | 0.1.1 | 24.00 | 385.00 | 409.00 | OK | |
| r-release-windows-x86_64 | 0.1.1 | 32.00 | 276.00 | 308.00 | OK | |
| r-oldrel-macos-arm64 | 0.1.1 | 7.00 | 80.00 | 87.00 | OK | |
| r-oldrel-macos-x86_64 | 0.1.1 | 23.00 | 413.00 | 436.00 | OK | |
| r-oldrel-windows-x86_64 | 0.1.1 | 46.00 | 374.00 | 420.00 | OK |
Version: 0.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [14s/24s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(dbSpatial)
>
> test_check("dbSpatial")
Saving _problems/test-extract-15.R
Saving _problems/test-spatial-functions-15.R
Saving _problems/test-spatial-functions-35.R
Saving _problems/test-spatial-functions-70.R
Saving _problems/test-spatial-functions-95.R
Saving _problems/test-spatial-functions-117.R
[ FAIL 6 | WARN 0 | SKIP 0 | PASS 0 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-extract.R:8:3'): $ extracts column values ──────────────────────
Error in `dbSendQuery(conn, statement, ...)`: Invalid Error: IO Error: Cannot open file "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension.tmp-72d0eb84-207d-4df8-bbc6-ecac01c33da7.duckdb_extension": Read-only file system
i Context: rapi_prepare
i Error type: INVALID
Backtrace:
▆
1. ├─dbSpatial::dbSpatial(...) at test-extract.R:8:3
2. │ ├─base::suppressMessages(loadSpatial(conn = conn))
3. │ │ └─base::withCallingHandlers(...)
4. │ └─dbSpatial::loadSpatial(conn = conn)
5. │ ├─DBI::dbExecute(conn, query)
6. │ └─DBI::dbExecute(conn, query)
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:::rethrow_rapi_prepare(conn@conn_ref, statement, env)
13. │ ├─rlang::try_fetch(...)
14. │ │ ├─base::tryCatch(...)
15. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
16. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
17. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
18. │ │ └─base::withCallingHandlers(...)
19. │ └─duckdb:::rapi_prepare(conn, query, env)
20. ├─duckdb (local) `<fn>`(...)
21. │ └─rlang::abort(error_parts, class = "duckdb_error", !!!fields)
22. │ └─rlang:::signal_abort(cnd, .file)
23. │ └─base::signalCondition(cnd)
24. └─rlang (local) `<fn>`(`<dckdb_rr>`)
25. └─handlers[[1L]](cnd)
26. └─duckdb:::rethrow_error_from_rapi(e, call)
27. └─rlang::abort(msg, call = call)
── Error ('test-spatial-functions.R:8:3'): dbSpatial constructor works ─────────
Error in `dbSendQuery(conn, statement, ...)`: Invalid Error: IO Error: Cannot open file "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension.tmp-f39baef1-1464-4355-8f8e-8c65323fb8b2.duckdb_extension": Read-only file system
i Context: rapi_prepare
i Error type: INVALID
Backtrace:
▆
1. ├─dbSpatial::dbSpatial(...) at test-spatial-functions.R:8:3
2. │ ├─base::suppressMessages(loadSpatial(conn = conn))
3. │ │ └─base::withCallingHandlers(...)
4. │ └─dbSpatial::loadSpatial(conn = conn)
5. │ ├─DBI::dbExecute(conn, query)
6. │ └─DBI::dbExecute(conn, query)
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:::rethrow_rapi_prepare(conn@conn_ref, statement, env)
13. │ ├─rlang::try_fetch(...)
14. │ │ ├─base::tryCatch(...)
15. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
16. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
17. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
18. │ │ └─base::withCallingHandlers(...)
19. │ └─duckdb:::rapi_prepare(conn, query, env)
20. ├─duckdb (local) `<fn>`(...)
