Last updated on 2026-03-31 00:50:33 CEST.
| Package | ERROR | OK |
|---|---|---|
| duckspatial | 8 | 6 |
| OTBsegm | 14 | |
| rpostgis | 1 | 13 |
| silviculture | 14 |
Current CRAN status: ERROR: 8, OK: 6
Version: 0.9.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [10s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(duckspatial)
Important: 'crs_column' and 'crs' arguments are deprecated and will be removed in the next version.
If possible, use the default values of these arguments to avoid future issues.
> library(duckdb)
Loading required package: DBI
>
> test_check("duckspatial")
Reading layer `countries' from data source
`/home/hornik/tmp/R.check/r-devel-clang/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-clang/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
Reading layer `rivers' from data source
`/home/hornik/tmp/R.check/r-devel-clang/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
v Temporary view view_test registered
v Arrow view view_test successfully imported.
i Table <table_test> dropped
v Table table_test successfully imported
v table table_test successfully imported.
i Table <rt_write_line> dropped
v Table rt_write_line successfully imported
v table rt_write_line successfully imported.
i Table <rt_write_polygon> dropped
v Table rt_write_polygon successfully imported
v table rt_write_polygon successfully imported.
i Table <rt_write_multipoint> dropped
v Table rt_write_multipoint successfully imported
v table rt_write_multipoint successfully imported.
v Temporary view rt_register_line registered
v Arrow view rt_register_line successfully imported.
v Temporary view rt_register_polygon registered
v Arrow view rt_register_polygon successfully imported.
v Temporary view rt_register_multipoint registered
v Arrow view rt_register_multipoint successfully imported.
i Table <countries_from_file_compat> dropped
v Table countries_from_file_compat successfully imported
Saving _problems/test-compatibility-112.R
[ FAIL 1 | WARN 2 | SKIP 17 | PASS 31 ]
══ Skipped tests (17) ══════════════════════════════════════════════════════════
• On CRAN (17): 'test-db_read.R:2:1', 'test-db_register.R:3:1',
'test-db_write.R:3:1', 'test-ddbs_area.R:3:1', 'test-ddbs_bbox.R:3:1',
'test-ddbs_combine.R:3:1', 'test-ddbs_concave_hull.R:3:1',
'test-ddbs_convex_hull.R:3:1', 'test-ddbs_distance.R:3:1',
'test-ddbs_envelope.R:3:1', 'test-ddbs_generate_points.R:5:1',
'test-ddbs_interpolate_aw.R:2:1', 'test-ddbs_join.R:3:1',
'test-ddbs_length.R:3:1', 'test-ddbs_transform.R:5:1',
'test-ddbs_union.R:3:1', 'test-utils.R:2:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-compatibility.R:112:5'): Compatibility: Writing from file path and reading back ──
Error in `ddbs_read_vector(conn, table_name)`: Geometry column wasn't found in table <countries_from_file_compat>.
Backtrace:
▆
1. └─duckspatial::ddbs_read_vector(conn, table_name) at test-compatibility.R:112:5
2. └─cli::cli_abort("Geometry column wasn't found in table <{name_list$query_name}>.")
3. └─rlang::abort(...)
[ FAIL 1 | WARN 2 | SKIP 17 | PASS 31 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.9.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [6s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(duckspatial)
Important: 'crs_column' and 'crs' arguments are deprecated and will be removed in the next version.
If possible, use the default values of these arguments to avoid future issues.
> library(duckdb)
Loading required package: DBI
>
> test_check("duckspatial")
Reading layer `countries' from data source
`/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
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
v Temporary view view_test registered
v Arrow view view_test successfully imported.
i Table <table_test> dropped
v Table table_test successfully imported
v table table_test successfully imported.
i Table <rt_write_line> dropped
v Table rt_write_line successfully imported
v table rt_write_line successfully imported.
i Table <rt_write_polygon> dropped
v Table rt_write_polygon successfully imported
v table rt_write_polygon successfully imported.
i Table <rt_write_multipoint> dropped
v Table rt_write_multipoint successfully imported
v table rt_write_multipoint successfully imported.
v Temporary view rt_register_line registered
v Arrow view rt_register_line successfully imported.
v Temporary view rt_register_polygon registered
v Arrow view rt_register_polygon successfully imported.
v Temporary view rt_register_multipoint registered
v Arrow view rt_register_multipoint successfully imported.
i Table <countries_from_file_compat> dropped
v Table countries_from_file_compat successfully imported
Saving _problems/test-compatibility-112.R
[ FAIL 1 | WARN 2 | SKIP 17 | PASS 31 ]
══ Skipped tests (17) ══════════════════════════════════════════════════════════
• On CRAN (17): 'test-db_read.R:2:1', 'test-db_register.R:3:1',
'test-db_write.R:3:1', 'test-ddbs_area.R:3:1', 'test-ddbs_bbox.R:3:1',
'test-ddbs_combine.R:3:1', 'test-ddbs_concave_hull.R:3:1',
'test-ddbs_convex_hull.R:3:1', 'test-ddbs_distance.R:3:1',
'test-ddbs_envelope.R:3:1', 'test-ddbs_generate_points.R:5:1',
'test-ddbs_interpolate_aw.R:2:1', 'test-ddbs_join.R:3:1',
'test-ddbs_length.R:3:1', 'test-ddbs_transform.R:5:1',
'test-ddbs_union.R:3:1', 'test-utils.R:2:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-compatibility.R:112:5'): Compatibility: Writing from file path and reading back ──
Error in `ddbs_read_vector(conn, table_name)`: Geometry column wasn't found in table <countries_from_file_compat>.
Backtrace:
▆
1. └─duckspatial::ddbs_read_vector(conn, table_name) at test-compatibility.R:112:5
2. └─cli::cli_abort("Geometry column wasn't found in table <{name_list$query_name}>.")
3. └─rlang::abort(...)
[ FAIL 1 | WARN 2 | SKIP 17 | PASS 31 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [7s/23s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(duckspatial)
duckspatial 1.0.0 attached
* Compatible with DuckDB v1.5.1
* This release introduces breaking changes
* See full release notes for migration guidance
Default output has changed:
duckspatial now returns lazy `duckspatial_df` (dbplyr) objects
instead of `sf` objects.
