Last updated on 2026-06-22 01:51:10 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.1 | 11.53 | 178.94 | 190.47 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.1.1 | 9.03 | 117.45 | 126.48 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.1.1 | 24.00 | 265.45 | 289.45 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 1.1.1 | 23.00 | 312.60 | 335.60 | ERROR | |
| r-devel-windows-x86_64 | 1.1.1 | 17.00 | 196.00 | 213.00 | OK | |
| r-patched-linux-x86_64 | 1.1.1 | 13.27 | 172.74 | 186.01 | OK | |
| r-release-linux-x86_64 | 1.1.1 | 11.78 | 154.27 | 166.05 | ERROR | |
| r-release-macos-arm64 | 1.1.1 | 3.00 | 47.00 | 50.00 | OK | |
| r-release-macos-x86_64 | 1.1.1 | 9.00 | 146.00 | 155.00 | OK | |
| r-release-windows-x86_64 | 1.1.1 | 16.00 | 189.00 | 205.00 | ERROR | |
| r-oldrel-macos-arm64 | 1.1.1 | 3.00 | 48.00 | 51.00 | OK | |
| r-oldrel-macos-x86_64 | 1.1.1 | 9.00 | 130.00 | 139.00 | OK | |
| r-oldrel-windows-x86_64 | 1.1.1 | 23.00 | 238.00 | 261.00 | OK |
Version: 1.1.1
Check: examples
Result: ERROR
Running examples in ‘duckspatial-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ddbs_install
> ### Title: Checks and installs the Spatial extension
> ### Aliases: ddbs_install
>
> ### ** Examples
>
> ## load packages
> library(duckspatial)
> library(duckdb)
Loading required package: DBI
>
> # connect to in memory database
> conn <- duckdb::dbConnect(duckdb::duckdb())
>
> # install the spatial extension
> ddbs_install(conn)
Error in `ddbs_install()`:
! Failed to install the spatial extension.
ℹ It could not be found in the core or community repositories.
ℹ Check that the extension name is correct:
<https://duckdb.org/docs/extensions/overview>
Backtrace:
▆
1. └─duckspatial::ddbs_install(conn)
2. └─cli::cli_abort(...)
3. └─rlang::abort(...)
Execution halted
Flavors: r-devel-linux-x86_64-debian-gcc, r-release-linux-x86_64
Version: 1.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [5s/5s]
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 1.1.1 attached
* Compatible with DuckDB >= v1.5.1
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(duckspatial.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
Error in `source_dir()`:
! Failed to evaluate './setup.R'.
Caused by error in `ddbs_install()`:
! Failed to install the spatial extension.
ℹ It could not be found in the core or community repositories.
ℹ Check that the extension name is correct:
<https://duckdb.org/docs/extensions/overview>
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_install(conn, upgrade = upgrade, quiet = TRUE)
19. └─cli::cli_abort(...)
20. └─rlang::abort(...)
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.1.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘aw_interpolation.qmd’ using html
<1b>[31m
processing file: aw_interpolation.qmd
<1b>[39m<1b>[31mError in `ddbs_install()`:
! Failed to install the spatial extension.
ℹ It could not be found in the core or community repositories.
ℹ Check that the extension name is correct:
<https://duckdb.org/docs/extensions/overview>
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_install(conn, upgrade = upgrade, quiet = TRUE)
6. └─cli::cli_abort(...)
7. └─rlang::abort(...)
<1b>[39m<1b>[31m
Quitting from aw_interpolation.qmd:68-79 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<1b>[39m<1b>[31m~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `ddbs_install()`:
! Failed to install the spatial extension.
ℹ It could not be<1b>[39m<1b>[31m found in the core or community repositories.
ℹ Check that the extension name is correct:
<https://duckdb.org/docs/extension<1b>[39m<1b>[31ms/overview>
---
Backtrace:
▆
1. └─duckspatial::ddbs_interpolate_aw(...)
2. └─duckspatial:::resolve_spatial_con<1b>[39m<1b>[31mnections(...)
3. └─duckspatial:::ddbs_default_conn()
4. └─duckspatial::ddbs_create_conn(dbdir = "memory", ..<1b>[39m<1b>[31m.)
5. └─duckspatial::ddbs_install(conn, upgrade = upgrade, quiet = TRUE)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<1b>[39m<1b>[31m~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<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 `ddbs_install()`:<1b>[39m
! Failed to install the spatial extension.
ℹ It could not be found in the core or community repositories.
ℹ Check that the extension name is correct:
<https://duckdb.org/docs/extensions/overview>
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_install(conn, upgrade = upgrade, quiet = TRUE)
6. └─cli::cli_abort(...)