21. │ └─rlang::abort(error_parts, class = "duckdb_error", !!!fields)
22. │ └─rlang:::signal_abort(cnd, .file)
23. │ └─base::signalCondition(cnd)
24. └─rlang (local) `<fn>`(`<dckdb_rr>`)
25. └─handlers[[1L]](cnd)
26. └─duckdb:::rethrow_error_from_rapi(e, call)
27. └─rlang::abort(msg, call = call)
── Error ('test-spatial-functions.R:28:3'): basic spatial functions work ───────
Error in `dbSendQuery(conn, statement, ...)`: Invalid Error: IO Error: Cannot open file "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension.tmp-506b45a5-9c09-400a-bba2-9da29b34e740.duckdb_extension": Read-only file system
i Context: rapi_prepare
i Error type: INVALID
Backtrace:
▆
1. ├─dbSpatial::dbSpatial(...) at test-spatial-functions.R:28:3
2. │ ├─base::suppressMessages(loadSpatial(conn = conn))
3. │ │ └─base::withCallingHandlers(...)
4. │ └─dbSpatial::loadSpatial(conn = conn)
5. │ ├─DBI::dbExecute(conn, query)
6. │ └─DBI::dbExecute(conn, query)
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:::rethrow_rapi_prepare(conn@conn_ref, statement, env)
13. │ ├─rlang::try_fetch(...)
14. │ │ ├─base::tryCatch(...)
15. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
16. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
17. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
18. │ │ └─base::withCallingHandlers(...)
19. │ └─duckdb:::rapi_prepare(conn, query, env)
20. ├─duckdb (local) `<fn>`(...)
21. │ └─rlang::abort(error_parts, class = "duckdb_error", !!!fields)
22. │ └─rlang:::signal_abort(cnd, .file)
23. │ └─base::signalCondition(cnd)
24. └─rlang (local) `<fn>`(`<dckdb_rr>`)
25. └─handlers[[1L]](cnd)
26. └─duckdb:::rethrow_error_from_rapi(e, call)
27. └─rlang::abort(msg, call = call)
── Error ('test-spatial-functions.R:63:3'): st_geometrytype returns expected types lazily ──
Error in `dbSendQuery(conn, statement, ...)`: Invalid Error: IO Error: Cannot open file "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension.tmp-63c18586-20e4-40b6-ae3e-58b18724bddf.duckdb_extension": Read-only file system
i Context: rapi_prepare
i Error type: INVALID
Backtrace:
▆
1. ├─dbSpatial::dbSpatial(...) at test-spatial-functions.R:63:3
2. │ ├─base::suppressMessages(loadSpatial(conn = conn))
3. │ │ └─base::withCallingHandlers(...)
4. │ └─dbSpatial::loadSpatial(conn = conn)
5. │ ├─DBI::dbExecute(conn, query)
6. │ └─DBI::dbExecute(conn, query)
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:::rethrow_rapi_prepare(conn@conn_ref, statement, env)
13. │ ├─rlang::try_fetch(...)
14. │ │ ├─base::tryCatch(...)
15. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
16. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
17. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
18. │ │ └─base::withCallingHandlers(...)
19. │ └─duckdb:::rapi_prepare(conn, query, env)
20. ├─duckdb (local) `<fn>`(...)
21. │ └─rlang::abort(error_parts, class = "duckdb_error", !!!fields)
22. │ └─rlang:::signal_abort(cnd, .file)
23. │ └─base::signalCondition(cnd)
24. └─rlang (local) `<fn>`(`<dckdb_rr>`)
25. └─handlers[[1L]](cnd)
26. └─duckdb:::rethrow_error_from_rapi(e, call)
27. └─rlang::abort(msg, call = call)
── Error ('test-spatial-functions.R:88:3'): st_join works with different predicates ──
Error in `dbSendQuery(conn, statement, ...)`: Invalid Error: IO Error: Cannot open file "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension.tmp-09d32b6e-432a-470e-9d8e-6e769207439f.duckdb_extension": Read-only file system
i Context: rapi_prepare
i Error type: INVALID
Backtrace:
▆
1. ├─dbSpatial::dbSpatial(...) at test-spatial-functions.R:88:3
2. │ ├─base::suppressMessages(loadSpatial(conn = conn))
3. │ │ └─base::withCallingHandlers(...)