To restore the previous behaviour:
ddbs_options(duckspatial.mode = 'sf')
> library(duckdb)
Loading required package: DBI
>
> test_check("duckspatial")
Reading layer `countries' from data source
`/data/gannet/ripley/R/packages/tests-clang/duckspatial.Rcheck/duckspatial/spatial/countries.geojson'
using driver `GeoJSON'
Simple feature collection with 257 features and 6 fields
Geometry type: POLYGON
Dimension: XY
Bounding box: xmin: -178.9125 ymin: -89.9 xmax: 180 ymax: 83.65187
Geodetic CRS: WGS 84
Reading layer `argentina' from data source
`/data/gannet/ripley/R/packages/tests-clang/duckspatial.Rcheck/duckspatial/spatial/argentina.geojson'
using driver `GeoJSON'
Simple feature collection with 1 feature and 6 fields
Geometry type: POLYGON
Dimension: XY
Bounding box: xmin: -73.52455 ymin: -52.39755 xmax: -53.62409 ymax: -21.81793
Geodetic CRS: WGS 84
Error in `source_dir()`:
! Failed to evaluate './setup.R'.
Caused by error in `duckdb_result()`:
! Invalid Error: Invalid Input Error: Initialization function "spatial_duckdb_cpp_init" from file "/data/gannet/ripley/.local/share/R/duckdb/extensions/v1.5.1/linux_amd64/spatial.duckdb_extension" threw an exception: "Missing DB manager"
ℹ Context: rapi_execute
ℹ Error type: INVALID
Backtrace:
▆
1. ├─testthat::test_check("duckspatial")
2. │ └─testthat::test_dir(...)
3. │ └─testthat:::test_files(...)
4. │ └─testthat:::test_files_serial(...)
5. │ └─testthat:::test_files_setup_state(...)
6. │ └─testthat::source_test_setup(".", env)
7. │ └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)
8. │ └─base::lapply(...)
9. │ └─testthat (local) FUN(X[[i]], ...)
10. │ └─testthat::source_file(...)
11. │ ├─base::withCallingHandlers(...)
12. │ └─base::eval(exprs, env)
13. │ └─base::eval(exprs, env)
14. │ ├─duckspatial::as_duckspatial_df(argentina_sf) at ./setup.R:15:1
15. │ └─duckspatial:::as_duckspatial_df.sf(argentina_sf)
16. │ └─duckspatial:::ddbs_default_conn()
17. │ └─duckspatial::ddbs_create_conn(dbdir = "memory", ...)
18. │ └─duckspatial::ddbs_load(conn, quiet = TRUE)
19. │ ├─base::suppressMessages(DBI::dbExecute(conn, glue::glue("LOAD {extension};")))
20. │ │ └─base::withCallingHandlers(...)
21. │ ├─DBI::dbExecute(conn, glue::glue("LOAD {extension};"))
22. │ └─DBI::dbExecute(conn, glue::glue("LOAD {extension};"))
23. │ ├─DBI::dbSendStatement(conn, statement, ...)
24. │ └─DBI::dbSendStatement(conn, statement, ...)
25. │ ├─DBI::dbSendQuery(conn, statement, ...)
26. │ └─duckdb::dbSendQuery(conn, statement, ...)
27. │ └─duckdb (local) .local(conn, statement, ...)
28. │ └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
29. │ └─duckdb:::duckdb_execute(res)
30. │ └─duckdb:::rethrow_rapi_execute(...)
31. │ ├─rlang::try_fetch(...)
32. │ │ ├─base::tryCatch(...)
33. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
34. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
35. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
36. │ │ └─base::withCallingHandlers(...)
37. │ └─duckdb:::rapi_execute(stmt, convert_opts)
38. ├─duckdb (local) `<fn>`(...)
39. │ └─rlang::abort(error_parts, class = "duckdb_error", !!!fields)
40. │ └─rlang:::signal_abort(cnd, .file)
41. │ └─base::signalCondition(cnd)
42. └─rlang (local) `<fn>`(`<dckdb_rr>`)
43. └─handlers[[1L]](cnd)
44. └─duckdb:::rethrow_error_from_rapi(e, call)
45. └─rlang::abort(msg, call = call)
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.0.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘aw_interpolation.qmd’ using html
<1b>[31m
processing file: aw_interpolation.qmd
<1b>[39m<1b>[31mError in `duckdb_result()`:
! Invalid Error: Invalid Input Error: Initialization function "spatial_duckdb_cpp_init" from file "/data/gannet/ripley/.local/share/R/duckdb/extensions/v1.5.1/linux_amd64/spatial.duckdb_extension" threw an exception: "Missing DB manager"
ℹ Context: rapi_execute
ℹ Error type: INVALID
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::suppressMessages(DBI::dbExecute(conn, glue::glue("LOAD {extension};")))
7. │ │ └─base::withCallingHandlers(...)
8. │ ├─DBI::dbExecute(conn, glue::glue("LOAD {extension};"))
9. │ └─DBI::dbExecute(conn, glue::glue("LOAD {extension};"))
10. │ ├─DBI::dbSendStatement(conn, statement, ...)
11. │ └─DBI::dbSendStatement(conn, statement, ...)
12. │ ├─DBI::dbSendQuery(conn, statement, ...)
13. │ └─duckdb::dbSendQuery(conn, statement, ...)
14. │ └─duckdb (local) .local(conn, statement, ...)
15. │ └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
16. │ └─duckdb:::duckdb_execute(res)
17. │ └─duckdb:::rethrow_rapi_execute(...)
18. │ ├─rlang::try_fetch(...)
19. │ │ ├─base::tryCatch(...)
20. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
21. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
22. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
23. │ │ └─base::withCallingHandlers(...)
24. │ └─duckdb:::rapi_execute(stmt, convert_opts)
25. ├─duckdb (local) `<fn>`(...)
26. │ └─rlang::abort(error_parts, class = "duckdb_error", !!!fields)
27. │ └─rlang:::signal_abort(cnd, .file)
28. │ └─base::signalCondition(cnd)
29. └─rlang (local) `<fn>`(`<dckdb_rr>`)
30. └─handlers[[1L]](cnd)
31. └─duckdb:::rethrow_error_from_rapi(e, call)
32. └─rlang::abort(msg, call = call)
<1b>[39m<1b>[31m
Quitting from aw_interpolation.qmd:68-79 [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/.local/share/R/duckdb/extensions/v1.5.1/linux_amd64/spatial.duckdb_extension" threw an exception: "Missing DB manager"
ℹ Context: rapi_execute
ℹ Error type: INVALID
---
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::suppressMessages(DBI::dbExecute(conn, glue::glue("LOAD {extension};")))
7. │ └─base::withCallingHandlers(...)
