Last updated on 2026-11-09 06:54:16 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.3.0 | 14.98 | 217.18 | 232.16 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.3.0 | 9.45 | 146.42 | 155.87 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.3.0 | 10.00 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.3.0 | 10.00 | 141.75 | 151.75 | OK | |
| r-devel-windows-x86_64 | 1.3.0 | 18.00 | 215.00 | 233.00 | OK | |
| r-patched-linux-x86_64 | 1.3.0 | OK | ||||
| r-release-linux-x86_64 | 1.3.0 | 14.07 | 210.82 | 224.89 | OK | |
| r-release-macos-arm64 | 1.3.0 | 3.00 | 40.00 | 43.00 | OK | |
| r-release-macos-x86_64 | 1.3.0 | 10.00 | 181.00 | 191.00 | OK | |
| r-release-windows-x86_64 | 1.3.0 | 20.00 | 238.00 | 258.00 | OK | |
| r-oldrel-macos-arm64 | 1.3.0 | 5.00 | 65.00 | 70.00 | OK | |
| r-oldrel-macos-x86_64 | 1.3.0 | 9.00 | 264.00 | 273.00 | OK | |
| r-oldrel-windows-x86_64 | 1.3.0 | 26.00 | 265.00 | 291.00 | OK |
Version: 1.3.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [11s/12s]
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 1.3.0 attached
* Compatible with DuckDB >= v1.5.6
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
`/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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
`/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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 keeps downloaded extensions and secrets in a temporary directory:
ℹ /home/hornik/tmp/scratch/RtmpyTJI2T/duckdb
This is removed when the R session ends.
• Extensions are re-downloaded each session.
• Secrets are lost.
ℹ Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
ℹ Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
ℹ See ?duckdb_storage for details and alternatives.
Reading layer `rivers' from data source
`/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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-nanoarrow_methods-54.R
Saving _problems/test-nanoarrow_methods-54.R
Saving _problems/test-nanoarrow_methods-64.R
Saving _problems/test-nanoarrow_methods-64.R
duckdb keeps downloaded extensions and secrets in a temporary directory:
i /home/hornik/tmp/scratch/RtmpyTJI2T/duckdb
This is removed when the R session ends.
* Extensions are re-downloaded each session.
* Secrets are lost.
i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
i See ?duckdb_storage for details and alternatives.
v spatial extension loaded
Saving _problems/test-nanoarrow_methods-150.R
Saving _problems/test-nanoarrow_methods-150.R
Saving _problems/test-utils_format-35.R
Saving _problems/test-utils_format-79.R
[ FAIL 8 | WARN 0 | SKIP 58 | PASS 19 ]
══ Skipped tests (58) ══════════════════════════════════════════════════════════
• On CRAN (58): 'test-collect_options.R:2:1', 'test-compatibility.R:2:1',
'test-connection-management.R:2:1', 'test-crs-persistence.R:1:1',
'test-db_extension.R:5:1', 'test-db_read.R:2:1', 'test-db_register.R:3:1',
'test-db_write.R:3:1', 'test-ddbs_affine.R:7:1',
'test-ddbs_as_spatial.R:6:1', 'test-ddbs_collect.R:2:1',
'test-ddbs_coordinates.R:6:1', 'test-ddbs_crs.R:3:1',
'test-ddbs_dimensions.R:7:1', 'test-ddbs_dimensions_ops.R:7:1',
'test-ddbs_extent_funs.R:6:1', 'test-ddbs_filter.R:3:1',
'test-ddbs_generate_points.R:6:1', 'test-ddbs_geom_conversion.R:6:1',
'test-ddbs_geom_validation.R:6:1', 'test-ddbs_interpolate_aw.R:2:1',
'test-ddbs_intersection_agg.R:6:1', 'test-ddbs_join.R:3:1',
'test-ddbs_macros.R:6:1', 'test-ddbs_measure.R:6:1', 'test-ddbs_mvt.R:6:1',
'test-ddbs_open_dataset.R:7:1', 'test-ddbs_ops_binary.R:6:1',
'test-ddbs_ops_unary.R:6:1', 'test-ddbs_ops_unary_line.R:7:1',
'test-ddbs_options.R:2:1', 'test-ddbs_predicates.R:6:1',
'test-ddbs_quadkey.R:6:1', 'test-ddbs_queries.R:6:1',
'test-ddbs_transform.R:5:1', 'test-ddbs_union.R:6:1',
'test-ddbs_write_dataset-fid.R:2:1',
'test-ddbs_write_dataset-validation.R:3:1', 'test-ddbs_write_dataset.R:2:1',
'test-ddbs_write_vector_cross_connection.R:3:1',
'test-duckdbfs-interop.R:7:1', 'test-duckspatial_df.R:6:1',
'test-duckspatial_df_dplyr_methods.R:11:1',
'test-duckspatial_df_sf_methods.R:6:1', 'test-formats_autodetect.R:1:1',
'test-get_query_list.R:1:1', 'test-helper-temp-spatial-files.R:1:1',
'test-import-strategies.R:1:1', 'test-import_view_to_connection.R:1:1',
'test-mixed-inputs.R:2:1', 'test-nanoarrow_methods.R:78:5',
'test-normalize_spatial_input.R:2:1',
'test-regression-inefficient-fallback.R:2:1',
'test-resolve_connections.R:2:1', 'test-resources.R:1:1',
'test-tmp_conn.R:2:1', 'test-utils.R:2:1', 'test-utils_not_exported.R:6:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-nanoarrow_methods.R:54:5'): as_nanoarrow_array_stream.duckspatial_df() / produces native geometry layouts when native = TRUE ──
Error in `duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)`: This build of the arrow package does not support Datasets
Backtrace:
▆
1. ├─testthat::expect_equal(native_extension(points_ddbs), "geoarrow.point") at test-nanoarrow_methods.R:54:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─duckspatial (local) native_extension(points_ddbs)
5. │ ├─nanoarrow::as_nanoarrow_array_stream(x, native = TRUE) at test-nanoarrow_methods.R:42:5
6. │ └─duckspatial:::as_nanoarrow_array_stream.duckspatial_df(x, native = TRUE)
7. │ ├─DBI::dbSendQuery(conn, query_sql, arrow = TRUE)
8. │ └─DBI::dbSendQuery(conn, query_sql, arrow = TRUE)
9. │ └─duckdb (local) .local(conn, statement, ...)
10. │ └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
11. │ └─duckdb:::duckdb_execute(res)
12. │ └─duckdb:::rethrow_rapi_execute(...)
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_execute(stmt, convert_opts)
20. ├─duckdb (local) `<fn>`(`<Table[,2]>`, 94352304419096, `<chr>`, TRUE)
21. │ └─arrow::Scanner$create(arrow_scannable, projection, filter)
22. │ └─arrow:::stop_if_no_datasets()
23. │ └─base::stop(...)