4. │ └─dbSpatial::loadSpatial(conn = conn)
5. │ ├─DBI::dbExecute(conn, query)
6. │ └─DBI::dbExecute(conn, query)
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:::rethrow_rapi_prepare(conn@conn_ref, statement, env)
13. │ ├─rlang::try_fetch(...)
14. │ │ ├─base::tryCatch(...)
15. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
16. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
17. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
18. │ │ └─base::withCallingHandlers(...)
19. │ └─duckdb:::rapi_prepare(conn, query, env)
20. ├─duckdb (local) `<fn>`(...)
21. │ └─rlang::abort(error_parts, class = "duckdb_error", !!!fields)
22. │ └─rlang:::signal_abort(cnd, .file)
23. │ └─base::signalCondition(cnd)
24. └─rlang (local) `<fn>`(`<dckdb_rr>`)
25. └─handlers[[1L]](cnd)
26. └─duckdb:::rethrow_error_from_rapi(e, call)
27. └─rlang::abort(msg, call = call)
── Error ('test-spatial-functions.R:110:3'): unsupported args warn ─────────────
Error in `dbSendQuery(conn, statement, ...)`: Invalid Error: IO Error: Cannot open file "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension.tmp-d00dab7b-59f7-401f-afa9-eed09f2fff85.duckdb_extension": Read-only file system
i Context: rapi_prepare
i Error type: INVALID
Backtrace:
▆
1. ├─dbSpatial::dbSpatial(...) at test-spatial-functions.R:110:3
2. │ ├─base::suppressMessages(loadSpatial(conn = conn))
3. │ │ └─base::withCallingHandlers(...)
4. │ └─dbSpatial::loadSpatial(conn = conn)
5. │ ├─DBI::dbExecute(conn, query)
6. │ └─DBI::dbExecute(conn, query)
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:::rethrow_rapi_prepare(conn@conn_ref, statement, env)
13. │ ├─rlang::try_fetch(...)
14. │ │ ├─base::tryCatch(...)
15. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
16. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
17. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
18. │ │ └─base::withCallingHandlers(...)
19. │ └─duckdb:::rapi_prepare(conn, query, env)
20. ├─duckdb (local) `<fn>`(...)
21. │ └─rlang::abort(error_parts, class = "duckdb_error", !!!fields)
22. │ └─rlang:::signal_abort(cnd, .file)
23. │ └─base::signalCondition(cnd)
24. └─rlang (local) `<fn>`(`<dckdb_rr>`)
25. └─handlers[[1L]](cnd)
26. └─duckdb:::rethrow_error_from_rapi(e, call)
27. └─rlang::abort(msg, call = call)
[ FAIL 6 | WARN 0 | SKIP 0 | PASS 0 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.1.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘class_structure.Rmd’ using rmarkdown
Quitting from class_structure.Rmd:32-52 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `dbSendQuery()`:
! Invalid Error: IO Error: Cannot open file "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension.tmp-52b0cc04-69ec-467e-acdf-8c69d1ecce0a.duckdb_extension": Read-only file system
ℹ Context: rapi_prepare
ℹ Error type: INVALID
---
Backtrace:
▆
1. └─dbSpatial::dbSpatial(...)
2. ├─base::suppressMessages(loadSpatial(conn = conn))
3. │ └─base::withCallingHandlers(...)
4. └─dbSpatial::loadSpatial(conn = conn)
5. ├─DBI::dbExecute(conn, query)
6. └─DBI::dbExecute(conn, query)
7. ├─DBI::dbSendStatement(conn, statement, ...)
8. └─DBI::dbSendStatement(conn, statement, ...)
9. ├─DBI::dbSendQuery(conn, statement, ...)