8. ├─DBI::dbExecute(conn, glue::glue("LOAD {extension};"))
9. └─DBI::dbExecute(conn, glue::glue("LOAD {extension};"))
10. ├─DBI::dbSendStatement(conn, statement, ...)
11. └─DBI::dbSendStatement(conn, statement, ...)
12. ├─DBI::dbSendQuery(conn, statement, ...)
13. └─duckdb::dbSendQuery(conn, statement, ...)
14. └─duckdb (local) .local(conn, statement, ...)
15. └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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:
! Could not evaluate cli `{}` expression: `extension`.
Caused by error:
! object 'extension' not found
--- failed re-building ‘aw_interpolation.qmd’
--- re-building ‘benchmark.qmd’ using html
<1b>[31m
processing file: benchmark.qmd
<1b>[39m<1b>[31moutput file: benchmark.knit.md
<1b>[39m<1b>[1mpandoc <1b>[22m
to: html
output-file: benchmark.html
standalone: true
embed-resources: true
wrap: none
default-image-extension: png
css:
- >-
/data/gannet/ripley/R/test-clang/quarto/rmarkdown/template/quarto_vignette/resources/vignette.css
variables: {}
<1b>[1mmetadata<1b>[22m
document-css: false
lang: en
engines:
- path: /data/gannet/ripley/Sources/quarto-1.9.36/share/extension-subtrees/julia-engine/_extensions/julia-engine/julia-engine.js
minimal: true
theme: none
title: Benchmark
date: '`r Sys.Date()`'
code-annotations: hover
urlcolor: blue
vignette: |
%\VignetteIndexEntry{Benchmark} %\VignetteEngine{quarto::html} %\VignetteEncoding{UTF-8}
knitr:
opts_chunk:
collapse: true
comment: '#>'
out.width: 100%
Output created: benchmark.html
--- finished re-building ‘benchmark.qmd’
--- re-building ‘duckspatial.qmd’ using html
<1b>[31m
processing file: duckspatial.qmd
<1b>[39m<1b>[31mError in `duckdb_result()`:
! Invalid Error: Invalid Input Error: Initialization function "spatial_duckdb_cpp_init" from file "/data/gannet/ripley/.local/share/R/duckdb/extensions/v1.5.1/linux_amd64/spatial.duckdb_extension" threw an exception: "Missing DB manager"
ℹ Context: rapi_execute
ℹ Error type: INVALID
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::suppressMessages(DBI::dbExecute(conn, glue::glue("LOAD {extension};")))
6. │ │ └─base::withCallingHandlers(...)
7. │ ├─DBI::dbExecute(conn, glue::glue("LOAD {extension};"))
8. │ └─DBI::dbExecute(conn, glue::glue("LOAD {extension};"))
9. │ ├─DBI::dbSendStatement(conn, statement, ...)
10. │ └─DBI::dbSendStatement(conn, statement, ...)
11. │ ├─DBI::dbSendQuery(conn, statement, ...)
12. │ └─duckdb::dbSendQuery(conn, statement, ...)
13. │ └─duckdb (local) .local(conn, statement, ...)
14. │ └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
15. │ └─duckdb:::duckdb_execute(res)
16. │ └─duckdb:::rethrow_rapi_execute(...)
17. │ ├─rlang::try_fetch(...)
18. │ │ ├─base::tryCatch(...)
19. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
20. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
21. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
22. │ │ └─base::withCallingHandlers(...)
23. │ └─duckdb:::rapi_execute(stmt, convert_opts)
24. ├─duckdb (local) `<fn>`(...)
25. │ └─rlang::abort(error_parts, class = "duckdb_error", !!!fields)
26. │ └─rlang:::signal_abort(cnd, .file)
27. │ └─base::signalCondition(cnd)
28. └─rlang (local) `<fn>`(`<dckdb_rr>`)
29. └─handlers[[1L]](cnd)
30. └─duckdb:::rethrow_error_from_rapi(e, call)
31. └─rlang::abort(msg, call = call)
<1b>[39m<1b>[31m
Quitting from duckspatial.qmd:68-77 [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/.local/share/R/duckdb/extensions/v1.5.1/linux_amd64/spatial.duckdb_extension" threw an exception: "Missing DB manager"
ℹ Context: rapi_execute
ℹ Error type: INVALID
---
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::suppressMessages(DBI::dbExecute(conn, glue::glue("LOAD {extension};")))
6. │ └─base::withCallingHandlers(...)
7. ├─DBI::dbExecute(conn, glue::glue("LOAD {extension};"))
8. └─DBI::dbExecute(conn, glue::glue("LOAD {extension};"))
9. ├─DBI::dbSendStatement(conn, statement, ...)
10. └─DBI::dbSendStatement(conn, statement, ...)
11. ├─DBI::dbSendQuery(conn, statement, ...)
12. └─duckdb::dbSendQuery(conn, statement, ...)
13. └─duckdb (local) .local(conn, statement, ...)
14. └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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:
! Could not evaluate cli `{}` expression: `extension`.