24. └─base::.handleSimpleError(...)
25. └─rlang (local) h(simpleError(msg, call))
26. └─handlers[[1L]](cnd)
27. └─duckdb:::rethrow_error_from_rapi(e, call)
28. └─rlang::abort(msg, call = call)
── Error ('test-nanoarrow_methods.R:54:5'): as_nanoarrow_array_stream.duckspatial_df() / produces native geometry layouts when native = TRUE ──
<duckdb_error/rlang_error/error/condition>
Error in `duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)`: Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
Backtrace:
▆
1. ├─testthat::expect_equal(native_extension(points_ddbs), "geoarrow.point") at test-nanoarrow_methods.R:54:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─duckspatial (local) native_extension(points_ddbs)
5. │ ├─nanoarrow::as_nanoarrow_array_stream(x, native = TRUE) at test-nanoarrow_methods.R:42:5
6. │ └─duckspatial:::as_nanoarrow_array_stream.duckspatial_df(x, native = TRUE)
7. │ ├─DBI::dbSendQuery(conn, query_sql, arrow = TRUE)
8. │ └─DBI::dbSendQuery(conn, query_sql, arrow = TRUE)
9. │ └─duckdb (local) .local(conn, statement, ...)
10. │ └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
11. │ └─duckdb:::duckdb_execute(res)
12. │ └─duckdb:::rethrow_rapi_execute(...)
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_execute(stmt, convert_opts)
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, class = "duckdb_error", call = call, !!!fields)
── Error ('test-nanoarrow_methods.R:60:5'): as_nanoarrow_array_stream.duckspatial_df() / uses chunk_size for streamed record batches ──
Error in `duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)`: This build of the arrow package does not support Datasets
Backtrace:
▆
1. ├─nanoarrow::as_nanoarrow_array_stream(...) at test-nanoarrow_methods.R:60:5
2. ├─duckspatial:::as_nanoarrow_array_stream.duckspatial_df(...)
3. │ ├─DBI::dbSendQuery(conn, query_sql, arrow = TRUE)
4. │ └─DBI::dbSendQuery(conn, query_sql, arrow = TRUE)
5. │ └─duckdb (local) .local(conn, statement, ...)
6. │ └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
7. │ └─duckdb:::duckdb_execute(res)
8. │ └─duckdb:::rethrow_rapi_execute(...)
9. │ ├─rlang::try_fetch(...)
10. │ │ ├─base::tryCatch(...)
11. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
12. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
13. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
14. │ │ └─base::withCallingHandlers(...)
15. │ └─duckdb:::rapi_execute(stmt, convert_opts)
16. ├─duckdb (local) `<fn>`(`<Table[,2]>`, 94352243003736, `<chr>`, TRUE)
17. │ └─arrow::Scanner$create(arrow_scannable, projection, filter)
18. │ └─arrow:::stop_if_no_datasets()
19. │ └─base::stop(...)
20. └─base::.handleSimpleError(...)
21. └─rlang (local) h(simpleError(msg, call))
22. └─handlers[[1L]](cnd)
23. └─duckdb:::rethrow_error_from_rapi(e, call)
24. └─rlang::abort(msg, call = call)
── Error ('test-nanoarrow_methods.R:60:5'): as_nanoarrow_array_stream.duckspatial_df() / uses chunk_size for streamed record batches ──
<duckdb_error/rlang_error/error/condition>
Error in `duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)`: Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
Backtrace:
▆
1. ├─nanoarrow::as_nanoarrow_array_stream(...) at test-nanoarrow_methods.R:60:5
2. ├─duckspatial:::as_nanoarrow_array_stream.duckspatial_df(...)
3. │ ├─DBI::dbSendQuery(conn, query_sql, arrow = TRUE)
4. │ └─DBI::dbSendQuery(conn, query_sql, arrow = TRUE)
5. │ └─duckdb (local) .local(conn, statement, ...)
6. │ └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
7. │ └─duckdb:::duckdb_execute(res)
8. │ └─duckdb:::rethrow_rapi_execute(...)
9. │ ├─rlang::try_fetch(...)
10. │ │ ├─base::tryCatch(...)
11. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
12. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
13. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
14. │ │ └─base::withCallingHandlers(...)
15. │ └─duckdb:::rapi_execute(stmt, convert_opts)
16. ├─duckdb (local) `<fn>`(...)
17. │ └─rlang::abort(error_parts, class = "duckdb_error", !!!fields)
18. │ └─rlang:::signal_abort(cnd, .file)
19. │ └─base::signalCondition(cnd)
20. └─rlang (local) `<fn>`(`<dckdb_rr>`)
21. └─handlers[[1L]](cnd)
22. └─duckdb:::rethrow_error_from_rapi(e, call)
23. └─rlang::abort(msg, class = "duckdb_error", call = call, !!!fields)
── Error ('test-nanoarrow_methods.R:150:5'): as_nanoarrow_array_stream.duckspatial_df() / works with geometry_schema (Native layout) ──
Error in `duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)`: This build of the arrow package does not support Datasets
Backtrace:
▆
1. ├─nanoarrow::as_nanoarrow_array_stream(points_ddbs, geometry_schema = target_schema) at test-nanoarrow_methods.R:150:5
2. ├─duckspatial:::as_nanoarrow_array_stream.duckspatial_df(...)
3. │ ├─DBI::dbSendQuery(conn, query_sql, arrow = TRUE)
4. │ └─DBI::dbSendQuery(conn, query_sql, arrow = TRUE)
5. │ └─duckdb (local) .local(conn, statement, ...)
6. │ └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
7. │ └─duckdb:::duckdb_execute(res)
8. │ └─duckdb:::rethrow_rapi_execute(...)
9. │ ├─rlang::try_fetch(...)
10. │ │ ├─base::tryCatch(...)
11. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
12. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
13. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
14. │ │ └─base::withCallingHandlers(...)
15. │ └─duckdb:::rapi_execute(stmt, convert_opts)
16. ├─duckdb (local) `<fn>`(`<Table[,2]>`, 94352384284616, `<chr>`, TRUE)
17. │ └─arrow::Scanner$create(arrow_scannable, projection, filter)
18. │ └─arrow:::stop_if_no_datasets()
19. │ └─base::stop(...)
20. └─base::.handleSimpleError(...)
21. └─rlang (local) h(simpleError(msg, call))
22. └─handlers[[1L]](cnd)
23. └─duckdb:::rethrow_error_from_rapi(e, call)
24. └─rlang::abort(msg, call = call)
── Error ('test-nanoarrow_methods.R:150:5'): as_nanoarrow_array_stream.duckspatial_df() / works with geometry_schema (Native layout) ──
<duckdb_error/rlang_error/error/condition>
Error in `duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)`: Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
Backtrace:
▆
1. ├─nanoarrow::as_nanoarrow_array_stream(points_ddbs, geometry_schema = target_schema) at test-nanoarrow_methods.R:150:5
2. ├─duckspatial:::as_nanoarrow_array_stream.duckspatial_df(...)
3. │ ├─DBI::dbSendQuery(conn, query_sql, arrow = TRUE)
4. │ └─DBI::dbSendQuery(conn, query_sql, arrow = TRUE)
5. │ └─duckdb (local) .local(conn, statement, ...)
6. │ └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
7. │ └─duckdb:::duckdb_execute(res)
8. │ └─duckdb:::rethrow_rapi_execute(...)
9. │ ├─rlang::try_fetch(...)
10. │ │ ├─base::tryCatch(...)
11. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
12. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
13. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
14. │ │ └─base::withCallingHandlers(...)
15. │ └─duckdb:::rapi_execute(stmt, convert_opts)
16. ├─duckdb (local) `<fn>`(...)
17. │ └─rlang::abort(error_parts, class = "duckdb_error", !!!fields)
18. │ └─rlang:::signal_abort(cnd, .file)
19. │ └─base::signalCondition(cnd)
20. └─rlang (local) `<fn>`(`<dckdb_rr>`)
21. └─handlers[[1L]](cnd)
22. └─duckdb:::rethrow_error_from_rapi(e, call)
23. └─rlang::abort(msg, class = "duckdb_error", call = call, !!!fields)
── Error ('test-utils_format.R:35:3'): get_parquet_crs handles column names with dots and special characters ──
Error in `parquet___WriterProperties___Builder__create()`: Cannot call parquet___WriterProperties___Builder__create(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. └─arrow::write_parquet(tbl, tmp_pq) at test-utils_format.R:35:3
2. ├─ParquetFileWriter$create(...)
3. │ └─arrow:::parquet___arrow___ParquetFileWriter__Open(...)
4. └─ParquetWriterProperties$create(...)
5. └─arrow:::parquet___WriterProperties___Builder__create()
── Error ('test-utils_format.R:79:3'): get_parquet_crs handles column names with spaces ──
Error in `parquet___WriterProperties___Builder__create()`: Cannot call parquet___WriterProperties___Builder__create(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. └─arrow::write_parquet(tbl, tmp_pq) at test-utils_format.R:79:3
2. ├─ParquetFileWriter$create(...)
3. │ └─arrow:::parquet___arrow___ParquetFileWriter__Open(...)
4. └─ParquetWriterProperties$create(...)
5. └─arrow:::parquet___WriterProperties___Builder__create()
[ FAIL 8 | WARN 0 | SKIP 58 | PASS 19 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.3.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘aw_interpolation.qmd’ using html
<1b>[31m
processing file: aw_interpolation.qmd
<1b>[39m<1b>[31mError in `duckdb_result()`:
! This build of the arrow package does not support Datasets
Backtrace:
▆
1. ├─duckspatial::ddbs_interpolate_aw(...)
2. │ └─duckspatial:::ddbs_handle_query(...)
3. │ ├─DBI::dbGetQuery(conn, query)
4. │ └─DBI::dbGetQuery(conn, query)
5. │ └─DBI (local) .local(conn, statement, ...)
6. │ ├─DBI::dbSendQuery(conn, statement, ...)
7. │ └─duckdb::dbSendQuery(conn, statement, ...)
8. │ └─duckdb (local) .local(conn, statement, ...)
9. │ └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
10. │ └─duckdb:::duckdb_execute(res)
11. │ └─duckdb:::rethrow_rapi_execute(...)
12. │ ├─rlang::try_fetch(...)
13. │ │ ├─base::tryCatch(...)
14. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
15. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
16. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
17. │ │ └─base::withCallingHandlers(...)
18. │ └─duckdb:::rapi_execute(stmt, convert_opts)
19. ├─duckdb (local) `<fn>`(`<Table[,2]>`, 94429981706696, `<chr>`, TRUE)
20. │ └─arrow::Scanner$create(arrow_scannable, projection, filter)
21. │ └─arrow:::stop_if_no_datasets()
22. │ └─base::stop(...)
23. └─base::.handleSimpleError(...)
24. └─rlang (local) h(simpleError(msg, call))
25. └─handlers[[1L]](cnd)
26. └─duckdb:::rethrow_error_from_rapi(e, call)
27. └─rlang::abort(msg, call = call)
<1b>[39m<1b>[31mError in `duckdb_result()`:
! Invalid Error: std::exception
ℹ Context: rapi_execute
ℹ Error type: INVALID
Backtrace:
▆
1. ├─duckspatial::ddbs_interpolate_aw(...)
2. │ └─duckspatial:::ddbs_handle_query(...)
3. │ ├─DBI::dbGetQuery(conn, query)
4. │ └─DBI::dbGetQuery(conn, query)
5. │ └─DBI (local) .local(conn, statement, ...)
6. │ ├─DBI::dbSendQuery(conn, statement, ...)
7. │ └─duckdb::dbSendQuery(conn, statement, ...)
8. │ └─duckdb (local) .local(conn, statement, ...)
9. │ └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
10. │ └─duckdb:::duckdb_execute(res)
11. │ └─duckdb:::rethrow_rapi_execute(...)
12. │ ├─rlang::try_fetch(...)
13. │ │ ├─base::tryCatch(...)
14. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
15. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
16. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
17. │ │ └─base::withCallingHandlers(...)
18. │ └─duckdb:::rapi_execute(stmt, convert_opts)
19. ├─duckdb (local) `<fn>`(...)
20. │ └─rlang::abort(error_parts, class = "duckdb_error", !!!fields)
21. │ └─rlang:::signal_abort(cnd, .file)
22. │ └─base::signalCondition(cnd)
23. └─rlang (local) `<fn>`(`<dckdb_rr>`)
24. └─handlers[[1L]](cnd)
25. └─duckdb:::rethrow_error_from_rapi(e, call)
26. └─rlang::abort(msg, class = "duckdb_error", call = call, !!!fields)
<1b>[39m<1b>[31m
Quitting from aw_interpolation.qmd:78-89 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<1b>[39m<1b>[31m~~~~~~~~~~~~~~~~~~
<error/duckdb_error>
Error in `duckdb_result()`:
! Invalid Error: std::exception
ℹ Context: rapi_execute
�<1b>[39m<1b>[31m� Error type: INVALID
---
Backtrace:
▆
1. └─duckspatial::ddbs_interpolate_aw(...)
2. └─duckspatial:::ddbs_handle_query(...)
3. ├─DBI::dbGetQuery(conn, query)
4. └─DBI::dbGetQuery(conn, query)
5. └─DBI (local) .local(conn, statement, ...)
6. ├─DBI::dbSendQuery(conn, statement, ...)
7. └─duckdb::dbSendQuery(conn, statement, ...)
8. └─duckdb (local) .local(conn, statement, ...)
9. └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<1b>[39m<1b>[31mExecution halted
<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 in `quarto_render()`:
✖ Error returned by quarto CLI.
-----------------------------
processing file: aw_interpolation.qmd
<1b>[31mError in `duckdb_result()`:<1b>[39m
! This build of the arrow package does not support Datasets
Backtrace:
▆
1. ├─duckspatial::ddbs_interpolate_aw(...)
2. │ └─duckspatial:::ddbs_handle_query(...)
3. │ ├─DBI::dbGetQuery(conn, query)
4. │ └─DBI::dbGetQuery(conn, query)
5. │ └─DBI (local) .local(conn, statement, ...)
6. │ ├─DBI::dbSendQuery(conn, statement, ...)
7. │ └─duckdb::dbSendQuery(conn, statement, ...)
8. │ └─duckdb (local) .local(conn, statement, ...)
9. │ └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow =
arrow)
10. │ └─duckdb:::duckdb_execute(res)
11. │ └─duckdb:::rethrow_rapi_execute(...)
12. │ ├─rlang::try_fetch(...)
13. │ │ ├─base::tryCatch(...)
14. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
15. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
16. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
17. │ │ └─base::withCallingHandlers(...)
18. │ └─duckdb:::rapi_execute(stmt, convert_opts)
19. ├─duckdb (local) `<fn>`(`<Table[,2]>`, 94429981706696, `<chr>`, TRUE)
20. │ └─arrow::Scanner$create(arrow_scannable, projection, filter)
21. │ └─arrow:::stop_if_no_datasets()
22. │ └─base::stop(...)
23. └─base::.handleSimpleError(...)
24. └─rlang (local) h(simpleError(msg, call))
25. └─handlers[[1L]](cnd)
26. └─duckdb:::rethrow_error_from_rapi(e, call)
27. └─rlang::abort(msg, call = call)
<1b>[31mError in `duckdb_result()`:<1b>[39m
! Invalid Error: std::exception
ℹ Context: rapi_execute
ℹ Error type: INVALID
Backtrace:
▆
1. ├─duckspatial::ddbs_interpolate_aw(...)
2. │ └─duckspatial:::ddbs_handle_query(...)
3. │ ├─DBI::dbGetQuery(conn, query)
4. │ └─DBI::dbGetQuery(conn, query)
5. │ └─DBI (local) .local(conn, statement, ...)
6. │ ├─DBI::dbSendQuery(conn, statement, ...)
7. │ └─duckdb::dbSendQuery(conn, statement, ...)
8. │ └─duckdb (local) .local(conn, statement, ...)
9. │ └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow =
arrow)
10. │ └─duckdb:::duckdb_execute(res)
11. │ └─duckdb:::rethrow_rapi_execute(...)
12. │ ├─rlang::try_fetch(...)
13. │ │ ├─base::tryCatch(...)
14. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
15. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
16. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
17. │ │ └─base::withCallingHandlers(...)
18. │ └─duckdb:::rapi_execute(stmt, convert_opts)
19. ├─duckdb (local) `<fn>`(...)
20. │ └─rlang::abort(error_parts, class = "duckdb_error", !!!fields)
21. │ └─rlang:::signal_abort(cnd, .file)
22. │ └─base::signalCondition(cnd)
23. └─rlang (local) `<fn>`(`<dckdb_rr>`)
24. └─handlers[[1L]](cnd)
25. └─duckdb:::rethrow_error_from_rapi(e, call)
26. └─rlang::abort(msg, class = "duckdb_error", call = call, !!!fields)
Quitting from aw_interpolation.qmd:78-89 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<1b>[31m~~~~~~~~~~~~~~~~~~<1b>[39m
<error/duckdb_error>
Error in `duckdb_result()`:
! Invalid Error: std::exception
ℹ Context: rapi_execute
�<1b>[31m� Error type: INVALID<1b>[39m
---
Backtrace:
▆
1. └─duckspatial::ddbs_interpolate_aw(...)
2. └─duckspatial:::ddbs_handle_query(...)
3. ├─DBI::dbGetQuery(conn, query)
4. └─DBI::dbGetQuery(conn, query)
5. └─DBI (local) .local(conn, statement, ...)
6. ├─DBI::dbSendQuery(conn, statement, ...)
7. └─duckdb::dbSendQuery(conn, statement, ...)
8. └─duckdb (local) .local(conn, statement, ...)
9. └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow =
arrow)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<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 ‘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:
- >-
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/quarto/rmarkdown/template/quarto_vignette/resources/vignette.css
<1b>[1mmetadata<1b>[22m
document-css: false
lang: en
minimal: true
theme: none
title: Benchmark
date: '`r Sys.Date()`'
code-annotations: hover
urlcolor: blue
vignette: |
%\VignetteIndexEntry{Benchmark} %\VignetteEncoding{UTF-8} %\VignetteEngine{quarto::html}
knitr:
opts_chunk:
collapse: true
comment: '#>'
out.width: 100%
editor_options:
chunk_output_type: console
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 `duckdb_result()`:
! This build of the arrow package does not support Datasets
Backtrace:
▆
1. ├─dplyr::fi<1b>[39m<1b>[31mlter(ddbs_is_valid(countries_ddbs), !is_valid)
2. ├─duckspatial::ddbs_is_valid(countries_ddbs)
3. │ └─duckspatial:::template_new_column(...)
4. │ └─duckspatial:::ddbs_handle_query(...)
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)
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>`(`<Table[,7]>`, 94645148304696, `<chr>`, TRUE)
23. │ └─arrow::Scanner$create(arrow_scannable, projection, filter)
24. │ └─arrow:::stop_if_no_datasets()
25. │ └─base::stop(...)
26. └─base::.handleSimpleError(...)
27. └─rlang (local) h(simpleError(msg, call))
28. └─handlers[[1L]](cnd)
29. └─duckdb:::rethrow_error_from_rapi(e, call)
30. └─rlang::abort(msg, call = call)
<1b>[39m<1b>[31mError in `duckdb_result()`:
! Invalid Error: std::exception
ℹ Context: rapi_execute
ℹ Error type: INVALID
Backtrace:
�<1b>[39m<1b>[31m�
1. ├─dplyr::filter(ddbs_is_valid(countries_ddbs), !is_valid)
2. ├─duckspatial::ddbs_is_valid(countries_ddbs)
3. <1b>[39m<1b>[31m│ └─duckspatial:::template_new_column(...)
4. │ └─duckspatial:::ddbs_handle_query(...)
5. │ ├─DBI::d<1b>[39m<1b>[31mbExecute(conn, query)
6. │ └─DBI::dbExecute(conn, query)
7. │ ├─DBI::dbSendStatement(conn, statement, <1b>[39m<1b>[31m...)
8. │ └─DBI::dbSendStatement(conn, statement, ...)
9. │ ├─DBI::dbSendQuery(conn, statement, ..<1b>[39m<1b>[31m.)
10. │ └─duckdb::dbSendQuery(conn, statement, ...)
11. │ └─duckdb (local) .local(conn, stateme<1b>[39m<1b>[31mnt, ...)
12. │ └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
13. │ <1b>[39m<1b>[31m └─duckdb:::duckdb_execute(res)
14. │ └─duckdb:::rethrow_rapi_execute(...)
15. │ <1b>[39m<1b>[31m ├─rlang::try_fetch(...)
16. │ │ ├─base::tryCatch(...)
17. │ │ │<1b>[39m<1b>[31m └─base (local) tryCatchList(expr, classes, parentenv, handlers)
18. │ │ │ └─base (local) try<1b>[39m<1b>[31mCatchOne(expr, names, parentenv, handlers[[1L]])
19. │ │ │ └─base (local) doTryCatch(return(exp<1b>[39m<1b>[31mr), name, parentenv, handler)
20. │ │ └─base::withCallingHandlers(...)
21. │ └<1b>[39m<1b>[31m─duckdb:::rapi_execute(stmt, convert_opts)
22. ├─duckdb (local) `<fn>`(...)
23. │ └─rlang::abort(error_parts, clas<1b>[39m<1b>[31ms = "duckdb_error", !!!fields)
24. │ └─rlang:::signal_abort(cnd, .file)
25. │ └─base::signalCondition(cnd)
<1b>[39m<1b>[31m26. └─rlang (local) `<fn>`(`<dckdb_rr>`)
27. └─handlers[[1L]](cnd)
28. └─duckdb:::rethrow_error_from_rapi(e,<1b>[39m<1b>[31m call)
29. └─rlang::abort(msg, class = "duckdb_error", call = call, !!!fields)
<1b>[39m<1b>[31m
Quitting from duckspatial.qmd:128-132 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<1b>[39m<1b>[31m~~~~~~~~~~~~~~~
<error/duckdb_error>
Error in `duckdb_result()`:
! Invalid Error: std::exception
ℹ Context: rapi_execute
ℹ Error type: INVALID
---
Backtrace:
▆
1. ├─dplyr::filter(ddbs_is_valid(countries_ddbs), !is_valid)
2. └─duckspatial::ddbs_is_valid(countries_ddbs)
3. └─duckspatial:::template_new_column(...)
4. └─duckspatial:::ddbs_handle_query(...)
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)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<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 `duckdb_result()`:<1b>[39m
! This build of the arrow package does not support Datasets
Backtrace:
▆
1. ├─dplyr::fi<1b>[31mlter(ddbs_is_valid(countries_ddbs), !is_valid)<1b>[39m
2. ├─duckspatial::ddbs_is_valid(countries_ddbs)
3. │ └─duckspatial:::template_new_column(...)
4. │ └─duckspatial:::ddbs_handle_query(...)
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)
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>`(`<Table[,7]>`, 94645148304696, `<chr>`, TRUE)
23. │ └─arrow::Scanner$create(arrow_scannable, projection, filter)
24. │ └─arrow:::stop_if_no_datasets()
25. │ └─base::stop(...)
26. └─base::.handleSimpleError(...)
27. └─rlang (local) h(simpleError(msg, call))
28. └─handlers[[1L]](cnd)
29. └─duckdb:::rethrow_error_from_rapi(e, call)
30. └─rlang::abort(msg, call = call)
<1b>[31mError in `duckdb_result()`:<1b>[39m
! Invalid Error: std::exception
ℹ Context: rapi_execute
ℹ Error type: INVALID
Backtrace:
�<1b>[31m�<1b>[39m
1. ├─dplyr::filter(ddbs_is_valid(countries_ddbs), !is_valid)
2. ├─duckspatial::ddbs_is_valid(countries_ddbs)
3. <1b>[31m│ └─duckspatial:::template_new_column(...)<1b>[39m
4. │ └─duckspatial:::ddbs_handle_query(...)
5. │ ├─DBI::d<1b>[31mbExecute(conn, query)<1b>[39m
6. │ └─DBI::dbExecute(conn, query)
7. │ ├─DBI::dbSendStatement(conn, statement, <1b>[31m...)<1b>[39m
8. │ └─DBI::dbSendStatement(conn, statement, ...)
9. │ ├─DBI::dbSendQuery(conn, statement, ..<1b>[31m.)<1b>[39m
10. │ └─duckdb::dbSendQuery(conn, statement, ...)
11. │ └─duckdb (local) .local(conn, stateme<1b>[31mnt, ...)<1b>[39m
12. │ └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow
= arrow)
13. │ <1b>[31m └─duckdb:::duckdb_execute(res)<1b>[39m
14. │ └─duckdb:::rethrow_rapi_execute(...)
15. │ <1b>[31m ├─rlang::try_fetch(...)<1b>[39m
16. │ │ ├─base::tryCatch(...)
17. │ │ │<1b>[31m └─base (local) tryCatchList(expr, classes, parentenv, handlers)<1b>[39m
18. │ │ │ └─base (local) try<1b>[31mCatchOne(expr, names, parentenv, handlers[[1L]])<1b>[39m
19. │ │ │ └─base (local) doTryCatch(return(exp<1b>[31mr), name, parentenv, handler)<1b>[39m
20. │ │ └─base::withCallingHandlers(...)
21. │ └<1b>[31m─duckdb:::rapi_execute(stmt, convert_opts)<1b>[39m
22. ├─duckdb (local) `<fn>`(...)
23. │ └─rlang::abort(error_parts, clas<1b>[31ms = "duckdb_error", !!!fields)<1b>[39m
24. │ └─rlang:::signal_abort(cnd, .file)
25. │ └─base::signalCondition(cnd)
<1b>[31m26. └─rlang (local) `<fn>`(`<dckdb_rr>`)<1b>[39m
27. └─handlers[[1L]](cnd)
28. └─duckdb:::rethrow_error_from_rapi(e,<1b>[31m call)<1b>[39m
29. └─rlang::abort(msg, class = "duckdb_error", call = call, !!!fields)
Quitting from duckspatial.qmd:128-132 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<1b>[31m~~~~~~~~~~~~~~~<1b>[39m
<error/duckdb_error>
Error in `duckdb_result()`:
! Invalid Error: std::exception
ℹ Context: rapi_execute
ℹ Error type: INVALID
---
Backtrace:
▆
1. ├─dplyr::filter(ddbs_is_valid(countries_ddbs), !is_valid)
2. └─duckspatial::ddbs_is_valid(countries_ddbs)
3. └─duckspatial:::template_new_column(...)
4. └─duckspatial:::ddbs_handle_query(...)
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)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<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>[31mError in `duckdb_result()`:
! This build of the arrow package does not support Datasets
Backtrace:
▆
1. ├─duckspati<1b>[39m<1b>[31mal::ddbs_join(x = points_sf, y = countries_sf, join = "within")
2. │ └─duckspatial:::ddbs_handle_query(...)
3. │ ├─DBI::dbExecute(conn, query)
4. │ └─DBI::dbExecute(conn, query)
5. │ ├─DBI::dbSendStatement(conn, statement, ...)
6. │ └─DBI::dbSendStatement(conn, statement, ...)
7. │ ├─DBI::dbSendQuery(conn, statement, ...)
8. │ └─duckdb::dbSendQuery(conn, statement, ...)
9. │ └─duckdb (local) .local(conn, statement, ...)
10. │ └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
11. │ └─duckdb:::duckdb_execute(res)
12. │ └─duckdb:::rethrow_rapi_execute(...)
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_execute(stmt, convert_opts)
20. ├─duckdb (local) `<fn>`(`<Table[,7]>`, 94559659870120, `<chr>`, TRUE)
21. │ └─arrow::Scanner$create(arrow_scannable, projection, filter)
22. │ └─arrow:::stop_if_no_datasets()
23. │ └─base::stop(...)
24. └─base::.handleSimpleError(...)
25. └─rlang (local) h(simpleError(msg, call))
26. └─handlers[[1L]](cnd)
27. └─duckdb:::rethrow_error_from_rapi(e, call)
28. └─rlang::abort(msg, call = call)
<1b>[39m<1b>[31mError in `duckdb_result()`:
! Invalid Error: std::exception
ℹ Context: rapi_execute
ℹ Error type: INVALID
Backtrace:
�<1b>[39m<1b>[31m�
1. ├─duckspatial::ddbs_join(x = points_sf, y = countries_sf, join = "within")
2. │ └─duckspatial:::ddbs_handle_q<1b>[39m<1b>[31muery(...)
3. │ ├─DBI::dbExecute(conn, query)
4. │ └─DBI::dbExecute(conn, query)
5. │ ├─DBI::dbSendStatement(conn, statement, ...)
6. │ └─DBI::dbSendStatement(conn, statement, ...)
7. │ ├─DBI::dbSendQuery(conn, statement, ...)
8. │ └─duckdb::dbSendQuery(conn, statement, ...)
9. │ └─duckdb (local) .local(conn, statement, ...)
10. │ └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
11. │ └─duckdb:::duckdb_execute(res)
12. │ └─duckdb:::rethrow_rapi_execute(...)
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_execute(stmt, convert_opts)
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, class = "duckdb_error", call = call, !!!fields)
<1b>[39m<1b>[31m
Quitting from spatial_joins.qmd:77-87 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/duckdb_error>
Error in `duckdb_result()`:
! Invalid Error: std::exception
ℹ Context: rapi_execute
ℹ Error type: INVALID
---
Backtrace:
▆
1. └─duckspatial::ddbs_join(x = points_sf, y = countries_sf, join = "within")
2. └─duckspatial:::ddbs_handle_query(...)
3. ├─DBI::dbExecute(conn, query)
4. └─DBI::dbExecute(conn, query)
5. ├─DBI::dbSendStatement(conn, statement, ...)
6. └─DBI::dbSendStatement(conn, statement, ...)
7. ├─DBI::dbSendQuery(conn, statement, ...)
8. └─duckdb::dbSendQuery(conn, statement, ...)
9. └─duckdb (local) .local(conn, statement, ...)
10. └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<1b>[39m<1b>[31mExecution halted
<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 in `quarto_render()`:
✖ Error returned by quarto CLI.
-----------------------------
processing file: spatial_joins.qmd
<1b>[31mError in `duckdb_result()`:<1b>[39m
! This build of the arrow package does not support Datasets
Backtrace:
▆
1. ├─duckspati<1b>[31mal::ddbs_join(x = points_sf, y = countries_sf, join = "within")<1b>[39m
2. │ └─duckspatial:::ddbs_handle_query(...)
3. │ ├─DBI::dbExecute(conn, query)
4. │ └─DBI::dbExecute(conn, query)
5. │ ├─DBI::dbSendStatement(conn, statement, ...)
6. │ └─DBI::dbSendStatement(conn, statement, ...)
7. │ ├─DBI::dbSendQuery(conn, statement, ...)
8. │ └─duckdb::dbSendQuery(conn, statement, ...)
9. │ └─duckdb (local) .local(conn, statement, ...)
10. │ └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow
= arrow)
11. │ └─duckdb:::duckdb_execute(res)
12. │ └─duckdb:::rethrow_rapi_execute(...)
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_execute(stmt, convert_opts)
20. ├─duckdb (local) `<fn>`(`<Table[,7]>`, 94559659870120, `<chr>`, TRUE)
21. │ └─arrow::Scanner$create(arrow_scannable, projection, filter)
22. │ └─arrow:::stop_if_no_datasets()
23. │ └─base::stop(...)
24. └─base::.handleSimpleError(...)
25. └─rlang (local) h(simpleError(msg, call))
26. └─handlers[[1L]](cnd)
27. └─duckdb:::rethrow_error_from_rapi(e, call)
28. └─rlang::abort(msg, call = call)
<1b>[31mError in `duckdb_result()`:<1b>[39m
! Invalid Error: std::exception
ℹ Context: rapi_execute
ℹ Error type: INVALID
Backtrace:
�<1b>[31m�<1b>[39m
1. ├─duckspatial::ddbs_join(x = points_sf, y = countries_sf, join = "within")
2. │ └─duckspatial:::ddbs_handle_q<1b>[31muery(...)<1b>[39m
3. │ ├─DBI::dbExecute(conn, query)
4. │ └─DBI::dbExecute(conn, query)
5. │ ├─DBI::dbSendStatement(conn, statement, ...)
6. │ └─DBI::dbSendStatement(conn, statement, ...)
7. │ ├─DBI::dbSendQuery(conn, statement, ...)
8. │ └─duckdb::dbSendQuery(conn, statement, ...)
9. │ └─duckdb (local) .local(conn, statement, ...)
10. │ └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow
= arrow)
11. │ └─duckdb:::duckdb_execute(res)
12. │ └─duckdb:::rethrow_rapi_execute(...)
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_execute(stmt, convert_opts)
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, class = "duckdb_error", call = call, !!!fields)
Quitting from spatial_joins.qmd:77-87 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/duckdb_error>
Error in `duckdb_result()`:
! Invalid Error: std::exception
ℹ Context: rapi_execute
ℹ Error type: INVALID
---
Backtrace:
▆
1. └─duckspatial::ddbs_join(x = points_sf, y = countries_sf, join = "within")
2. └─duckspatial:::ddbs_handle_query(...)
3. ├─DBI::dbExecute(conn, query)
4. └─DBI::dbExecute(conn, query)
5. ├─DBI::dbSendStatement(conn, statement, ...)
6. └─DBI::dbSendStatement(conn, statement, ...)
7. ├─DBI::dbSendQuery(conn, statement, ...)
8. └─duckdb::dbSendQuery(conn, statement, ...)
9. └─duckdb (local) .local(conn, statement, ...)
10. └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow =
arrow)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<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 ‘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-debian-gcc
Version: 1.3.0
Check: tests
Result: ERROR
Running ‘testthat.R’
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 1.3.0 attached
* Compatible with DuckDB >= v1.5.6
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/localhost/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/localhost/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 storing downloaded extensions and secrets under ~/.duckdb:
ℹ /data/localhost/ripley/.duckdb
This persists across sessions and is shared with the DuckDB CLI and other clients.
ℹ Run duckdb(shared_home = FALSE) to use a temporary directory instead.
ℹ See ?duckdb_storage for details and alternatives.
duckdb was built with libc++ (not libstdc++) on Linux, so DuckDB extensions are disabled:
• Loading a prebuilt (libstdc++) extension could crash R (https://github.com/duckdb/duckdb-r/issues/1107).
• INSTALL/LOAD of an extension will error, and automatic extension loading is off.
ℹ Pass duckdb(allow_extensions = FALSE) to accept this and silence this message.
ℹ Pass duckdb(allow_extensions = TRUE) to attempt loading anyway (may crash R).
ℹ See ?duckdb for details.
Error in `source_dir()`:
! Failed to evaluate './setup.R'.
Caused by error in `value[[3L]]()`:
! Failed to load the spatial extension.
✖ DuckDB extension loading (INSTALL / LOAD) is disabled for this driver. ℹ
Recreate the driver with duckdb(allow_extensions = TRUE) to enable it (this
may crash R on a Linux build not compiled with libstdc++; see
https://github.com/duckdb/duckdb-r/issues/1107). ℹ See ?duckdb for details. ℹ
Context: load_extension
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. └─testthat::test_check("duckspatial")
2. └─testthat::test_dir(...)
3. └─testthat:::test_files(...)
4. └─testthat:::test_files_serial(...)
5. └─testthat:::test_files_setup_state(...)
6. └─testthat::source_test_setup(".", env)
7. └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)
8. └─base::lapply(...)
9. └─testthat (local) FUN(X[[i]], ...)
10. └─testthat::source_file(...)
11. ├─base::withCallingHandlers(...)
12. └─base::eval(exprs, env)
13. └─base::eval(exprs, env)
14. ├─duckspatial::as_duckspatial_df(argentina_sf) at ./setup.R:15:1
15. └─duckspatial:::as_duckspatial_df.sf(argentina_sf)
16. └─duckspatial::ddbs_default_conn()
17. └─duckspatial::ddbs_create_conn(dbdir = "memory", ...)
18. └─duckspatial::ddbs_load(conn, quiet = TRUE)
19. └─base::tryCatch(...)
20. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
21. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
22. └─value[[3L]](cond)
23. └─cli::cli_abort(...)
24. └─rlang::abort(...)
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.3.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘aw_interpolation.qmd’ using html
<1b>[31m
processing file: aw_interpolation.qmd
<1b>[39m<1b>[31mError in `value[[3L]]()`:
! Failed to load the spatial extension.
✖ DuckDB extension loading (INSTALL / LOAD) is disabled for this driver. ℹ
Recreate the driver with duckdb(allow_extensions = TRUE) to enable it (this
may crash R on a Linux build not compiled with libstdc++; see
https://github.com/duckdb/duckdb-r/issues/1107). ℹ See ?duckdb for details. ℹ
Context: load_extension
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_interpolate_aw(...)
2. └─duckspatial:::resolve_spatial_connections(...)
3. └─duckspatial::ddbs_default_conn()
4. └─duckspatial::ddbs_create_conn(dbdir = "memory", ...)
5. └─duckspatial::ddbs_load(conn, quiet = TRUE)
6. └─base::tryCatch(...)
7. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
8. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
9. └─value[[3L]](cond)
10. └─cli::cli_abort(...)
11. └─rlang::abort(...)
<1b>[39m<1b>[31m
Quitting from aw_interpolation.qmd:78-89 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `value[[3L]]()`:
! Failed to load the spatial extension.
✖ DuckDB extension loading (INSTALL / LOAD) is disabled for this driver. ℹ
Recreate the driver with duckdb(allow_extensions = TRUE) to enable it (this
may crash R on a Linux build not compiled with libstdc++; see
https://github.com/duckdb/duckdb-r/issues/1107). ℹ See ?duckdb for details. ℹ
Context: load_extension
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_interpolate_aw(...)
2. └─duckspatial:::resolve_spatial_connections(...)
3. └─duckspatial::ddbs_default_conn()
4. └─duckspatial::ddbs_create_conn(dbdir = "memory", ...)
5. └─duckspatial::ddbs_load(conn, quiet = TRUE)
6. └─base::tryCatch(...)
7. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
8. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
9. └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Execution halted
<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 in `quarto_render()`:
✖ Error returned by quarto CLI.
-----------------------------
processing file: aw_interpolation.qmd
<1b>[31mError in `value[[3L]]()`:<1b>[39m
! Failed to load the spatial extension.
✖ DuckDB extension loading (INSTALL / LOAD) is disabled for this driver. ℹ
Recreate the driver with duckdb(allow_extensions = TRUE) to enable it (this
may crash R on a Linux build not compiled with libstdc++; see
https://github.com/duckdb/duckdb-r/issues/1107). ℹ See ?duckdb for details. ℹ
Context: load_extension
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_interpolate_aw(...)
2. └─duckspatial:::resolve_spatial_connections(...)
3. └─duckspatial::ddbs_default_conn()
4. └─duckspatial::ddbs_create_conn(dbdir = "memory", ...)
5. └─duckspatial::ddbs_load(conn, quiet = TRUE)
6. └─base::tryCatch(...)
7. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
8. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
9. └─value[[3L]](cond)
10. └─cli::cli_abort(...)
11. └─rlang::abort(...)
Quitting from aw_interpolation.qmd:78-89 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `value[[3L]]()`:
! Failed to load the spatial extension.
✖ DuckDB extension loading (INSTALL / LOAD) is disabled for this driver. ℹ
Recreate the driver with duckdb(allow_extensions = TRUE) to enable it (this
may crash R on a Linux build not compiled with libstdc++; see
https://github.com/duckdb/duckdb-r/issues/1107). ℹ See ?duckdb for details. ℹ
Context: load_extension
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_interpolate_aw(...)
2. └─duckspatial:::resolve_spatial_connections(...)
3. └─duckspatial::ddbs_default_conn()
4. └─duckspatial::ddbs_create_conn(dbdir = "memory", ...)
5. └─duckspatial::ddbs_load(conn, quiet = TRUE)
6. └─base::tryCatch(...)
7. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
8. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
9. └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Execution halted
<1b>[33mWARN: Error encountered when rendering files<1b>[39m
Caused by error in `processx::run()`:
! System command 'quarto' failed
--- 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/localhost/ripley/R/test-clang/quarto/rmarkdown/template/quarto_vignette/resources/vignette.css
<1b>[1mmetadata<1b>[22m
document-css: false
lang: en
minimal: true
theme: none
title: Benchmark
date: '`r Sys.Date()`'
code-annotations: hover
urlcolor: blue
vignette: |
%\VignetteIndexEntry{Benchmark} %\VignetteEncoding{UTF-8} %\VignetteEngine{quarto::html}
knitr:
opts_chunk:
collapse: true
comment: '#>'
out.width: 100%
editor_options:
chunk_output_type: console
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.
✖ DuckDB extension loading (INSTALL / LOAD) is disabled for this driver. ℹ
Recreate the driver with duckdb(allow_extensions = TRUE) to enable it (this
may crash R on a Linux build not compiled with libstdc++; see
https://github.com/duckdb/duckdb-r/issues/1107). ℹ See ?duckdb for details. ℹ
Context: load_extension
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]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<1b>[39m<1b>[31m~~~~~~~~~~~~~
<error/rlang_error>
Error in `value[[3L]]()`:
! Failed to load the spatial extension.
✖ DuckDB extension loading (INSTALL / LOAD) is disabled for this driver. ℹ
Recreate the driver with duckdb(allow_extensions = TRUE) to enable it (this
may crash R on a Linux build not compiled with libstdc++; see
https://github.com/duckdb/duckdb-r/issues/1107). ℹ See ?duckdb for details. ℹ
Context: load_extension
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)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Execution 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.
✖ DuckDB extension loading (INSTALL / LOAD) is disabled for this driver. ℹ
Recreate the driver with duckdb(allow_extensions = TRUE) to enable it (this
may crash R on a Linux build not compiled with libstdc++; see
https://github.com/duckdb/duckdb-r/issues/1107). ℹ See ?duckdb for details. ℹ
Context: load_extension
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]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<1b>[31m~~~~~~~~~~~~~<1b>[39m
<error/rlang_error>
Error in `value[[3L]]()`:
! Failed to load the spatial extension.
✖ DuckDB extension loading (INSTALL / LOAD) is disabled for this driver. ℹ
Recreate the driver with duckdb(allow_extensions = TRUE) to enable it (this
may crash R on a Linux build not compiled with libstdc++; see
https://github.com/duckdb/duckdb-r/issues/1107). ℹ See ?duckdb for details. ℹ
Context: load_extension
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)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Execution halted
<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>[31mError in `value[[3L]]()`:
! Failed to load the spatial extension.
✖ DuckDB extension loading (INSTALL / LOAD) is disabled for this driver. ℹ
Recreate the driver with duckdb(allow_extensions = TRUE) to enable it (this
may crash R on a Linux build not compiled with libstdc++; see
https://github.com/duckdb/duckdb-r/issues/1107). ℹ See ?duckdb for details. ℹ
Context: load_extension
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_join(x = points_sf, y = countries_sf, join = "within")
2. └─duckspatial:::resolve_spatial_connections(...)
3. └─duckspatial::ddbs_default_conn()
4. └─duckspatial::ddbs_create_conn(dbdir = "memory", ...)
5. └─duckspatial::ddbs_load(conn, quiet = TRUE)
6. └─base::tryCatch(...)
7. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
8. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
9. └─value[[3L]](cond)
10. └─cli::cli_abort(...)
11. └─rlang::abort(...)
<1b>[39m<1b>[31m
Quitting from spatial_joins.qmd:77-87 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `value[[3L]]()`:
! Failed to load the spatial extension.
✖ DuckDB extension loading (INSTALL / LOAD) is disabled for this driver. ℹ
Recreate the driver with duckdb(allow_extensions = TRUE) to enable it (this
may crash R on a Linux build not compiled with libstdc++; see
https://github.com/duckdb/duckdb-r/issues/1107). ℹ See ?duckdb for details. ℹ
Context: load_extension
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_join(x = points_sf, y = countries_sf, join = "within")
2. └─duckspatial:::resolve_spatial_connections(...)
3. └─duckspatial::ddbs_default_conn()
4. └─duckspatial::ddbs_create_conn(dbdir = "memory", ...)
5. └─duckspatial::ddbs_load(conn, quiet = TRUE)
6. └─base::tryCatch(...)
7. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
8. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
9. └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Execution halted
<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 in `quarto_render()`:
✖ Error returned by quarto CLI.
-----------------------------
processing file: spatial_joins.qmd
<1b>[31mError in `value[[3L]]()`:<1b>[39m
! Failed to load the spatial extension.
✖ DuckDB extension loading (INSTALL / LOAD) is disabled for this driver. ℹ
Recreate the driver with duckdb(allow_extensions = TRUE) to enable it (this
may crash R on a Linux build not compiled with libstdc++; see
https://github.com/duckdb/duckdb-r/issues/1107). ℹ See ?duckdb for details. ℹ
Context: load_extension
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_join(x = points_sf, y = countries_sf, join = "within")
2. └─duckspatial:::resolve_spatial_connections(...)
3. └─duckspatial::ddbs_default_conn()
4. └─duckspatial::ddbs_create_conn(dbdir = "memory", ...)
5. └─duckspatial::ddbs_load(conn, quiet = TRUE)
6. └─base::tryCatch(...)
7. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
8. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
9. └─value[[3L]](cond)
10. └─cli::cli_abort(...)
11. └─rlang::abort(...)
Quitting from spatial_joins.qmd:77-87 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `value[[3L]]()`:
! Failed to load the spatial extension.
✖ DuckDB extension loading (INSTALL / LOAD) is disabled for this driver. ℹ
Recreate the driver with duckdb(allow_extensions = TRUE) to enable it (this
may crash R on a Linux build not compiled with libstdc++; see
https://github.com/duckdb/duckdb-r/issues/1107). ℹ See ?duckdb for details. ℹ
Context: load_extension
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_join(x = points_sf, y = countries_sf, join = "within")
2. └─duckspatial:::resolve_spatial_connections(...)
3. └─duckspatial::ddbs_default_conn()
4. └─duckspatial::ddbs_create_conn(dbdir = "memory", ...)
5. └─duckspatial::ddbs_load(conn, quiet = TRUE)
6. └─base::tryCatch(...)
7. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
8. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
9. └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Execution halted
<1b>[33mWARN: Error encountered when rendering files<1b>[39m
Caused by error in `processx::run()`:
! System command 'quarto' failed
--- 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