10. └─duckdb::dbSendQuery(conn, statement, ...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'class_structure.Rmd' failed with diagnostics:
Invalid Error: IO Error: Cannot open file "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension.tmp-52b0cc04-69ec-467e-acdf-8c69d1ecce0a.duckdb_extension": Read-only file system
ℹ Context: rapi_prepare
ℹ Error type: INVALID
--- failed re-building ‘class_structure.Rmd’
--- re-building ‘getting_started.Rmd’ using rmarkdown
Quitting from getting_started.Rmd:40-53 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `dbSendQuery()`:
! Invalid Error: IO Error: Cannot open file "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension.tmp-41084edb-79cf-44d0-9441-f0414ab0c5ef.duckdb_extension": Read-only file system
ℹ Context: rapi_prepare
ℹ Error type: INVALID
---
Backtrace:
▆
1. └─dbSpatial::dbSpatial(...)
2. ├─base::suppressMessages(loadSpatial(conn = conn))
3. │ └─base::withCallingHandlers(...)
4. └─dbSpatial::loadSpatial(conn = conn)
5. ├─DBI::dbExecute(conn, query)
6. └─DBI::dbExecute(conn, query)
7. ├─DBI::dbSendStatement(conn, statement, ...)
8. └─DBI::dbSendStatement(conn, statement, ...)
9. ├─DBI::dbSendQuery(conn, statement, ...)
10. └─duckdb::dbSendQuery(conn, statement, ...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'getting_started.Rmd' failed with diagnostics:
Invalid Error: IO Error: Cannot open file "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension.tmp-41084edb-79cf-44d0-9441-f0414ab0c5ef.duckdb_extension": Read-only file system
ℹ Context: rapi_prepare
ℹ Error type: INVALID
--- failed re-building ‘getting_started.Rmd’
--- re-building ‘spatial_operations.Rmd’ using rmarkdown
Quitting from spatial_operations.Rmd:24-35 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `dbSendQuery()`:
! Invalid Error: IO Error: Cannot open file "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension.tmp-c78343fc-cc60-430c-8e77-9e3f1747b34b.duckdb_extension": Read-only file system
ℹ Context: rapi_prepare
ℹ Error type: INVALID
---
Backtrace:
▆
1. └─dbSpatial::dbSpatial(...)
2. ├─base::suppressMessages(loadSpatial(conn = conn))
3. │ └─base::withCallingHandlers(...)
4. └─dbSpatial::loadSpatial(conn = conn)
5. ├─DBI::dbExecute(conn, query)
6. └─DBI::dbExecute(conn, query)
7. ├─DBI::dbSendStatement(conn, statement, ...)
8. └─DBI::dbSendStatement(conn, statement, ...)
9. ├─DBI::dbSendQuery(conn, statement, ...)
10. └─duckdb::dbSendQuery(conn, statement, ...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'spatial_operations.Rmd' failed with diagnostics:
Invalid Error: IO Error: Cannot open file "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension.tmp-c78343fc-cc60-430c-8e77-9e3f1747b34b.duckdb_extension": Read-only file system
ℹ Context: rapi_prepare
ℹ Error type: INVALID
--- failed re-building ‘spatial_operations.Rmd’
SUMMARY: processing the following files failed:
‘class_structure.Rmd’ ‘getting_started.Rmd’ ‘spatial_operations.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [0m/13m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(dbSpatial)
>
> test_check("dbSpatial")
[gannet:1822683:0:1822683] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x449)
==== backtrace (tid:1822683) ====
0 /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7f3ea378cdf4]
1 /lib64/libucs.so.0(+0x17aed) [0x7f3ea378eaed]
2 /lib64/libucs.so.0(+0x17cbd) [0x7f3ea378ecbd]
3 /lib64/libc.so.6(+0x1a040) [0x7f3eb8629040]
4 /data/gannet/ripley/R/test-clang/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x1196990) [0x7f3d80b96990]
5 /data/gannet/ripley/R/test-clang/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x1168568) [0x7f3d80b68568]
6 /data/gannet/ripley/R/test-clang/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x773384) [0x7f3d80173384]
7 /data/gannet/ripley/R/test-clang/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x771719) [0x7f3d80171719]
8 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper29LoadExternalExtensionInternalERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEERNS_19ExtensionActiveLoadE+0x18f) [0x7f3dda07f85f]
9 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper21LoadExternalExtensionERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEE+0x4a) [0x7f3dda07f60a]
10 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZNK6duckdb12PhysicalLoad15GetDataInternalERNS_16ExecutionContextERNS_9DataChunkERNS_19OperatorSourceInputE+0x151) [0x7f3ddae6d401]
11 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor15FetchFromSourceERNS_9DataChunkE+0x98) [0x7f3ddb6a10c8]
12 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor7ExecuteEm+0x146) [0x7f3ddb69dca6]