Caused by error:
! object 'extension' not found
--- failed re-building ‘duckspatial.qmd’
--- re-building ‘spatial_joins.qmd’ using html
<1b>[31m
processing file: spatial_joins.qmd
<1b>[39m<1b>[31m[gannet:4105154:0:4106529] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x100000002)
<1b>[39m<1b>[31m==== backtrace (tid:4106529) ====
0 /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7ffb6e3b7df4]
1 /lib64/libucs.so.0(+0x17aed) [0x7ffb6e3b9aed]
2 /lib64/libucs.so.0(+0x17cbd) [0x7ffb6e3b9cbd]
3 /lib64/libc.so.6(+0x1a040) [0x7ffb84928040]
4 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.5.1/linux_amd64/spatial.duckdb_extension(+0xc17cc8) [0x7ffa44817cc8]
5 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.5.1/linux_amd64/spatial.duckdb_extension(+0xc1b387) [0x7ffa4481b387]
6 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.5.1/linux_amd64/spatial.duckdb_extension(+0xc1b504) [0x7ffa4481b504]
7 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.5.1/linux_amd64/spatial.duckdb_extension(+0x11442ea) [0x7ffa44d442ea]
8 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.5.1/linux_amd64/spatial.duckdb_extension(+0x758844) [0x7ffa44358844]
9 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.5.1/linux_amd64/spatial.duckdb_extension(+0x756bd9) [0x7ffa44356bd9]
10 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper29LoadExternalExtensionInternalERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEERNS_19ExtensionActiveLoadE+0x195) [0x7ffaa7079825]
11 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper21LoadExternalExtensionERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEE+0x4a) [0x7ffaa70795ca]
12 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZNK6duckdb12PhysicalLoad15GetDataInternalERNS_16ExecutionContextERNS_9DataChunkERNS_19OperatorSourceInputE+0x151) [0x7ffaa7e6c831]
13 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor15FetchFromSourceERNS_9DataChunkE+0x9b) [0x7ffaa8693fdb]
14 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor7ExecuteEm+0x146) [0x7ffaa8690bb6]
15 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12PipelineTask11ExecuteTaskENS_17TaskExecutionModeE+0x154) [0x7ffaa8690824]
16 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12ExecutorTask7ExecuteENS_17TaskExecutionModeE+0xa0) [0x7ffaa868a5a0]
17 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb13TaskScheduler14ExecuteForeverEPNSt3__16atomicIbEE+0x39a) [0x7ffaa869720a]
18 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(+0x1aa2ccc) [0x7ffaa86a2ccc]
19 /lib64/libc.so.6(+0x71f14) [0x7ffb8497ff14]
20 /lib64/libc.so.6(+0xf532c) [0x7ffb84a0332c]
=================================
*** caught segfault ***
address 0x4d2003ea3c2, cause 'unknown'
Traceback:
1: rapi_execute(stmt, convert_opts)
2: withCallingHandlers(expr, condition = function(cnd) { { .__handler_frame__. <- TRUE .__setup_frame__. <- frame if (inherits(cnd, "message")) { except <- c("warning", "error") } else if (inherits(cnd, "warning")) { except <- "error" } else { except <- "" } } while (!is_null(cnd)) { if (inherits(cnd, "error")) { out <- handlers[[1L]](cnd) if (!inherits(out, "rlang_zap")) throw(out) } inherit <- .subset2(.subset2(cnd, "rlang"), "inherit") if (is_false(inherit)) { return() } cnd <- .subset2(cnd, "parent") }})
3: doTryCatch(return(expr), name, parentenv, handler)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
5: tryCatchList(expr, classes, parentenv, handlers)
6: tryCatch(withCallingHandlers(expr, condition = function(cnd) { { .__handler_frame__. <- TRUE .__setup_frame__. <- frame if (inherits(cnd, "message")) { except <- c("warning", "error") } else if (inherits(cnd, "warning")) { except <- "error" } else { except <- "" } } while (!is_null(cnd)) { if (inherits(cnd, "error")) { out <- handlers[[1L]](cnd) if (!inherits(out, "rlang_zap")) throw(out) } inherit <- .subset2(.subset2(cnd, "rlang"), "inherit") if (is_false(inherit)) { return() } cnd <- .subset2(cnd, "parent") }}), stackOverflowError = handlers[[1L]])
7: rlang::try_fetch(rapi_execute(stmt, convert_opts), error = function(e) { rethrow_error_from_rapi(e, call)})
8: rethrow_rapi_execute(res@stmt_lst$ref, duckdb_convert_opts_impl(res@connection@convert_opts, arrow = res@arrow))
9: duckdb_execute(res)
10: duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
11: .local(conn, statement, ...)
12: dbSendQuery(conn, statement, ...)
13: dbSendQuery(conn, statement, ...)
14: dbSendStatement(conn, statement, ...)
15: dbSendStatement(conn, statement, ...)
16: DBI::dbExecute(conn, glue::glue("LOAD {extension};"))
17: DBI::dbExecute(conn, glue::glue("LOAD {extension};"))
18: withCallingHandlers(expr, message = function(c) if (inherits(c, classes)) tryInvokeRestart("muffleMessage"))
19: suppressMessages(DBI::dbExecute(conn, glue::glue("LOAD {extension};")))
20: ddbs_load(conn, quiet = TRUE)
21: ddbs_create_conn(dbdir = "memory", ...)
22: ddbs_default_conn()
23: resolve_spatial_connections(x, y, conn, conn_x, conn_y, quiet = quiet)
24: ddbs_join(x = points_sf, y = countries_sf, join = "within")
25: eval(expr, envir)
26: eval(expr, envir)
27: withVisible(eval(expr, envir))
28: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
29: eval(call)
30: eval(call)
31: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
32: doWithOneRestart(return(expr), restart)
33: withOneRestart(expr, restarts[[1L]])
34: withRestartList(expr, restarts[-nr])
35: doWithOneRestart(return(expr), restart)
36: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
37: withRestartList(expr, restarts)
38: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
39: evaluate::evaluate(...)
40: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
41: in_dir(input_dir(), expr)
42: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
43: eng_r(options)
44: block_exec(params)
45: call_block(x)
46: process_group(group)
47: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
48: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
49: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
50: process_file(text, output)
51: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
52: rmarkdown::render(input = input, output_format = output_format, knit_root_dir = knit_root_dir, params = params, run_pandoc = FALSE, envir = env)
53: execute(params$input, params$format, params$tempDir, params$libDir, params$dependencies, params$cwd, params$params, params$resourceDir, params$handledLanguages, params$markdown)
54: .main()
An irrecoverable exception occurred. R is aborting now ...
<1b>[39m<1b>[33mWARN: Error encountered when rendering files<1b>[39m
Error: processing vignette 'spatial_joins.qmd' failed with diagnostics:
! Error running quarto CLI from R.
Caused by error:
! Could not parse cli `{}` expression: ` { .__han…`.
Caused by error:
! <text>:1:49: unexpected symbol
1: { .__handler_frame__. <- TRUE .__setup_frame__.
^
--- failed re-building ‘spatial_joins.qmd’
SUMMARY: processing the following files failed:
‘aw_interpolation.qmd’ ‘duckspatial.qmd’ ‘spatial_joins.qmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.9.0
Check: tests
Result: ERROR
Running 'testthat.R' [6s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(duckspatial)
Important: 'crs_column' and 'crs' arguments are deprecated and will be removed in the next version.