7. └─rlang::abort(...)
Quitting from aw_interpolation.qmd:68-79 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<1b>[31m~~~~~~~~~~~~~~~~~~<1b>[39m
<error/rlang_error>
Error in `ddbs_install()`:
! Failed to install the spatial extension.
ℹ It could not be<1b>[31m found in the core or community repositories.<1b>[39m
ℹ Check that the extension name is correct:
<https://duckdb.org/docs/extension<1b>[31ms/overview><1b>[39m
---
Backtrace:
▆
1. └─duckspatial::ddbs_interpolate_aw(...)
2. └─duckspatial:::resolve_spatial_con<1b>[31mnections(...)<1b>[39m
3. └─duckspatial:::ddbs_default_conn()
4. └─duckspatial::ddbs_create_conn(dbdir = "memory", ..<1b>[31m.)<1b>[39m
5. └─duckspatial::ddbs_install(conn, upgrade = upgrade, quiet = TRUE)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<1b>[31m~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<1b>[39m
<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
variables: {}
<1b>[1mmetadata<1b>[22m
document-css: false
lang: en
engines:
- path: /opt/quarto/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 `ddbs_install()`:
! Failed to install the spatial extension.
ℹ It could not be found in the core or community repositories.
ℹ Check that the extension name is correct:
<https://duckdb.org/docs/extensions/overview>
Backtrace:
▆
1. └─duckspatial::ddbs_open_dataset(...)
2. └─duckspatial:::ddbs_default_conn()
3. └─duckspatial::ddbs_create_conn(dbdir = "memory", ...)
4. └─duckspatial::ddbs_install(conn, upgrade = upgrade, quiet = TRUE)
5. └─cli::cli_abort(...)
6. └─rlang::abort(...)
<1b>[39m<1b>[31m
Quitting from duckspatial.qmd:68-77 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<1b>[39m<1b>[31m~~~~~~~~~~~~~
<error/rlang_error>
Error in `ddbs_install()`:
! Failed to install the spatial extension.
ℹ It could not be foun<1b>[39m<1b>[31md in the core or community repositories.
ℹ Check that the extension name is correct:
<https://duckdb.org/docs/extensions/overview>
---
Backtrace:
▆
1. └─duckspatial::ddbs_open_dataset(...)
2. └─duckspatial:::ddbs_default_conn()
3. └─duckspatial::ddbs_create_conn(dbdir = "memory", ...)
4. └─duckspatial::ddbs_install(conn, upgrade = upgrade, quiet = TRUE)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<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 `ddbs_install()`:<1b>[39m
! Failed to install the spatial extension.
ℹ It could not be found in the core or community repositories.
ℹ Check that the extension name is correct:
<https://duckdb.org/docs/extensions/overview>
Backtrace:
▆
1. └─duckspatial::ddbs_open_dataset(...)
2. └─duckspatial:::ddbs_default_conn()
3. └─duckspatial::ddbs_create_conn(dbdir = "memory", ...)
4. └─duckspatial::ddbs_install(conn, upgrade = upgrade, quiet = TRUE)
5. └─cli::cli_abort(...)
6. └─rlang::abort(...)
Quitting from duckspatial.qmd:68-77 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<1b>[31m~~~~~~~~~~~~~<1b>[39m
<error/rlang_error>
Error in `ddbs_install()`:
! Failed to install the spatial extension.
ℹ It could not be foun<1b>[31md in the core or community repositories.<1b>[39m
ℹ Check that the extension name is correct:
<https://duckdb.org/docs/extensions/overview>
---
Backtrace:
▆
1. └─duckspatial::ddbs_open_dataset(...)
2. └─duckspatial:::ddbs_default_conn()
3. └─duckspatial::ddbs_create_conn(dbdir = "memory", ...)
4. └─duckspatial::ddbs_install(conn, upgrade = upgrade, quiet = TRUE)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<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 `ddbs_install()`:
! Failed to install the spatial extension.
ℹ It could not be found in the core or community repositories.
ℹ Check that the extension name is correct:
<https://duckdb.org/docs/extensions/overview>
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_install(conn, upgrade = upgrade, quiet = TRUE)
6. └─cli::cli_abort(...)
7. └─rlang::abort(...)
<1b>[39m<1b>[31m
Quitting from spatial_joins.qmd:67-77 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<1b>[39m<1b>[31m~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `ddbs_install()`:
! Failed to install the spatial extension.
ℹ It could not be found in the core or community repositories.
ℹ Check that the extension name is correct:
<https://duckdb.org/docs/extensions/overview>
---
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_install(conn, upgrade = upgrade, quiet = TRUE)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 `ddbs_install()`:<1b>[39m
! Failed to install the spatial extension.
ℹ It could not be found in the core or community repositories.
ℹ Check that the extension name is correct:
<https://duckdb.org/docs/extensions/overview>
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_install(conn, upgrade = upgrade, quiet = TRUE)
6. └─cli::cli_abort(...)
7. └─rlang::abort(...)
Quitting from spatial_joins.qmd:67-77 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<1b>[31m~~~~~~~~~~~~~~~<1b>[39m
<error/rlang_error>
Error in `ddbs_install()`:
! Failed to install the spatial extension.
ℹ It could not be found in the core or community repositories.
ℹ Check that the extension name is correct:
<https://duckdb.org/docs/extensions/overview>
---
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_install(conn, upgrade = upgrade, quiet = TRUE)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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-debian-gcc
Version: 1.1.1
Check: examples
Result: ERROR
Running examples in ‘duckspatial-Ex.R’ failed
The error most likely occurred in:
> ### Name: ddbs_install
> ### Title: Checks and installs the Spatial extension
> ### Aliases: ddbs_install
>
> ### ** Examples
>
> ## load packages
> library(duckspatial)
> library(duckdb)
Loading required package: DBI
>
> # connect to in memory database
> conn <- duckdb::dbConnect(duckdb::duckdb())
>
> # install the spatial extension
> ddbs_install(conn)
ℹ spatial extension version "b68b309" is already installed. Use `upgrade = TRUE` to upgrade.
>
> # install the h3 community extension
> ddbs_install(conn, extension = "h3")
Error in `ddbs_install()`:
! Failed to install the h3 extension.
ℹ It could not be found in the core or community repositories.
ℹ Check that the extension name is correct:
<https://duckdb.org/docs/extensions/overview>
Backtrace:
▆
1. └─duckspatial::ddbs_install(conn, extension = "h3")
2. └─cli::cli_abort(...)
3. └─rlang::abort(...)
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-release-windows-x86_64
Version: 1.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [7s/28s]
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 1.1.1 attached
* Compatible with DuckDB >= v1.5.1
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(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
[gannet:1731932:0:1736875] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x449)
==== backtrace (tid:1736875) ====
0 /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7f5c080e3df4]
1 /lib64/libucs.so.0(+0x17aed) [0x7f5c080e5aed]
2 /lib64/libucs.so.0(+0x17cbd) [0x7f5c080e5cbd]
3 /lib64/libc.so.6(+0x1a040) [0x7f5c1e128040]
4 /data/gannet/ripley/R/test-clang/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x1196990) [0x7f5ad8b96990]
5 /data/gannet/ripley/R/test-clang/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x1168568) [0x7f5ad8b68568]
6 /data/gannet/ripley/R/test-clang/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x773384) [0x7f5ad8173384]
7 /data/gannet/ripley/R/test-clang/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x771719) [0x7f5ad8171719]
8 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper29LoadExternalExtensionInternalERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEERNS_19ExtensionActiveLoadE+0x18f) [0x7f5b4147f85f]
9 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper21LoadExternalExtensionERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEE+0x4a) [0x7f5b4147f60a]
10 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZNK6duckdb12PhysicalLoad15GetDataInternalERNS_16ExecutionContextERNS_9DataChunkERNS_19OperatorSourceInputE+0x151) [0x7f5b4226d401]
11 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor15FetchFromSourceERNS_9DataChunkE+0x98) [0x7f5b42aa10c8]
12 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor7ExecuteEm+0x146) [0x7f5b42a9dca6]
13 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12PipelineTask11ExecuteTaskENS_17TaskExecutionModeE+0x154) [0x7f5b42a9d914]
14 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12ExecutorTask7ExecuteENS_17TaskExecutionModeE+0xa0) [0x7f5b42a97570]
15 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb13TaskScheduler14ExecuteForeverEPNSt3__16atomicIbEE+0x39a) [0x7f5b42aa432a]
16 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(+0x1aafe9c) [0x7f5b42aafe9c]
17 /lib64/libc.so.6(+0x71f14) [0x7f5c1e17ff14]
18 /lib64/libc.so.6(+0xf532c) [0x7f5c1e20332c]
=================================
*** caught segfault ***
address 0x4d2001a6d5c, 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: as_duckspatial_df.sf(argentina_sf)
24: duckspatial::as_duckspatial_df(argentina_sf)
25: eval(exprs, env)
26: eval(exprs, env)
27: withCallingHandlers(invisible(eval(exprs, env)), error = function(err) { cli::cli_abort("Failed to evaluate {.path {path}}.", parent = err, call = error_call)})
28: source_file(path, env = env, chdir = chdir, wrap = wrap, shuffle = shuffle, error_call = error_call)
29: FUN(X[[i]], ...)
30: lapply(files, function(path) { source_file(path, env = env, chdir = chdir, wrap = wrap, shuffle = shuffle, error_call = error_call)})
31: source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)
32: source_test_setup(".", env)
33: test_files_setup_state(test_dir, test_package, load_helpers, env)
34: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call)
35: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle)
36: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
37: test_check("duckspatial")
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.1.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘aw_interpolation.qmd’ using html
<1b>[31m
processing file: aw_interpolation.qmd
<1b>[39m<1b>[31m[gannet:1739982:0:1739982] Caught signal 11 (Segmentation fault: Sent by the kernel at address (nil))
<1b>[39m<1b>[31m==== backtrace (tid:1739982) ====
0 /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7fa67dae3df4]
1 /lib64/libucs.so.0(+0x17aed) [0x7fa67dae5aed]
2 /lib64/libucs.so.0(+0x17cbd) [0x7fa67dae5cbd]
3 /lib64/libc.so.6(+0x1a040) [0x7fa694629040]
4 /data/gannet/ripley/R/test-clang/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x1196990) [0x7fa4ccb96990]
5 /data/gannet/ripley/R/test-clang/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x1168568) [0x7fa4ccb68568]
6 /data/gannet/ripley/R/test-clang/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x773384) [0x7fa4cc173384]
7 /data/gannet/ripley/R/test-clang/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x771719) [0x7fa4cc171719]
8 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper29LoadExternalExtensionInternalERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEERNS_19ExtensionActiveLoadE+0x18f) [0x7fa5b6e7f85f]
9 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper21LoadExternalExtensionERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEE+0x4a) [0x7fa5b6e7f60a]
10 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZNK6duckdb12PhysicalLoad15GetDataInternalERNS_16ExecutionContextERNS_9DataChunkERNS_19OperatorSourceInputE+0x151) [0x7fa5b7c6d401]
11 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor15FetchFromSourceERNS_9DataChunkE+0x98) [0x7fa5b84a10c8]
12 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor7ExecuteEm+0x146) [0x7fa5b849dca6]
13 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12PipelineTask11ExecuteTaskENS_17TaskExecutionModeE+0x112) [0x7fa5b849d8d2]
14 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12ExecutorTask7ExecuteENS_17TaskExecutionModeE+0xa0) [0x7fa5b8497570]
15 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb8Executor11ExecuteTaskEb+0x1c0) [0x7fa5b849c8d0]
16 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb13ClientContext19ExecuteTaskInternalERNS_17ClientContextLockERNS_15BaseQueryResultEb+0x40) [0x7fa5b82a8c60]
17 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb18PendingQueryResult15ExecuteInternalERNS_17ClientContextLockE+0x7a) [0x7fa5b82ab3ba]
18 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb13ClientContext7ExecuteERKNSt3__112basic_stringIcNS1_11char_traitsIcEENS1_9allocatorIcEEEERNS_10shared_ptrINS_21PreparedStatementDataELb1EEERKNS_22PendingQueryParametersE+0xa0) [0x7fa5b82ab100]
19 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb17PreparedStatement7ExecuteERNSt3__113unordered_mapINS1_12basic_stringIcNS1_11char_traitsIcEENS1_9allocatorIcEEEENS_18BoundParameterDataENS_33CaseInsensitiveStringHashFunctionENS_29CaseInsensitiveStringEqualityENS6_INS1_4pairIKS8_S9_EEEEEEb+0x1c3) [0x7fa5b82ce3a3]
20 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb17PreparedStatement7ExecuteERNS_6vectorINS_5ValueELb1ENSt3__19allocatorIS2_EEEEb+0x172) [0x7fa5b82ce642]
21 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(+0x1087fc) [0x7fa5b6b087fc]
22 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_duckdb_rapi_execute+0x63) [0x7fa5b6b72f73]
23 /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8f524) [0x561bfaf47524]
24 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdae08) [0x561bfaf92e08]
25 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc918c) [0x561bfaf8118c]
26 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x561bfaf80945]
27 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc93e4) [0x561bfaf813e4]
28 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x26e) [0x561bfaf80a0e]
29 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc93e4) [0x561bfaf813e4]
30 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdcf10) [0x561bfaf94f10]
31 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcd5c9) [0x561bfaf855c9]
32 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc918c) [0x561bfaf8118c]
33 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x561bfaf80945]
34 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0aa9) [0x561bfaf98aa9]
35 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdff9b) [0x561bfaf97f9b]
36 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9867) [0x561bfaf81867]
37 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f8) [0x561bfaf80d98]
38 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc93e4) [0x561bfaf813e4]
39 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdcf10) [0x561bfaf94f10]
40 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcd5c9) [0x561bfaf855c9]
41 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc918c) [0x561bfaf8118c]
42 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x561bfaf80945]
43 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0aa9) [0x561bfaf98aa9]
44 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdff9b) [0x561bfaf97f9b]
45 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9867) [0x561bfaf81867]
46 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f8) [0x561bfaf80d98]
47 /data/gannet/ripley/R/test-clang/rlang/libs/rlang.so(+0x4983) [0x7fa6920b7983]
48 /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8d673) [0x561bfaf45673]
49 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcfbc4) [0x561bfaf87bc4]
50 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc918c) [0x561bfaf8118c]
51 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x561bfaf80945]
52 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0aa9) [0x561bfaf98aa9]
53 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdff9b) [0x561bfaf97f9b]
54 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9867) [0x561bfaf81867]
55 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f8) [0x561bfaf80d98]
56 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe5e08) [0x561bfaf9de08]
57 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x561bfaf80b70]
58 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe50fb) [0x561bfaf9d0fb]
59 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x561bfaf80b70]
60 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0aa9) [0x561bfaf98aa9]
61 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdff9b) [0x561bfaf97f9b]
=================================
*** caught segfault ***
address 0x4d2001a8cce, 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(target, source, conn, quiet = quiet)
24: ddbs_interpolate_aw(target = grid, source = nc, tid = "target_id", sid = "source_id", extensive = "BIR74", weight = "total", mode = "sf")
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 'aw_interpolation.qmd' failed with diagnostics:
! Error running quarto CLI from R.
Caused by error:
! Could not parse cli `{}` expression: ` { .__han…`.
Caused by error:
! <text>:1:49: unexpected symbol
1: { .__handler_frame__. <- TRUE .__setup_frame__.
^
--- failed re-building ‘aw_interpolation.qmd’
--- re-building ‘benchmark.qmd’ using html
<1b>[31m
processing file: benchmark.qmd
<1b>[39m<1b>[31moutput file: benchmark.knit.md
<1b>[39m<1b>[1mpandoc <1b>[22m
to: html
output-file: benchmark.html
standalone: true
embed-resources: true
wrap: none
default-image-extension: png
css:
- >-
/data/gannet/ripley/R/test-clang/quarto/rmarkdown/template/quarto_vignette/resources/vignette.css
variables: {}
<1b>[1mmetadata<1b>[22m
document-css: false
lang: en
engines:
- path: /data/gannet/ripley/Sources/quarto-1.9.36/share/extension-subtrees/julia-engine/_extensions/julia-engine/julia-engine.js
minimal: true
theme: none
title: Benchmark
date: '`r Sys.Date()`'
code-annotations: hover
urlcolor: blue
vignette: |
%\VignetteIndexEntry{Benchmark} %\VignetteEngine{quarto::html} %\VignetteEncoding{UTF-8}
knitr:
opts_chunk:
collapse: true
comment: '#>'
out.width: 100%
Output created: benchmark.html
--- finished re-building ‘benchmark.qmd’
--- re-building ‘duckspatial.qmd’ using html
<1b>[31m
processing file: duckspatial.qmd
<1b>[39m<1b>[31m[gannet:1750494:0:1751466] Caught signal 11 (Segmentation fault: address not mapped to object at address 0xe)
<1b>[39m<1b>[31m==== backtrace (tid:1751466) ====
0 /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7f80029b2df4]
1 /lib64/libucs.so.0(+0x17aed) [0x7f80029b4aed]
2 /lib64/libucs.so.0(+0x17cbd) [0x7f80029b4cbd]
3 /lib64/libc.so.6(+0x1a040) [0x7f801b429040]
4 /data/gannet/ripley/R/test-clang/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x1198570) [0x7f7ebcb98570]
5 /data/gannet/ripley/R/test-clang/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x1168568) [0x7f7ebcb68568]
6 /data/gannet/ripley/R/test-clang/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x773384) [0x7f7ebc173384]
7 /data/gannet/ripley/R/test-clang/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x771719) [0x7f7ebc171719]
8 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper29LoadExternalExtensionInternalERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEERNS_19ExtensionActiveLoadE+0x18f) [0x7f800667f85f]
9 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper21LoadExternalExtensionERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEE+0x4a) [0x7f800667f60a]
10 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZNK6duckdb12PhysicalLoad15GetDataInternalERNS_16ExecutionContextERNS_9DataChunkERNS_19OperatorSourceInputE+0x151) [0x7f800746d401]
11 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor15FetchFromSourceERNS_9DataChunkE+0x98) [0x7f8007ca10c8]
12 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor7ExecuteEm+0x146) [0x7f8007c9dca6]
13 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12PipelineTask11ExecuteTaskENS_17TaskExecutionModeE+0x154) [0x7f8007c9d914]
14 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12ExecutorTask7ExecuteENS_17TaskExecutionModeE+0xa0) [0x7f8007c97570]
15 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb13TaskScheduler14ExecuteForeverEPNSt3__16atomicIbEE+0x39a) [0x7f8007ca432a]
16 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(+0x1aafe9c) [0x7f8007cafe9c]
17 /lib64/libc.so.6(+0x71f14) [0x7f801b480f14]
18 /lib64/libc.so.6(+0xf532c) [0x7f801b50432c]
=================================
*** caught segfault ***
address 0x4d2001ab5de, 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$ref, duckdb_convert_opts_impl(res@connection@convert_opts, arrow = res@arrow))
9: duckdb_execute(res)
10: duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
11: .local(conn, statement, ...)
12: dbSendQuery(conn, statement, ...)
13: dbSendQuery(conn, statement, ...)
14: dbSendStatement(conn, statement, ...)
15: dbSendStatement(conn, statement, ...)
16: DBI::dbExecute(conn, glue::glue("LOAD {extension};"))
17: DBI::dbExecute(conn, glue::glue("LOAD {extension};"))
18: withCallingHandlers(expr, message = function(c) if (inherits(c, classes)) tryInvokeRestart("muffleMessage"))
19: suppressMessages(DBI::dbExecute(conn, glue::glue("LOAD {extension};")))
20: ddbs_load(conn, quiet = TRUE)
21: ddbs_create_conn(dbdir = "memory", ...)
22: ddbs_default_conn()
23: ddbs_open_dataset(system.file("spatial/countries.geojson", package = "duckspatial"))
24: eval(expr, envir)
25: eval(expr, envir)
26: withVisible(eval(expr, envir))
27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$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$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
28: eval(call)
29: eval(call)
30: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: evaluate::evaluate(...)
39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
40: in_dir(input_dir(), expr)
41: 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$render, options)))
42: eng_r(options)
43: block_exec(params)
44: call_block(x)
45: process_group(group)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
49: process_file(text, output)
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51: rmarkdown::render(input = input, output_format = output_format, knit_root_dir = knit_root_dir, params = params, run_pandoc = FALSE, envir = env)
52: execute(params$input, params$format, params$tempDir, params$libDir, params$dependencies, params$cwd, params$params, params$resourceDir, params$handledLanguages, params$markdown)
53: .main()
An irrecoverable exception occurred. R is aborting now ...
<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 parse cli `{}` expression: ` { .__han…`.
Caused by error:
! <text>:1:49: unexpected symbol
1: { .__handler_frame__. <- TRUE .__setup_frame__.
^
--- failed re-building ‘duckspatial.qmd’
--- re-building ‘spatial_joins.qmd’ using html
<1b>[31m
processing file: spatial_joins.qmd
<1b>[39m<1b>[31m[gannet:1754352:0:1756351] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x11d)
<1b>[39m<1b>[31m==== backtrace (tid:1756351) ====
0 /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7fdc845b7df4]
1 /lib64/libucs.so.0(+0x17aed) [0x7fdc845b9aed]
2 /lib64/libucs.so.0(+0x17cbd) [0x7fdc845b9cbd]
3 /lib64/libc.so.6(+0x1a040) [0x7fdc9ab28040]
4 /data/gannet/ripley/R/test-clang/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x1198570) [0x7fdb5cb98570]
5 /data/gannet/ripley/R/test-clang/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x1168568) [0x7fdb5cb68568]
6 /data/gannet/ripley/R/test-clang/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x773384) [0x7fdb5c173384]
7 /data/gannet/ripley/R/test-clang/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x771719) [0x7fdb5c171719]
8 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper29LoadExternalExtensionInternalERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEERNS_19ExtensionActiveLoadE+0x18f) [0x7fdbbd27f85f]
9 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper21LoadExternalExtensionERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEE+0x4a) [0x7fdbbd27f60a]
10 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZNK6duckdb12PhysicalLoad15GetDataInternalERNS_16ExecutionContextERNS_9DataChunkERNS_19OperatorSourceInputE+0x151) [0x7fdbbe06d401]
11 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor15FetchFromSourceERNS_9DataChunkE+0x98) [0x7fdbbe8a10c8]
12 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor7ExecuteEm+0x146) [0x7fdbbe89dca6]
13 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12PipelineTask11ExecuteTaskENS_17TaskExecutionModeE+0x154) [0x7fdbbe89d914]
14 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12ExecutorTask7ExecuteENS_17TaskExecutionModeE+0xa0) [0x7fdbbe897570]
15 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb13TaskScheduler14ExecuteForeverEPNSt3__16atomicIbEE+0x39a) [0x7fdbbe8a432a]
16 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(+0x1aafe9c) [0x7fdbbe8afe9c]
17 /lib64/libc.so.6(+0x71f14) [0x7fdc9ab7ff14]
18 /lib64/libc.so.6(+0xf532c) [0x7fdc9ac0332c]
=================================
*** caught segfault ***
address 0x4d2001ac4f0, 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: 1.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [5s/7s]
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 1.1.1 attached
* Compatible with DuckDB >= v1.5.1
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(duckspatial.mode = 'sf')
> 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
Error in `source_dir()`:
! Failed to evaluate './setup.R'.
Caused by error in `ddbs_install()`:
! Failed to install the spatial extension.
ℹ It could not be found in the core or community repositories.
ℹ Check that the extension name is correct:
<https://duckdb.org/docs/extensions/overview>
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_install(conn, upgrade = upgrade, quiet = TRUE)
19. └─cli::cli_abort(...)
20. └─rlang::abort(...)
Execution halted
Flavor: r-release-linux-x86_64
Version: 1.1.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘aw_interpolation.qmd’ using html
<1b>[31m
processing file: aw_interpolation.qmd
<1b>[39m<1b>[31mError in `ddbs_install()`:
! Failed to install the spatial extension.
ℹ It could not be found in the core or community reposit<1b>[39m<1b>[31mories.
ℹ Check that the extension name is correct:
<https://duckdb.org/docs/extensions/overview>
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_install(conn, upgrade = upgrade, quiet = TRUE)
6. └─cli::cli_abort(...)
7. └─rlang::abort(...)
<1b>[39m<1b>[31m
Quitting from aw_interpolation.qmd:68-79 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<1b>[39m<1b>[31m~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `ddbs_install()`:
! Failed to install the spatial extension.
ℹ It could not be found in the core or community repositories.
ℹ Check that the extension name is correct:
<https://duckdb.org/docs/extensions/overview>
---
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_install(conn, upgrade = upgrade, quiet = TRUE)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 `ddbs_install()`:<1b>[39m
! Failed to install the spatial extension.
ℹ It could not be found in the core or community reposit<1b>[31mories.<1b>[39m
ℹ Check that the extension name is correct:
<https://duckdb.org/docs/extensions/overview>
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_install(conn, upgrade = upgrade, quiet = TRUE)
6. └─cli::cli_abort(...)
7. └─rlang::abort(...)
Quitting from aw_interpolation.qmd:68-79 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<1b>[31m~~~~~~~~~~~~~~~~~~<1b>[39m
<error/rlang_error>
Error in `ddbs_install()`:
! Failed to install the spatial extension.
ℹ It could not be found in the core or community repositories.
ℹ Check that the extension name is correct:
<https://duckdb.org/docs/extensions/overview>
---
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_install(conn, upgrade = upgrade, quiet = TRUE)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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:
- >-
/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/quarto/rmarkdown/template/quarto_vignette/resources/vignette.css
variables: {}
<1b>[1mmetadata<1b>[22m
document-css: false
lang: en
engines:
- path: /opt/quarto/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 `ddbs_install()`:
! Failed to install the spatial extension.
ℹ It could not be found in the core or community repositories.
ℹ Check that the extension name is correct:
<https://duckdb.org/docs/extensions/overview>
Backtrace:
▆
1. └─duckspatial::ddbs_open_dataset(...)
2. └─duckspatial:::ddbs_default_conn()
3. └─duckspatial::ddbs_create_conn(dbdir = "memory", ...)
4. └─duckspatial::ddbs_install(conn, upgrade = upgrade, quiet = TRUE)
5. └─cli::cli_abort(...)
6. └─rlang::abort(...)
<1b>[39m<1b>[31m
Quitting from duckspatial.qmd:68-77 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<1b>[39m<1b>[31m~~~~~~~~~~~~~
<error/rlang_error>
Error in `ddbs_install()`:
! Failed to install the spatial extension.
ℹ It could not be foun<1b>[39m<1b>[31md in the core or community repositories.
ℹ Check that the extension name is correct:
<https://duckdb.org/docs/extensions/overview>
---
Backtrace:
▆
1. └─duckspatial::ddbs_open_dataset(...)
2. └─duckspatial:::ddbs_default_conn()
3. └─duckspatial::ddbs_create_conn(dbdir = "memory", ...)
4. └─duckspatial::ddbs_install(conn, upgrade = upgrade, quiet = TRUE)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 `ddbs_install()`:<1b>[39m
! Failed to install the spatial extension.
ℹ It could not be found in the core or community repositories.
ℹ Check that the extension name is correct:
<https://duckdb.org/docs/extensions/overview>
Backtrace:
▆
1. └─duckspatial::ddbs_open_dataset(...)
2. └─duckspatial:::ddbs_default_conn()
3. └─duckspatial::ddbs_create_conn(dbdir = "memory", ...)
4. └─duckspatial::ddbs_install(conn, upgrade = upgrade, quiet = TRUE)
5. └─cli::cli_abort(...)
6. └─rlang::abort(...)
Quitting from duckspatial.qmd:68-77 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<1b>[31m~~~~~~~~~~~~~<1b>[39m
<error/rlang_error>
Error in `ddbs_install()`:
! Failed to install the spatial extension.
ℹ It could not be foun<1b>[31md in the core or community repositories.<1b>[39m
ℹ Check that the extension name is correct:
<https://duckdb.org/docs/extensions/overview>
---
Backtrace:
▆
1. └─duckspatial::ddbs_open_dataset(...)
2. └─duckspatial:::ddbs_default_conn()
3. └─duckspatial::ddbs_create_conn(dbdir = "memory", ...)
4. └─duckspatial::ddbs_install(conn, upgrade = upgrade, quiet = TRUE)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 `ddbs_install()`:
! Failed to install the spatial extension.
ℹ It could not be found in the core or community reposit<1b>[39m<1b>[31mories.
ℹ Check that the extension name is correct:
<https://duckdb.org/docs/extensions/overview>
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_install(conn, upgrade = upgrade, quiet = TRUE)
6. └─cli::cli_abort(...)
7. └─rlang::abort(...)
<1b>[39m<1b>[31m
Quitting from spatial_joins.qmd:67-77 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<1b>[39m<1b>[31m~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `ddbs_install()`:
! Failed to install the spatial extension.
ℹ It could not be fo<1b>[39m<1b>[31mund in the core or community repositories.
ℹ Check that the extension name is correct:
<https://duckdb.org/docs/extensions/o<1b>[39m<1b>[31mverview>
---
Backtrace:
▆
1. └─duckspatial::ddbs_join(x = points_sf, y = countries_sf, join = "within")
2. └─d<1b>[39m<1b>[31muckspatial:::resolve_spatial_connections(...)
3. └─duckspatial:::ddbs_default_conn()
4. └─duckspatial::ddbs_<1b>[39m<1b>[31mcreate_conn(dbdir = "memory", ...)
5. └─duckspatial::ddbs_install(conn, upgrade = upgrade, quiet = TRUE)
~~~~~~~~~~<1b>[39m<1b>[31m~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 `ddbs_install()`:<1b>[39m
! Failed to install the spatial extension.
ℹ It could not be found in the core or community reposit<1b>[31mories.<1b>[39m
ℹ Check that the extension name is correct:
<https://duckdb.org/docs/extensions/overview>
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_install(conn, upgrade = upgrade, quiet = TRUE)
6. └─cli::cli_abort(...)
7. └─rlang::abort(...)
Quitting from spatial_joins.qmd:67-77 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<1b>[31m~~~~~~~~~~~~~~~<1b>[39m
<error/rlang_error>
Error in `ddbs_install()`:
! Failed to install the spatial extension.
ℹ It could not be fo<1b>[31mund in the core or community repositories.<1b>[39m
ℹ Check that the extension name is correct:
<https://duckdb.org/docs/extensions/o<1b>[31mverview><1b>[39m
---
Backtrace:
▆
1. └─duckspatial::ddbs_join(x = points_sf, y = countries_sf, join = "within")
2. └─d<1b>[31muckspatial:::resolve_spatial_connections(...)<1b>[39m
3. └─duckspatial:::ddbs_default_conn()
4. └─duckspatial::ddbs_<1b>[31mcreate_conn(dbdir = "memory", ...)<1b>[39m
5. └─duckspatial::ddbs_install(conn, upgrade = upgrade, quiet = TRUE)
~~~~~~~~~~<1b>[31m~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<1b>[39m
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-release-linux-x86_64