13 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12PipelineTask11ExecuteTaskENS_17TaskExecutionModeE+0x112) [0x7f3ddb69d8d2]
14 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12ExecutorTask7ExecuteENS_17TaskExecutionModeE+0xa0) [0x7f3ddb697570]
15 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb8Executor11ExecuteTaskEb+0x1c0) [0x7f3ddb69c8d0]
16 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb13ClientContext19ExecuteTaskInternalERNS_17ClientContextLockERNS_15BaseQueryResultEb+0x40) [0x7f3ddb4a8c60]
17 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb18PendingQueryResult15ExecuteInternalERNS_17ClientContextLockE+0x7a) [0x7f3ddb4ab3ba]
18 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb13ClientContext7ExecuteERKNSt3__112basic_stringIcNS1_11char_traitsIcEENS1_9allocatorIcEEEERNS_10shared_ptrINS_21PreparedStatementDataELb1EEERKNS_22PendingQueryParametersE+0xa0) [0x7f3ddb4ab100]
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) [0x7f3ddb4ce3a3]
20 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb17PreparedStatement7ExecuteERNS_6vectorINS_5ValueELb1ENSt3__19allocatorIS2_EEEEb+0x172) [0x7f3ddb4ce642]
21 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(+0x1087fc) [0x7f3dd9d087fc]
22 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_duckdb_rapi_execute+0x63) [0x7f3dd9d72f73]
23 /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8f524) [0x55d06d1d1524]
24 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdae08) [0x55d06d21ce08]
25 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc918c) [0x55d06d20b18c]
26 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55d06d20a945]
27 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc93e4) [0x55d06d20b3e4]
28 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x26e) [0x55d06d20aa0e]
29 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc93e4) [0x55d06d20b3e4]
30 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdcf10) [0x55d06d21ef10]
31 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcd5c9) [0x55d06d20f5c9]
32 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc918c) [0x55d06d20b18c]
33 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55d06d20a945]
34 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0aa9) [0x55d06d222aa9]
35 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdff9b) [0x55d06d221f9b]
36 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9867) [0x55d06d20b867]
37 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f8) [0x55d06d20ad98]
38 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc93e4) [0x55d06d20b3e4]
39 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdcf10) [0x55d06d21ef10]
40 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcd5c9) [0x55d06d20f5c9]
41 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc918c) [0x55d06d20b18c]
42 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55d06d20a945]
43 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0aa9) [0x55d06d222aa9]
44 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdff9b) [0x55d06d221f9b]
45 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9867) [0x55d06d20b867]
46 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f8) [0x55d06d20ad98]
47 /data/gannet/ripley/R/test-clang/rlang/libs/rlang.so(+0x4983) [0x7f3eb6484983]
48 /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8d673) [0x55d06d1cf673]
49 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcfbc4) [0x55d06d211bc4]
50 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc918c) [0x55d06d20b18c]
51 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55d06d20a945]
52 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0aa9) [0x55d06d222aa9]
53 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdff9b) [0x55d06d221f9b]
54 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9867) [0x55d06d20b867]
55 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f8) [0x55d06d20ad98]
56 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe5e08) [0x55d06d227e08]
57 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x55d06d20ab70]
58 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe50fb) [0x55d06d2270fb]
59 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x55d06d20ab70]
60 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0aa9) [0x55d06d222aa9]
61 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdff9b) [0x55d06d221f9b]
=================================
*** caught segfault ***
address 0x4d2001bcfdb, 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$ref, duckdb_convert_opts_impl(res@connection@convert_opts, arrow = res@arrow))
9: duckdb_execute(res)
10: duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
11: .local(conn, statement, ...)