If possible, use the default values of these arguments to avoid future issues.
> library(duckdb)
Loading required package: DBI
>
> test_check("duckspatial")
Reading layer `countries' from data source
`D:\RCompile\CRANpkg\lib\4.6\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
`D:\RCompile\CRANpkg\lib\4.6\duckspatial\spatial\argentina.geojson'
using driver `GeoJSON'
Simple feature collection with 1 feature and 6 fields
Geometry type: POLYGON
Dimension: XY
Bounding box: xmin: -73.52455 ymin: -52.39755 xmax: -53.62409 ymax: -21.81793
Geodetic CRS: WGS 84
Reading layer `rivers' from data source
`D:\RCompile\CRANpkg\lib\4.6\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
v Temporary view view_test registered
Saving _problems/test-compatibility-28.R
i Table <rt_write_line> dropped
v Table rt_write_line successfully imported
Saving _problems/test-compatibility-63.R
v Temporary view rt_register_line registered
Saving _problems/test-compatibility-92.R
i Table <countries_from_file_compat> dropped
v Table countries_from_file_compat successfully imported
Saving _problems/test-compatibility-112.R
[ FAIL 4 | WARN 1 | SKIP 17 | PASS 3 ]
══ Skipped tests (17) ══════════════════════════════════════════════════════════
• On CRAN (17): 'test-db_read.R:2:1', 'test-db_register.R:3:1',
'test-db_write.R:3:1', 'test-ddbs_area.R:3:1', 'test-ddbs_bbox.R:3:1',
'test-ddbs_combine.R:3:1', 'test-ddbs_concave_hull.R:3:1',
'test-ddbs_convex_hull.R:3:1', 'test-ddbs_distance.R:3:1',
'test-ddbs_envelope.R:3:1', 'test-ddbs_generate_points.R:5:1',
'test-ddbs_interpolate_aw.R:2:1', 'test-ddbs_join.R:3:1',
'test-ddbs_length.R:3:1', 'test-ddbs_transform.R:5:1',
'test-ddbs_union.R:3:1', 'test-utils.R:2:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-compatibility.R:28:5'): Compatibility: Arrow Views behave like Persistent Tables ──
Error in `dbSendQuery(conn, statement, ...)`: Unknown column type for prepare: GEOMETRY
i Context: rapi_prepare
Backtrace:
▆
1. ├─duckspatial::ddbs_read_vector(conn, "view_test", crs = 4326) at test-compatibility.R:28:5
2. │ ├─DBI::dbListFields(conn, name_list$query_name)
3. │ └─DBI::dbListFields(conn, name_list$query_name)
4. │ ├─DBI::dbGetQuery(...)
5. │ └─DBI::dbGetQuery(...)
6. │ └─DBI (local) .local(conn, statement, ...)
7. │ ├─DBI::dbSendQuery(conn, statement, ...)
8. │ └─duckdb::dbSendQuery(conn, statement, ...)
9. │ └─duckdb (local) .local(conn, statement, ...)
10. │ └─duckdb:::rethrow_rapi_prepare(conn@conn_ref, statement, env)
11. │ ├─rlang::try_fetch(...)
12. │ │ ├─base::tryCatch(...)
13. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
14. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
15. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
16. │ │ └─base::withCallingHandlers(...)
17. │ └─duckdb:::rapi_prepare(conn, query, env)
18. ├─duckdb (local) `<fn>`("rapi_prepare", "Unknown column type for prepare: GEOMETRY")
19. │ └─rlang::abort(error_parts, class = "duckdb_error", !!!fields)
20. │ └─rlang:::signal_abort(cnd, .file)
21. │ └─base::signalCondition(cnd)
22. └─rlang (local) `<fn>`(`<dckdb_rr>`)
23. └─handlers[[1L]](cnd)
24. └─duckdb:::rethrow_error_from_rapi(e, call)
25. └─rlang::abort(msg, call = call)
── Error ('test-compatibility.R:63:9'): Round trip: write -> read for various geometry types ──
Error in `get_geom_name(conn, name_list$query_name)`: The table <rt_write_line> does not exist.
Backtrace:
▆
1. └─duckspatial::ddbs_read_vector(conn, table_name) at test-compatibility.R:63:9
2. └─duckspatial:::get_geom_name(conn, name_list$query_name)
3. └─cli::cli_abort("The table <{x}> does not exist.")
4. └─rlang::abort(...)
── Error ('test-compatibility.R:92:9'): Round trip: register -> read for various geometry types ──
Error in `dbSendQuery(conn, statement, ...)`: Unknown column type for prepare: GEOMETRY
i Context: rapi_prepare
Backtrace:
▆
1. ├─duckspatial::ddbs_read_vector(conn, view_name) at test-compatibility.R:92:9
2. │ ├─DBI::dbListFields(conn, name_list$query_name)
3. │ └─DBI::dbListFields(conn, name_list$query_name)
4. │ ├─DBI::dbGetQuery(...)
5. │ └─DBI::dbGetQuery(...)
6. │ └─DBI (local) .local(conn, statement, ...)
7. │ ├─DBI::dbSendQuery(conn, statement, ...)
8. │ └─duckdb::dbSendQuery(conn, statement, ...)
9. │ └─duckdb (local) .local(conn, statement, ...)
10. │ └─duckdb:::rethrow_rapi_prepare(conn@conn_ref, statement, env)
11. │ ├─rlang::try_fetch(...)
12. │ │ ├─base::tryCatch(...)
13. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
14. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
15. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
16. │ │ └─base::withCallingHandlers(...)
17. │ └─duckdb:::rapi_prepare(conn, query, env)
18. ├─duckdb (local) `<fn>`("rapi_prepare", "Unknown column type for prepare: GEOMETRY")
19. │ └─rlang::abort(error_parts, class = "duckdb_error", !!!fields)
20. │ └─rlang:::signal_abort(cnd, .file)
21. │ └─base::signalCondition(cnd)
22. └─rlang (local) `<fn>`(`<dckdb_rr>`)
23. └─handlers[[1L]](cnd)
24. └─duckdb:::rethrow_error_from_rapi(e, call)
25. └─rlang::abort(msg, call = call)
── Error ('test-compatibility.R:112:5'): Compatibility: Writing from file path and reading back ──
Error in `get_geom_name(conn, name_list$query_name)`: The table <countries_from_file_compat> does not exist.