12: dbSendQuery(conn, statement, ...)
13: dbSendQuery(conn, statement, ...)
14: dbSendStatement(conn, statement, ...)
15: dbSendStatement(conn, statement, ...)
16: DBI::dbExecute(conn, query)
17: DBI::dbExecute(conn, query)
18: loadSpatial(conn = conn)
19: withCallingHandlers(expr, message = function(c) if (inherits(c, classes)) tryInvokeRestart("muffleMessage"))
20: suppressMessages(loadSpatial(conn = conn))
21: dbSpatial(conn = con, name = "test_pts", value = df, x_colName = "x", y_colName = "y", overwrite = TRUE)
22: eval(code, test_env)
23: eval(code, test_env)
24: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
25: doTryCatch(return(expr), name, parentenv, handler)
26: tryCatchOne(expr, names, parentenv, handlers[[1L]])
27: tryCatchList(expr, classes, parentenv, handlers)
28: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
29: doWithOneRestart(return(expr), restart)
30: withOneRestart(expr, restarts[[1L]])
31: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
32: test_code(code, parent.frame())
33: test_that("$ extracts column values", { skip_if_not_installed("duckdb") con <- DBI::dbConnect(duckdb::duckdb()) on.exit(DBI::dbDisconnect(con, shutdown = TRUE)) df <- data.frame(id = 1:3, x = c(0, 10, 20), y = c(0, 10, 20)) pts <- dbSpatial(conn = con, name = "test_pts", value = df, x_colName = "x", y_colName = "y", overwrite = TRUE) expect_identical(pts$id, 1:3)})
34: eval(code, test_env)
35: eval(code, test_env)
36: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
37: doTryCatch(return(expr), name, parentenv, handler)
38: tryCatchOne(expr, names, parentenv, handlers[[1L]])
39: tryCatchList(expr, classes, parentenv, handlers)
40: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
41: doWithOneRestart(return(expr), restart)
42: withOneRestart(expr, restarts[[1L]])
43: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
44: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
45: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
46: FUN(X[[i]], ...)
47: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
48: doTryCatch(return(expr), name, parentenv, handler)
49: tryCatchOne(expr, names, parentenv, handlers[[1L]])
50: tryCatchList(expr, classes, parentenv, handlers)
51: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
52: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
53: 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)
54: 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)
55: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
56: test_check("dbSpatial")
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.1.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘class_structure.Rmd’ using rmarkdown
Quitting from class_structure.Rmd:32-52 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `duckdb_result()`:
! Invalid Error: Invalid Input Error: Initialization function "spatial_duckdb_cpp_init" from file "/data/gannet/ripley/R/test-clang/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension" threw an exception: "Missing DB manager"
ℹ Context: rapi_execute
ℹ Error type: INVALID
---
Backtrace:
▆
1. └─dbSpatial::dbSpatial(...)
2. ├─base::suppressMessages(loadSpatial(conn = conn))
3. │ └─base::withCallingHandlers(...)
4. └─dbSpatial::loadSpatial(conn = conn)
5. ├─DBI::dbExecute(conn, query)
6. └─DBI::dbExecute(conn, query)
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)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'class_structure.Rmd' failed with diagnostics:
Invalid Error: Invalid Input Error: Initialization function "spatial_duckdb_cpp_init" from file "/data/gannet/ripley/R/test-clang/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension" threw an exception: "Missing DB manager"
ℹ Context: rapi_execute
ℹ Error type: INVALID
--- failed re-building ‘class_structure.Rmd’
--- re-building ‘getting_started.Rmd’ using rmarkdown
Quitting from getting_started.Rmd:40-53 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `duckdb_result()`:
! Invalid Error: Invalid Input Error: Initialization function "spatial_duckdb_cpp_init" from file "/data/gannet/ripley/R/test-clang/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension" threw an exception: "Missing DB manager"
ℹ Context: rapi_execute
ℹ Error type: INVALID
---
Backtrace:
▆
1. └─dbSpatial::dbSpatial(...)
2. ├─base::suppressMessages(loadSpatial(conn = conn))
3. │ └─base::withCallingHandlers(...)
4. └─dbSpatial::loadSpatial(conn = conn)
5. ├─DBI::dbExecute(conn, query)
6. └─DBI::dbExecute(conn, query)
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)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'getting_started.Rmd' failed with diagnostics:
Invalid Error: Invalid Input Error: Initialization function "spatial_duckdb_cpp_init" from file "/data/gannet/ripley/R/test-clang/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension" threw an exception: "Missing DB manager"
ℹ Context: rapi_execute
ℹ Error type: INVALID
--- failed re-building ‘getting_started.Rmd’
--- re-building ‘spatial_operations.Rmd’ using rmarkdown
[gannet:1906020:0:1906020] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x449)
==== backtrace (tid:1906020) ====
0 /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7f2b8879bdf4]
1 /lib64/libucs.so.0(+0x17aed) [0x7f2b8879daed]
2 /lib64/libucs.so.0(+0x17cbd) [0x7f2b8879dcbd]
3 /lib64/libc.so.6(+0x1a040) [0x7f2ba1928040]
4 /data/gannet/ripley/R/test-clang/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x1196990) [0x7f2ab8b96990]
5 /data/gannet/ripley/R/test-clang/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x1168568) [0x7f2ab8b68568]
6 /data/gannet/ripley/R/test-clang/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x773384) [0x7f2ab8173384]
7 /data/gannet/ripley/R/test-clang/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x771719) [0x7f2ab8171719]
8 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper29LoadExternalExtensionInternalERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEERNS_19ExtensionActiveLoadE+0x18f) [0x7f2b8ca7f85f]
9 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper21LoadExternalExtensionERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEE+0x4a) [0x7f2b8ca7f60a]
10 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZNK6duckdb12PhysicalLoad15GetDataInternalERNS_16ExecutionContextERNS_9DataChunkERNS_19OperatorSourceInputE+0x151) [0x7f2b8d86d401]
11 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor15FetchFromSourceERNS_9DataChunkE+0x98) [0x7f2b8e0a10c8]
12 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor7ExecuteEm+0x146) [0x7f2b8e09dca6]
13 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12PipelineTask11ExecuteTaskENS_17TaskExecutionModeE+0x112) [0x7f2b8e09d8d2]
14 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12ExecutorTask7ExecuteENS_17TaskExecutionModeE+0xa0) [0x7f2b8e097570]
15 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb8Executor11ExecuteTaskEb+0x1c0) [0x7f2b8e09c8d0]
16 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb13ClientContext19ExecuteTaskInternalERNS_17ClientContextLockERNS_15BaseQueryResultEb+0x40) [0x7f2b8dea8c60]
17 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb18PendingQueryResult15ExecuteInternalERNS_17ClientContextLockE+0x7a) [0x7f2b8deab3ba]
18 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb13ClientContext7ExecuteERKNSt3__112basic_stringIcNS1_11char_traitsIcEENS1_9allocatorIcEEEERNS_10shared_ptrINS_21PreparedStatementDataELb1EEERKNS_22PendingQueryParametersE+0xa0) [0x7f2b8deab100]
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) [0x7f2b8dece3a3]
20 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb17PreparedStatement7ExecuteERNS_6vectorINS_5ValueELb1ENSt3__19allocatorIS2_EEEEb+0x172) [0x7f2b8dece642]
21 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(+0x1087fc) [0x7f2b8c7087fc]
22 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_duckdb_rapi_execute+0x63) [0x7f2b8c772f73]
23 /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8f524) [0x55da4f202524]
24 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdae08) [0x55da4f24de08]
25 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc918c) [0x55da4f23c18c]
26 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55da4f23b945]
27 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc93e4) [0x55da4f23c3e4]
28 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x26e) [0x55da4f23ba0e]
29 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc93e4) [0x55da4f23c3e4]
30 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdcf10) [0x55da4f24ff10]
31 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcd5c9) [0x55da4f2405c9]
32 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc918c) [0x55da4f23c18c]
33 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55da4f23b945]
34 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0aa9) [0x55da4f253aa9]