Backtrace:
▆
1. └─duckspatial::ddbs_read_vector(conn, table_name) at test-compatibility.R:112:5
2. └─duckspatial:::get_geom_name(conn, name_list$query_name)
3. └─cli::cli_abort("The table <{x}> does not exist.")
4. └─rlang::abort(...)
[ FAIL 4 | WARN 1 | SKIP 17 | PASS 3 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.9.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'aw_interpolation.Rmd' using rmarkdown
Quitting from aw_interpolation.Rmd:67-78 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `get_geom_name()`:
! The table <temp_view_88b435b9_c66c_4621_a265_423bc1960d0f> does not
exist.
---
Backtrace:
▆
1. └─duckspatial::ddbs_interpolate_aw(...)
2. └─duckspatial:::get_geom_name(conn, t_list$query_name)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'aw_interpolation.Rmd' failed with diagnostics:
The table <temp_view_88b435b9_c66c_4621_a265_423bc1960d0f> does not
exist.
--- failed re-building 'aw_interpolation.Rmd'
--- re-building 'benchmark.Rmd' using rmarkdown
--- finished re-building 'benchmark.Rmd'
--- re-building 'duckspatial.Rmd' using rmarkdown
--- finished re-building 'duckspatial.Rmd'
--- re-building 'spatial_joins.Rmd' using rmarkdown
--- finished re-building 'spatial_joins.Rmd'
SUMMARY: processing the following file failed:
'aw_interpolation.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.9.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [9s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(duckspatial)
Important: 'crs_column' and 'crs' arguments are deprecated and will be removed in the next version.
If possible, use the default values of these arguments to avoid future issues.
> library(duckdb)
Loading required package: DBI
>
> test_check("duckspatial")
Reading layer `countries' from data source
`/home/hornik/tmp/R.check/r-patched-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-patched-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
Reading layer `rivers' from data source
`/home/hornik/tmp/R.check/r-patched-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
v Temporary view view_test registered
Saving _problems/test-compatibility-28.R
i Table <rt_write_line> dropped
v Table rt_write_line successfully imported
Saving _problems/test-compatibility-63.R
v Temporary view rt_register_line registered
Saving _problems/test-compatibility-92.R
i Table <countries_from_file_compat> dropped
v Table countries_from_file_compat successfully imported
Saving _problems/test-compatibility-112.R
[ FAIL 4 | WARN 1 | SKIP 17 | PASS 3 ]
══ Skipped tests (17) ══════════════════════════════════════════════════════════
• On CRAN (17): 'test-db_read.R:2:1', 'test-db_register.R:3:1',
'test-db_write.R:3:1', 'test-ddbs_area.R:3:1', 'test-ddbs_bbox.R:3:1',
'test-ddbs_combine.R:3:1', 'test-ddbs_concave_hull.R:3:1',
'test-ddbs_convex_hull.R:3:1', 'test-ddbs_distance.R:3:1',
'test-ddbs_envelope.R:3:1', 'test-ddbs_generate_points.R:5:1',
'test-ddbs_interpolate_aw.R:2:1', 'test-ddbs_join.R:3:1',
'test-ddbs_length.R:3:1', 'test-ddbs_transform.R:5:1',
'test-ddbs_union.R:3:1', 'test-utils.R:2:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-compatibility.R:28:5'): Compatibility: Arrow Views behave like Persistent Tables ──
Error in `dbSendQuery(conn, statement, ...)`: Unknown column type for prepare: GEOMETRY
i Context: rapi_prepare
Backtrace:
▆
1. ├─duckspatial::ddbs_read_vector(conn, "view_test", crs = 4326) at test-compatibility.R:28:5
2. │ ├─DBI::dbListFields(conn, name_list$query_name)
3. │ └─DBI::dbListFields(conn, name_list$query_name)
4. │ ├─DBI::dbGetQuery(...)
5. │ └─DBI::dbGetQuery(...)
6. │ └─DBI (local) .local(conn, statement, ...)
7. │ ├─DBI::dbSendQuery(conn, statement, ...)
8. │ └─duckdb::dbSendQuery(conn, statement, ...)
9. │ └─duckdb (local) .local(conn, statement, ...)
10. │ └─duckdb:::rethrow_rapi_prepare(conn@conn_ref, statement, env)
11. │ ├─rlang::try_fetch(...)
12. │ │ ├─base::tryCatch(...)
13. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
14. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
15. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
16. │ │ └─base::withCallingHandlers(...)
17. │ └─duckdb:::rapi_prepare(conn, query, env)
18. ├─duckdb (local) `<fn>`("rapi_prepare", "Unknown column type for prepare: GEOMETRY")
19. │ └─rlang::abort(error_parts, class = "duckdb_error", !!!fields)
20. │ └─rlang:::signal_abort(cnd, .file)
21. │ └─base::signalCondition(cnd)
22. └─rlang (local) `<fn>`(`<dckdb_rr>`)
23. └─handlers[[1L]](cnd)
24. └─duckdb:::rethrow_error_from_rapi(e, call)
25. └─rlang::abort(msg, call = call)
── Error ('test-compatibility.R:63:9'): Round trip: write -> read for various geometry types ──
Error in `get_geom_name(conn, name_list$query_name)`: The table <rt_write_line> does not exist.
Backtrace:
▆
1. └─duckspatial::ddbs_read_vector(conn, table_name) at test-compatibility.R:63:9
2. └─duckspatial:::get_geom_name(conn, name_list$query_name)
3. └─cli::cli_abort("The table <{x}> does not exist.")
4. └─rlang::abort(...)
── Error ('test-compatibility.R:92:9'): Round trip: register -> read for various geometry types ──
Error in `dbSendQuery(conn, statement, ...)`: Unknown column type for prepare: GEOMETRY
i Context: rapi_prepare
Backtrace:
▆
1. ├─duckspatial::ddbs_read_vector(conn, view_name) at test-compatibility.R:92:9
2. │ ├─DBI::dbListFields(conn, name_list$query_name)
3. │ └─DBI::dbListFields(conn, name_list$query_name)
4. │ ├─DBI::dbGetQuery(...)
5. │ └─DBI::dbGetQuery(...)
6. │ └─DBI (local) .local(conn, statement, ...)
7. │ ├─DBI::dbSendQuery(conn, statement, ...)
8. │ └─duckdb::dbSendQuery(conn, statement, ...)
9. │ └─duckdb (local) .local(conn, statement, ...)
10. │ └─duckdb:::rethrow_rapi_prepare(conn@conn_ref, statement, env)
11. │ ├─rlang::try_fetch(...)
12. │ │ ├─base::tryCatch(...)
13. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
14. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
15. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
16. │ │ └─base::withCallingHandlers(...)
17. │ └─duckdb:::rapi_prepare(conn, query, env)
18. ├─duckdb (local) `<fn>`("rapi_prepare", "Unknown column type for prepare: GEOMETRY")
19. │ └─rlang::abort(error_parts, class = "duckdb_error", !!!fields)
20. │ └─rlang:::signal_abort(cnd, .file)
21. │ └─base::signalCondition(cnd)
22. └─rlang (local) `<fn>`(`<dckdb_rr>`)
23. └─handlers[[1L]](cnd)
24. └─duckdb:::rethrow_error_from_rapi(e, call)
25. └─rlang::abort(msg, call = call)
── Error ('test-compatibility.R:112:5'): Compatibility: Writing from file path and reading back ──
Error in `get_geom_name(conn, name_list$query_name)`: The table <countries_from_file_compat> does not exist.
Backtrace:
▆
1. └─duckspatial::ddbs_read_vector(conn, table_name) at test-compatibility.R:112:5
2. └─duckspatial:::get_geom_name(conn, name_list$query_name)
3. └─cli::cli_abort("The table <{x}> does not exist.")
4. └─rlang::abort(...)
[ FAIL 4 | WARN 1 | SKIP 17 | PASS 3 ]
Error:
! Test failures.
Execution halted
Flavor: r-patched-linux-x86_64
Version: 0.9.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘aw_interpolation.Rmd’ using rmarkdown
Quitting from aw_interpolation.Rmd:67-78 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `get_geom_name()`:
! The table <temp_view_92cee292_3158_4205_92a1_916d96c236f4> does not
exist.
---
Backtrace:
▆
1. └─duckspatial::ddbs_interpolate_aw(...)
2. └─duckspatial:::get_geom_name(conn, t_list$query_name)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'aw_interpolation.Rmd' failed with diagnostics:
The table <temp_view_92cee292_3158_4205_92a1_916d96c236f4> does not
exist.
--- failed re-building ‘aw_interpolation.Rmd’
--- re-building ‘benchmark.Rmd’ using rmarkdown
--- finished re-building ‘benchmark.Rmd’
--- re-building ‘duckspatial.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘duckspatial.Rmd’
--- re-building ‘spatial_joins.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘spatial_joins.Rmd’
SUMMARY: processing the following file failed:
‘aw_interpolation.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-patched-linux-x86_64
Version: 0.9.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [9s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(duckspatial)
Important: 'crs_column' and 'crs' arguments are deprecated and will be removed in the next version.
If possible, use the default values of these arguments to avoid future issues.
> library(duckdb)
Loading required package: DBI
>
> test_check("duckspatial")
Reading layer `countries' from data source
`/home/hornik/tmp/R.check/r-release-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-release-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
Reading layer `rivers' from data source
`/home/hornik/tmp/R.check/r-release-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
v Temporary view view_test registered
v Arrow view view_test successfully imported.
i Table <table_test> dropped
v Table table_test successfully imported
v table table_test successfully imported.
i Table <rt_write_line> dropped
v Table rt_write_line successfully imported
v table rt_write_line successfully imported.
i Table <rt_write_polygon> dropped
v Table rt_write_polygon successfully imported
v table rt_write_polygon successfully imported.
i Table <rt_write_multipoint> dropped
v Table rt_write_multipoint successfully imported
v table rt_write_multipoint successfully imported.
v Temporary view rt_register_line registered
v Arrow view rt_register_line successfully imported.
v Temporary view rt_register_polygon registered
v Arrow view rt_register_polygon successfully imported.
v Temporary view rt_register_multipoint registered
v Arrow view rt_register_multipoint successfully imported.
i Table <countries_from_file_compat> dropped
v Table countries_from_file_compat successfully imported
Saving _problems/test-compatibility-112.R
[ FAIL 1 | WARN 2 | SKIP 17 | PASS 31 ]
══ Skipped tests (17) ══════════════════════════════════════════════════════════
• On CRAN (17): 'test-db_read.R:2:1', 'test-db_register.R:3:1',
'test-db_write.R:3:1', 'test-ddbs_area.R:3:1', 'test-ddbs_bbox.R:3:1',
'test-ddbs_combine.R:3:1', 'test-ddbs_concave_hull.R:3:1',
'test-ddbs_convex_hull.R:3:1', 'test-ddbs_distance.R:3:1',
'test-ddbs_envelope.R:3:1', 'test-ddbs_generate_points.R:5:1',
'test-ddbs_interpolate_aw.R:2:1', 'test-ddbs_join.R:3:1',
'test-ddbs_length.R:3:1', 'test-ddbs_transform.R:5:1',
'test-ddbs_union.R:3:1', 'test-utils.R:2:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-compatibility.R:112:5'): Compatibility: Writing from file path and reading back ──
Error in `ddbs_read_vector(conn, table_name)`: Geometry column wasn't found in table <countries_from_file_compat>.
Backtrace:
▆
1. └─duckspatial::ddbs_read_vector(conn, table_name) at test-compatibility.R:112:5
2. └─cli::cli_abort("Geometry column wasn't found in table <{name_list$query_name}>.")
3. └─rlang::abort(...)
[ FAIL 1 | WARN 2 | SKIP 17 | PASS 31 ]
Error:
! Test failures.
Execution halted
Flavor: r-release-linux-x86_64
Version: 0.9.0
Check: tests
Result: ERROR
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(duckspatial)
Important: 'crs_column' and 'crs' arguments are deprecated and will be removed in the next version.
If possible, use the default values of these arguments to avoid future issues.
> library(duckdb)
Loading required package: DBI
>
> test_check("duckspatial")
Reading layer `countries' from data source
`D:\RCompile\CRANpkg\lib\4.5\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
`D:\RCompile\CRANpkg\lib\4.5\duckspatial\spatial\argentina.geojson'
using driver `GeoJSON'
Simple feature collection with 1 feature and 6 fields
Geometry type: POLYGON
Dimension: XY
Bounding box: xmin: -73.52455 ymin: -52.39755 xmax: -53.62409 ymax: -21.81793
Geodetic CRS: WGS 84
Reading layer `rivers' from data source
`D:\RCompile\CRANpkg\lib\4.5\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
v Temporary view view_test registered
v Arrow view view_test successfully imported.
i Table <table_test> dropped
v Table table_test successfully imported
v table table_test successfully imported.
i Table <rt_write_line> dropped
v Table rt_write_line successfully imported
v table rt_write_line successfully imported.
i Table <rt_write_polygon> dropped
v Table rt_write_polygon successfully imported
v table rt_write_polygon successfully imported.
i Table <rt_write_multipoint> dropped
v Table rt_write_multipoint successfully imported
v table rt_write_multipoint successfully imported.
v Temporary view rt_register_line registered
v Arrow view rt_register_line successfully imported.
v Temporary view rt_register_polygon registered
v Arrow view rt_register_polygon successfully imported.
v Temporary view rt_register_multipoint registered
v Arrow view rt_register_multipoint successfully imported.
i Table <countries_from_file_compat> dropped
v Table countries_from_file_compat successfully imported
Saving _problems/test-compatibility-112.R
[ FAIL 1 | WARN 2 | SKIP 17 | PASS 31 ]
══ Skipped tests (17) ══════════════════════════════════════════════════════════
• On CRAN (17): 'test-db_read.R:2:1', 'test-db_register.R:3:1',
'test-db_write.R:3:1', 'test-ddbs_area.R:3:1', 'test-ddbs_bbox.R:3:1',
'test-ddbs_combine.R:3:1', 'test-ddbs_concave_hull.R:3:1',
'test-ddbs_convex_hull.R:3:1', 'test-ddbs_distance.R:3:1',
'test-ddbs_envelope.R:3:1', 'test-ddbs_generate_points.R:5:1',
'test-ddbs_interpolate_aw.R:2:1', 'test-ddbs_join.R:3:1',
'test-ddbs_length.R:3:1', 'test-ddbs_transform.R:5:1',
'test-ddbs_union.R:3:1', 'test-utils.R:2:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-compatibility.R:112:5'): Compatibility: Writing from file path and reading back ──
Error in `ddbs_read_vector(conn, table_name)`: Geometry column wasn't found in table <countries_from_file_compat>.
Backtrace:
▆
1. └─duckspatial::ddbs_read_vector(conn, table_name) at test-compatibility.R:112:5
2. └─cli::cli_abort("Geometry column wasn't found in table <{name_list$query_name}>.")
3. └─rlang::abort(...)
[ FAIL 1 | WARN 2 | SKIP 17 | PASS 31 ]
Error:
! Test failures.
Execution halted
Flavor: r-release-windows-x86_64
Version: 0.9.0
Check: tests
Result: ERROR
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(duckspatial)
Important: 'crs_column' and 'crs' arguments are deprecated and will be removed in the next version.
If possible, use the default values of these arguments to avoid future issues.
> library(duckdb)
Loading required package: DBI
>
> test_check("duckspatial")
Reading layer `countries' from data source
`D:\RCompile\CRANpkg\lib\4.4\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
`D:\RCompile\CRANpkg\lib\4.4\duckspatial\spatial\argentina.geojson'
using driver `GeoJSON'
Simple feature collection with 1 feature and 6 fields
Geometry type: POLYGON
Dimension: XY
Bounding box: xmin: -73.52455 ymin: -52.39755 xmax: -53.62409 ymax: -21.81793
Geodetic CRS: WGS 84
Reading layer `rivers' from data source
`D:\RCompile\CRANpkg\lib\4.4\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
v Temporary view view_test registered
v Arrow view view_test successfully imported.
i Table <table_test> dropped
v Table table_test successfully imported
v table table_test successfully imported.
i Table <rt_write_line> dropped
v Table rt_write_line successfully imported
v table rt_write_line successfully imported.
i Table <rt_write_polygon> dropped
v Table rt_write_polygon successfully imported
v table rt_write_polygon successfully imported.
i Table <rt_write_multipoint> dropped
v Table rt_write_multipoint successfully imported
v table rt_write_multipoint successfully imported.
v Temporary view rt_register_line registered
v Arrow view rt_register_line successfully imported.
v Temporary view rt_register_polygon registered
v Arrow view rt_register_polygon successfully imported.
v Temporary view rt_register_multipoint registered
v Arrow view rt_register_multipoint successfully imported.
i Table <countries_from_file_compat> dropped
v Table countries_from_file_compat successfully imported
Saving _problems/test-compatibility-112.R
[ FAIL 1 | WARN 2 | SKIP 17 | PASS 31 ]
══ Skipped tests (17) ══════════════════════════════════════════════════════════
• On CRAN (17): 'test-db_read.R:2:1', 'test-db_register.R:3:1',
'test-db_write.R:3:1', 'test-ddbs_area.R:3:1', 'test-ddbs_bbox.R:3:1',
'test-ddbs_combine.R:3:1', 'test-ddbs_concave_hull.R:3:1',
'test-ddbs_convex_hull.R:3:1', 'test-ddbs_distance.R:3:1',
'test-ddbs_envelope.R:3:1', 'test-ddbs_generate_points.R:5:1',
'test-ddbs_interpolate_aw.R:2:1', 'test-ddbs_join.R:3:1',
'test-ddbs_length.R:3:1', 'test-ddbs_transform.R:5:1',
'test-ddbs_union.R:3:1', 'test-utils.R:2:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-compatibility.R:112:5'): Compatibility: Writing from file path and reading back ──
Error in `ddbs_read_vector(conn, table_name)`: Geometry column wasn't found in table <countries_from_file_compat>.
Backtrace:
▆
1. └─duckspatial::ddbs_read_vector(conn, table_name) at test-compatibility.R:112:5
2. └─cli::cli_abort("Geometry column wasn't found in table <{name_list$query_name}>.")
3. └─rlang::abort(...)
[ FAIL 1 | WARN 2 | SKIP 17 | PASS 31 ]
Error:
! Test failures.
Execution halted
Flavor: r-oldrel-windows-x86_64
Current CRAN status: OK: 14
Current CRAN status: ERROR: 1, OK: 13
Version: 1.6.0
Check: package dependencies
Result: ERROR
Package required but not available: ‘RPostgreSQL’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-devel-macos-arm64
Current CRAN status: OK: 14