35 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdff9b) [0x55da4f252f9b]
36 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9867) [0x55da4f23c867]
37 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f8) [0x55da4f23bd98]
38 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc93e4) [0x55da4f23c3e4]
39 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdcf10) [0x55da4f24ff10]
40 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcd5c9) [0x55da4f2405c9]
41 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc918c) [0x55da4f23c18c]
42 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55da4f23b945]
43 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0aa9) [0x55da4f253aa9]
44 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdff9b) [0x55da4f252f9b]
45 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9867) [0x55da4f23c867]
46 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f8) [0x55da4f23bd98]
47 /data/gannet/ripley/R/test-clang/rlang/libs/rlang.so(+0x4983) [0x7f2b9f300983]
48 /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8d673) [0x55da4f200673]
49 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcfbc4) [0x55da4f242bc4]
50 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc918c) [0x55da4f23c18c]
51 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55da4f23b945]
52 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0aa9) [0x55da4f253aa9]
53 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdff9b) [0x55da4f252f9b]
54 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9867) [0x55da4f23c867]
55 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f8) [0x55da4f23bd98]
56 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe5e08) [0x55da4f258e08]
57 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x55da4f23bb70]
58 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe50fb) [0x55da4f2580fb]
59 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x55da4f23bb70]
60 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0aa9) [0x55da4f253aa9]
61 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdff9b) [0x55da4f252f9b]
=================================
*** caught segfault ***
address 0x4d2001d1564, 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, query)
17: DBI::dbExecute(conn, query)
18: loadSpatial(conn = conn)
19: withCallingHandlers(expr, message = function(c) if (inherits(c, classes)) tryInvokeRestart("muffleMessage"))
20: suppressMessages(loadSpatial(conn = conn))
21: dbSpatial(conn = con, name = "pts", value = df, x_colName = "x", y_colName = "y", overwrite = TRUE)
22: eval(expr, envir)
23: eval(expr, envir)
24: withVisible(eval(expr, envir))
25: 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)})
26: eval(call)
27: eval(call)
28: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
29: doWithOneRestart(return(expr), restart)
30: withOneRestart(expr, restarts[[1L]])
31: withRestartList(expr, restarts[-nr])
32: doWithOneRestart(return(expr), restart)
33: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
34: withRestartList(expr, restarts)
35: withRestarts(with_handlers({ for (expr in tle$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)
36: evaluate::evaluate(...)
37: 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$render, options))
38: in_dir(input_dir(), expr)
39: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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)))
40: eng_r(options)
41: block_exec(params)
42: call_block(x)
43: process_group(group)
44: 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) })
45: 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()))
46: 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)
47: process_file(text, output)
48: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
49: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
50: vweave_rmarkdown(...)
51: engine$weave(file, quiet = quiet, encoding = enc)
52: doTryCatch(return(expr), name, parentenv, handler)
53: tryCatchOne(expr, names, parentenv, handlers[[1L]])
54: tryCatchList(expr, classes, parentenv, handlers)
55: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)), domain = NA)})
56: tools:::.buildOneVignette("spatial_operations.Rmd", "/data/gannet/ripley/R/packages/tests-clang/dbSpatial.Rcheck/vign_test/dbSpatial", TRUE, FALSE, "spatial_operations", "UTF-8", "/tmp/Rtmp5uetsS/working_dir/Rtmp3EQfwF/file1c6429e184f94.rds")
An irrecoverable exception occurred. R is aborting now ...
SUMMARY: processing the following files failed:
‘class_structure.Rmd’ ‘getting_started.Rmd’ ‘spatial_operations.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang