Last updated on 2026-08-01 05:55:34 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.2.1 | 13.75 | 185.00 | 198.75 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.2.1 | 9.91 | 137.71 | 147.62 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 1.2.1 | 26.00 | 256.92 | 282.92 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 1.2.1 | 10.00 | 136.09 | 146.09 | OK | |
| r-devel-windows-x86_64 | 1.2.1 | 20.00 | 184.00 | 204.00 | OK | |
| r-patched-linux-x86_64 | 1.2.1 | 17.90 | 178.73 | 196.63 | OK | |
| r-release-linux-x86_64 | 1.2.1 | 12.96 | 191.98 | 204.94 | OK | |
| r-release-macos-arm64 | 1.2.1 | 3.00 | 38.00 | 41.00 | OK | |
| r-release-macos-x86_64 | 1.2.1 | 10.00 | 140.00 | 150.00 | OK | |
| r-release-windows-x86_64 | 1.2.1 | 16.00 | 204.00 | 220.00 | OK | |
| r-oldrel-macos-arm64 | 1.2.1 | 3.00 | 40.00 | 43.00 | OK | |
| r-oldrel-macos-x86_64 | 1.2.1 | 9.00 | 118.00 | 127.00 | OK | |
| r-oldrel-windows-x86_64 | 1.2.1 | 25.00 | 250.00 | 275.00 | OK |
Version: 1.2.1
Check: for new files in some other directories
Result: NOTE
Found the following files/directories:
‘~/tmp/scratch/Rtmp09ycnr’ ‘~/tmp/scratch/Rtmp0YiEt0’
‘~/tmp/scratch/Rtmp0lXxEx’ ‘~/tmp/scratch/Rtmp1zWfH5’
‘~/tmp/scratch/Rtmp2154E8’ ‘~/tmp/scratch/Rtmp23TVOO’
‘~/tmp/scratch/Rtmp26vVY9’ ‘~/tmp/scratch/Rtmp2nvxMF’
‘~/tmp/scratch/Rtmp2x1trl’ ‘~/tmp/scratch/Rtmp3dj8Iz’
‘~/tmp/scratch/Rtmp4DHxA4’ ‘~/tmp/scratch/Rtmp4lX3vS’
‘~/tmp/scratch/Rtmp4qu3Uu’ ‘~/tmp/scratch/Rtmp52S6Gp’
‘~/tmp/scratch/Rtmp5TimaF’ ‘~/tmp/scratch/Rtmp5TozX9’
‘~/tmp/scratch/Rtmp5vr3au’ ‘~/tmp/scratch/Rtmp6GQzyK’
‘~/tmp/scratch/Rtmp7B4CbF’ ‘~/tmp/scratch/Rtmp8EdvAz’
‘~/tmp/scratch/Rtmp8ORS4P’ ‘~/tmp/scratch/Rtmp8ZhZSc’
‘~/tmp/scratch/Rtmp8qDFhF’ ‘~/tmp/scratch/Rtmp9N7kk6’
‘~/tmp/scratch/RtmpAnamj4’ ‘~/tmp/scratch/RtmpAsENKg’
‘~/tmp/scratch/RtmpBUGMWD’ ‘~/tmp/scratch/RtmpCH74GG’
‘~/tmp/scratch/RtmpDeJaoV’ ‘~/tmp/scratch/RtmpDlcWeE’
‘~/tmp/scratch/RtmpDtFnjV’ ‘~/tmp/scratch/RtmpEPcpgS’
‘~/tmp/scratch/RtmpErXxyn’ ‘~/tmp/scratch/RtmpFmrLLi’
‘~/tmp/scratch/RtmpG4UMRN’ ‘~/tmp/scratch/RtmpG88k0Z’
‘~/tmp/scratch/RtmpHnYbg2’ ‘~/tmp/scratch/RtmpIOzcSt’
‘~/tmp/scratch/RtmpIQRQc3’ ‘~/tmp/scratch/RtmpIxvS2D’
‘~/tmp/scratch/RtmpJQxrA1’ ‘~/tmp/scratch/RtmpJqW69r’
‘~/tmp/scratch/RtmpJuHIe7’ ‘~/tmp/scratch/RtmpJzNVKD’
‘~/tmp/scratch/RtmpKWVpzb’ ‘~/tmp/scratch/RtmpKgXqJB’
‘~/tmp/scratch/RtmpKzDUdv’ ‘~/tmp/scratch/RtmpLA4yYQ’
‘~/tmp/scratch/RtmpLZzrFj’ ‘~/tmp/scratch/RtmpMDjF9Z’
‘~/tmp/scratch/RtmpMZWMLk’ ‘~/tmp/scratch/RtmpModcRJ’
‘~/tmp/scratch/RtmpN2BqIG’ ‘~/tmp/scratch/RtmpNE4ByF’
‘~/tmp/scratch/RtmpNNYFrj’ ‘~/tmp/scratch/RtmpNSUAmd’
‘~/tmp/scratch/RtmpNnecEo’ ‘~/tmp/scratch/RtmpODE6FV’
‘~/tmp/scratch/RtmpOQq2WS’ ‘~/tmp/scratch/RtmpOtWimQ’
‘~/tmp/scratch/RtmpPPoXK9’ ‘~/tmp/scratch/RtmpPXq1zi’
‘~/tmp/scratch/RtmpPiI1fU’ ‘~/tmp/scratch/RtmpPtKiQN’
‘~/tmp/scratch/RtmpPv84Wk’ ‘~/tmp/scratch/RtmpQSDoM5’
‘~/tmp/scratch/RtmpQUKs70’ ‘~/tmp/scratch/RtmpQuclWM’
‘~/tmp/scratch/RtmpRKhCjU’ ‘~/tmp/scratch/RtmpRzWaOp’
‘~/tmp/scratch/RtmpSJAlzN’ ‘~/tmp/scratch/RtmpSfItkn’
‘~/tmp/scratch/RtmpSlRSle’ ‘~/tmp/scratch/RtmpTFkfpd’
‘~/tmp/scratch/RtmpTmU4dq’ ‘~/tmp/scratch/RtmpURZ07I’
‘~/tmp/scratch/RtmpUT4qI0’ ‘~/tmp/scratch/RtmpUWDjNn’
‘~/tmp/scratch/RtmpUgDjOc’ ‘~/tmp/scratch/RtmpVjGxCz’
‘~/tmp/scratch/RtmpWFc11p’ ‘~/tmp/scratch/RtmpWgdyJj’
‘~/tmp/scratch/RtmpWvmPo6’ ‘~/tmp/scratch/RtmpWweN5N’
‘~/tmp/scratch/RtmpXGeHZJ’ ‘~/tmp/scratch/RtmpXjcgad’
‘~/tmp/scratch/RtmpYMoy2t’ ‘~/tmp/scratch/RtmpZMFLgh’
‘~/tmp/scratch/Rtmpa3OtAW’ ‘~/tmp/scratch/RtmpaAwbpf’
‘~/tmp/scratch/RtmpaXKokz’ ‘~/tmp/scratch/Rtmpaa56wG’
‘~/tmp/scratch/Rtmpbdc5Yq’ ‘~/tmp/scratch/Rtmpbocuvt’
‘~/tmp/scratch/RtmpbzPOll’ ‘~/tmp/scratch/Rtmpc2xymA’
‘~/tmp/scratch/RtmpcGxCmU’ ‘~/tmp/scratch/RtmpcPgKA5’
‘~/tmp/scratch/RtmpcfGkBu’ ‘~/tmp/scratch/RtmpcmVT0Z’
‘~/tmp/scratch/RtmpdUOiyG’ ‘~/tmp/scratch/RtmpdbdVNn’
‘~/tmp/scratch/Rtmpdy72PD’ ‘~/tmp/scratch/RtmpeFpvBz’
‘~/tmp/scratch/RtmpeGC9Rc’ ‘~/tmp/scratch/RtmpeZYmLB’
‘~/tmp/scratch/RtmpeomLKB’ ‘~/tmp/scratch/RtmpevBrSK’
‘~/tmp/scratch/RtmpgO6JbX’ ‘~/tmp/scratch/RtmpgT6wUk’
‘~/tmp/scratch/Rtmpgx7Sxr’ ‘~/tmp/scratch/RtmphBPwAd’
‘~/tmp/scratch/RtmphE0VLS’ ‘~/tmp/scratch/RtmphHpNdZ’
‘~/tmp/scratch/RtmphMct10’ ‘~/tmp/scratch/Rtmphi0euy’
‘~/tmp/scratch/Rtmpi2nFpc’ ‘~/tmp/scratch/RtmpiS1adP’
‘~/tmp/scratch/RtmpijZftT’ ‘~/tmp/scratch/RtmpjPHlWW’
‘~/tmp/scratch/Rtmpjxbyyu’ ‘~/tmp/scratch/RtmpkIOVhN’
‘~/tmp/scratch/RtmplXUHNP’ ‘~/tmp/scratch/RtmpnIrCIO’
‘~/tmp/scratch/RtmpnQ4J08’ ‘~/tmp/scratch/RtmpnQ8FAk’
‘~/tmp/scratch/RtmpoE4bDy’ ‘~/tmp/scratch/RtmpopeZGI’
‘~/tmp/scratch/Rtmpp5QOKK’ ‘~/tmp/scratch/Rtmpp9aZo1’
‘~/tmp/scratch/RtmppU9Wrg’ ‘~/tmp/scratch/RtmppWbLQk’
‘~/tmp/scratch/RtmpqEhIc9’ ‘~/tmp/scratch/RtmpqhXsbx’
‘~/tmp/scratch/RtmprSkWnc’ ‘~/tmp/scratch/Rtmprgei8u’
‘~/tmp/scratch/RtmproEP6Z’ ‘~/tmp/scratch/RtmprqavPP’
‘~/tmp/scratch/Rtmps2Esqi’ ‘~/tmp/scratch/RtmpsyEXfZ’
‘~/tmp/scratch/Rtmptb2ogR’ ‘~/tmp/scratch/RtmpuB6doM’
‘~/tmp/scratch/Rtmpukx2QN’ ‘~/tmp/scratch/RtmpuonUZM’
‘~/tmp/scratch/RtmpvBIxOc’ ‘~/tmp/scratch/Rtmpwqy94b’
‘~/tmp/scratch/Rtmpx2tpdj’ ‘~/tmp/scratch/Rtmpx4pVhS’
‘~/tmp/scratch/RtmpxGpLtU’ ‘~/tmp/scratch/RtmpyYytmE’
‘~/tmp/scratch/RtmpyhgeZN’ ‘~/tmp/scratch/Rtmpyw4WOR’
‘~/tmp/scratch/RtmpzG315o’ ‘~/tmp/scratch/Rtmpzr4eqy’
‘~/tmp/scratch/RtmpzzqUe0’ ‘~/tmp/scratch/xvfb-run.1oDaW5’
‘~/tmp/scratch/xvfb-run.2LLH6H’ ‘~/tmp/scratch/xvfb-run.3G5B46’
‘~/tmp/scratch/xvfb-run.6uTHZA’ ‘~/tmp/scratch/xvfb-run.88Hyun’
‘~/tmp/scratch/xvfb-run.8MJWyS’ ‘~/tmp/scratch/xvfb-run.8XRY77’
‘~/tmp/scratch/xvfb-run.8pFf1G’ ‘~/tmp/scratch/xvfb-run.8ywUP2’
‘~/tmp/scratch/xvfb-run.97AjXL’ ‘~/tmp/scratch/xvfb-run.9WOcC3’
‘~/tmp/scratch/xvfb-run.AyKdeS’ ‘~/tmp/scratch/xvfb-run.BXpCGi’
‘~/tmp/scratch/xvfb-run.BexMJu’ ‘~/tmp/scratch/xvfb-run.DffE5Z’
‘~/tmp/scratch/xvfb-run.Gw5FRd’ ‘~/tmp/scratch/xvfb-run.GzFtNa’
‘~/tmp/scratch/xvfb-run.Hr0RtF’ ‘~/tmp/scratch/xvfb-run.Iay3e9’
‘~/tmp/scratch/xvfb-run.JZ6KGN’ ‘~/tmp/scratch/xvfb-run.KQf3qE’
‘~/tmp/scratch/xvfb-run.KtfzNX’ ‘~/tmp/scratch/xvfb-run.M3xR8j’
‘~/tmp/scratch/xvfb-run.N5Lq9f’ ‘~/tmp/scratch/xvfb-run.NIrn6A’
‘~/tmp/scratch/xvfb-run.O3CcEs’ ‘~/tmp/scratch/xvfb-run.O9amJC’
‘~/tmp/scratch/xvfb-run.OqiYx3’ ‘~/tmp/scratch/xvfb-run.RlXkFU’
‘~/tmp/scratch/xvfb-run.SZ7sqn’ ‘~/tmp/scratch/xvfb-run.T9s946’
‘~/tmp/scratch/xvfb-run.U3FenL’ ‘~/tmp/scratch/xvfb-run.U8HDJp’
‘~/tmp/scratch/xvfb-run.UqV9iT’ ‘~/tmp/scratch/xvfb-run.V0cFB2’
‘~/tmp/scratch/xvfb-run.VYohoV’ ‘~/tmp/scratch/xvfb-run.Vienaa’
‘~/tmp/scratch/xvfb-run.WMA2Rc’ ‘~/tmp/scratch/xvfb-run.YtaXZb’
‘~/tmp/scratch/xvfb-run.Yub2tR’ ‘~/tmp/scratch/xvfb-run.ZIcnaA’
‘~/tmp/scratch/xvfb-run.Ziu1Nr’ ‘~/tmp/scratch/xvfb-run.ZpIk4S’
‘~/tmp/scratch/xvfb-run.aj3G0a’ ‘~/tmp/scratch/xvfb-run.asoA81’
‘~/tmp/scratch/xvfb-run.cnl7mm’ ‘~/tmp/scratch/xvfb-run.dnAxFW’
‘~/tmp/scratch/xvfb-run.dpsBo3’ ‘~/tmp/scratch/xvfb-run.fUgAaA’
‘~/tmp/scratch/xvfb-run.gb46K3’ ‘~/tmp/scratch/xvfb-run.h2DP3V’
‘~/tmp/scratch/xvfb-run.k624Hx’ ‘~/tmp/scratch/xvfb-run.mexsEe’
‘~/tmp/scratch/xvfb-run.oMzodl’ ‘~/tmp/scratch/xvfb-run.p62N2u’
‘~/tmp/scratch/xvfb-run.q461YR’ ‘~/tmp/scratch/xvfb-run.q5YUc5’
‘~/tmp/scratch/xvfb-run.rM6CuW’ ‘~/tmp/scratch/xvfb-run.rv5C7i’
‘~/tmp/scratch/xvfb-run.rw8H0q’ ‘~/tmp/scratch/xvfb-run.sBRoVh’
‘~/tmp/scratch/xvfb-run.t1hEaS’ ‘~/tmp/scratch/xvfb-run.w9tllf’
‘~/tmp/scratch/xvfb-run.xh9YoZ’ ‘~/tmp/scratch/xvfb-run.xjU62e’
‘~/tmp/scratch/xvfb-run.xxeQGt’
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.2.1
Check: tests
Result: ERROR
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(duckspatial)
duckspatial 1.2.1 attached
* Compatible with DuckDB >= v1.5.4.2
Default output has changed on v1.0.0:
duckspatial now returns lazy `duckspatial_df` (dbplyr) objects
instead of `sf` objects.
To restore the previous behaviour:
ddbs_options(mode = 'sf')
> library(duckdb)
Loading required package: DBI
>
> test_check("duckspatial")
Reading layer `countries' from data source
`/data/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
duckdb keeps downloaded extensions and secrets in a temporary directory:
ℹ /tmp/RtmpzqWVyB/working_dir/RtmprxmteP/duckdb
This is removed when the R session ends.
• Extensions are re-downloaded each session.
• Secrets are lost.
ℹ Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
ℹ Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
ℹ See ?duckdb_storage for details and alternatives.
duckdb was built with libc++ (not libstdc++) on Linux, so DuckDB extensions are disabled:
• Loading a prebuilt (libstdc++) extension could crash R (https://github.com/duckdb/duckdb-r/issues/1107).
• INSTALL/LOAD of an extension will error, and automatic extension loading is off.
ℹ Pass duckdb(allow_extensions = FALSE) to accept this and silence this message.
ℹ Pass duckdb(allow_extensions = TRUE) to attempt loading anyway (may crash R).
ℹ See ?duckdb for details.
Error in `source_dir()`:
! Failed to evaluate './setup.R'.
Caused by error in `ddbs_install()`:
! Failed to install the spatial extension.
✖ core: DuckDB extension loading (INSTALL / LOAD) is disabled for this driver.
ℹ Recreate the driver with duckdb(allow_extensions = TRUE) to enable it (this
may crash R on a Linux build not compiled with libstdc++; see
https://github.com/duckdb/duckdb-r/issues/1107). ℹ See ?duckdb for details. ℹ
Context: load_extension
✖ community: DuckDB extension loading (INSTALL / LOAD) is disabled for this
driver. ℹ Recreate the driver with duckdb(allow_extensions = TRUE) to enable
it (this may crash R on a Linux build not compiled with libstdc++; see
https://github.com/duckdb/duckdb-r/issues/1107). ℹ See ?duckdb for details. ℹ
Context: load_extension
ℹ It might not be available for this version of DuckDB, or the install location
may not be writable.
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-fedora-clang
Version: 1.2.1
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.
✖ core: DuckDB extension loading (INSTALL / LOAD) is disabled for this driver.
ℹ Recreate the driver with duckdb(allow_extensions = TRUE) to enable it (this
may crash R on a Linux build not compiled with libstdc++; see
https://github.com/duckdb/duckdb-r/issues/1107). ℹ See ?duckdb for details. ℹ
Context: load_extension
✖ community: DuckDB extension loading (INSTALL / LOAD) is disabled for this
driver. ℹ Recreate the driver with duckdb(allow_extensions = TRUE) to enable
it (this may crash R on a Linux build not compiled with libstdc++; see
https://github.com/duckdb/duckdb-r/issues/1107). ℹ See ?duckdb for details. ℹ
Context: load_extension
ℹ It might not be available for this version of DuckDB, or the install location
may not be writable.
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:78-89 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `ddbs_install()`:
! Failed to install the spatial extension.
✖ core: DuckDB extension loading (INSTALL / LOAD) is disabled for this driver.
ℹ Recreate the driver with duckdb(allow_extensions = TRUE) to enable it (this
may crash R on a Linux build not compiled with libstdc++; see
https://github.com/duckdb/duckdb-r/issues/1107). ℹ See ?duckdb for details. ℹ
Context: load_extension
✖ community: DuckDB extension loading (INSTALL / LOAD) is disabled for this
driver. ℹ Recreate the driver with duckdb(allow_extensions = TRUE) to enable
it (this may crash R on a Linux build not compiled with libstdc++; see
https://github.com/duckdb/duckdb-r/issues/1107). ℹ See ?duckdb for details. ℹ
Context: load_extension
ℹ It might not be available for this version of DuckDB, or the install location
may not be writable.
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)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<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.
✖ core: DuckDB extension loading (INSTALL / LOAD) is disabled for this
driver.
ℹ Recreate the driver with duckdb(allow_extensions = TRUE) to enable it (this
may crash R on a Linux build not compiled with libstdc++; see
https://github.com/duckdb/duckdb-r/issues/1107). ℹ See ?duckdb for details. ℹ
Context: load_extension
✖ community: DuckDB extension loading (INSTALL / LOAD) is disabled for this
driver. ℹ Recreate the driver with duckdb(allow_extensions = TRUE) to enable
it (this may crash R on a Linux build not compiled with libstdc++; see
https://github.com/duckdb/duckdb-r/issues/1107). ℹ See ?duckdb for details. ℹ
Context: load_extension
ℹ It might not be available for this version of DuckDB, or the install
location
may not be writable.
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:78-89 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `ddbs_install()`:
! Failed to install the spatial extension.
✖ core: DuckDB extension loading (INSTALL / LOAD) is disabled for this
driver.
ℹ Recreate the driver with duckdb(allow_extensions = TRUE) to enable it (this
may crash R on a Linux build not compiled with libstdc++; see
https://github.com/duckdb/duckdb-r/issues/1107). ℹ See ?duckdb for details. ℹ
Context: load_extension
✖ community: DuckDB extension loading (INSTALL / LOAD) is disabled for this
driver. ℹ Recreate the driver with duckdb(allow_extensions = TRUE) to enable
it (this may crash R on a Linux build not compiled with libstdc++; see
https://github.com/duckdb/duckdb-r/issues/1107). ℹ See ?duckdb for details. ℹ
Context: load_extension
ℹ It might not be available for this version of DuckDB, or the install
location
may not be writable.
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)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<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:
- >-
/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 `ddbs_install()`:
! Failed to install the spatial extension.
✖ core: DuckDB extension loading (INSTALL / LOAD) is disabled for this driver.
ℹ Recreate the driver with duckdb(allow_extensions = TRUE) to enable it (this
may crash R on a Linux build not compiled with libstdc++; see
https://github.com/duckdb/duckdb-r/issues/1107). ℹ See ?duckdb for details. ℹ
Context: load_extension
✖ community: DuckDB extension loading (INSTALL / LOAD) is disabled for this
driver. ℹ Recreate the driver with duckdb(allow_extensions = TRUE) to enable
it (this may crash R on a Linux build not compiled with libstdc++; see
https://github.com/duckdb/duckdb-r/issues/1107). ℹ See ?duckdb for details. ℹ
Context: load_extension
ℹ It might not be available for this version of DuckDB, or the install location
may not be writable.
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:78-87 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `ddbs_install()`:
! Failed to install the spatial extension.
✖ core: DuckDB extension loading (INSTALL / LOAD) is disabled for this driver.
ℹ Recreate the driver with duckdb(allow_extensions = TRUE) to enable it (this
may crash R on a Linux build not compiled with libstdc++; see
https://github.com/duckdb/duckdb-r/issues/1107). ℹ See ?duckdb for details. ℹ
Context: load_extension
✖ community: DuckDB extension loading (INSTALL / LOAD) is disabled for this
driver. ℹ Recreate the driver with duckdb(allow_extensions = TRUE) to enable
it (this may crash R on a Linux build not compiled with libstdc++; see
https://github.com/duckdb/duckdb-r/issues/1107). ℹ See ?duckdb for details. ℹ
Context: load_extension
ℹ It might not be available for this version of DuckDB, or the install location
may not be writable.
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.
✖ core: DuckDB extension loading (INSTALL / LOAD) is disabled for this
driver.
ℹ Recreate the driver with duckdb(allow_extensions = TRUE) to enable it (this
may crash R on a Linux build not compiled with libstdc++; see
https://github.com/duckdb/duckdb-r/issues/1107). ℹ See ?duckdb for details. ℹ
Context: load_extension
✖ community: DuckDB extension loading (INSTALL / LOAD) is disabled for this
driver. ℹ Recreate the driver with duckdb(allow_extensions = TRUE) to enable
it (this may crash R on a Linux build not compiled with libstdc++; see
https://github.com/duckdb/duckdb-r/issues/1107). ℹ See ?duckdb for details. ℹ
Context: load_extension
ℹ It might not be available for this version of DuckDB, or the install
location
may not be writable.
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:78-87 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `ddbs_install()`:
! Failed to install the spatial extension.
✖ core: DuckDB extension loading (INSTALL / LOAD) is disabled for this
driver.
ℹ Recreate the driver with duckdb(allow_extensions = TRUE) to enable it (this
may crash R on a Linux build not compiled with libstdc++; see
https://github.com/duckdb/duckdb-r/issues/1107). ℹ See ?duckdb for details. ℹ
Context: load_extension
✖ community: DuckDB extension loading (INSTALL / LOAD) is disabled for this
driver. ℹ Recreate the driver with duckdb(allow_extensions = TRUE) to enable
it (this may crash R on a Linux build not compiled with libstdc++; see
https://github.com/duckdb/duckdb-r/issues/1107). ℹ See ?duckdb for details. ℹ
Context: load_extension
ℹ It might not be available for this version of DuckDB, or the install
location
may not be writable.
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.
✖ core: DuckDB extension loading (INSTALL / LOAD) is dis<1b>[39m<1b>[31mabled for this driver.
ℹ Recreate the driver with duckdb(allow_extensions = TRUE) to enable it (this
may crash R on a Linux build not compiled with libstdc++; see
https://github.com/duckdb/duckdb-r/issues/1107). ℹ See ?duckdb for details. ℹ
Context: load_extension
✖ community: DuckDB extension loading (INSTALL / LOAD) is disabled for this
driver. ℹ Recreate the driver with duckdb(allow_extensions = TRUE) to enable
it (this may crash R on a Linux build not compiled with libstdc++; see
https://github.com/duckdb/duckdb-r/issues/1107). ℹ See ?duckdb for details. ℹ
Context: load_extension
ℹ It might not be available for this version of DuckDB, or the install location
may not be writable.
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:77-87 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<1b>[39m<1b>[31m~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `ddbs_install()`:
! Failed to install the spatial extension.
✖ core: DuckDB extension loading (INSTALL / LOAD) is disabled for this driver.
ℹ Recreate the driver with duckdb(allow_extensions = TRUE) to enable it (this
may crash R on a Linux build not compiled with libstdc++; see
https://github.com/duckdb/duckdb-r/issues/1107). ℹ See ?duckdb for details. ℹ
Context: load_extension
✖ community: DuckDB extension loading (INSTALL / LOAD) is disabled for this
driver. ℹ Recreate the driver with duckdb(allow_extensions = TRUE) to enable
it (this may crash R on a Linux build not compiled with libstdc++; see
https://github.com/duckdb/duckdb-r/issues/1107). ℹ See ?duckdb for details. ℹ
Context: load_extension
ℹ It might not be available for this version of DuckDB, or the install location
may not be writable.
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.
✖ core: DuckDB extension loading (INSTALL / LOAD) is dis<1b>[31mabled for this<1b>[39m
<1b>[31mdriver.<1b>[39m
ℹ Recreate the driver with duckdb(allow_extensions = TRUE) to enable it (this
may crash R on a Linux build not compiled with libstdc++; see
https://github.com/duckdb/duckdb-r/issues/1107). ℹ See ?duckdb for details. ℹ
Context: load_extension
✖ community: DuckDB extension loading (INSTALL / LOAD) is disabled for this
driver. ℹ Recreate the driver with duckdb(allow_extensions = TRUE) to enable
it (this may crash R on a Linux build not compiled with libstdc++; see
https://github.com/duckdb/duckdb-r/issues/1107). ℹ See ?duckdb for details. ℹ
Context: load_extension
ℹ It might not be available for this version of DuckDB, or the install
location
may not be writable.
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:77-87 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<1b>[31m~~~~~~~~~~~~~~~<1b>[39m
<error/rlang_error>
Error in `ddbs_install()`:
! Failed to install the spatial extension.
✖ core: DuckDB extension loading (INSTALL / LOAD) is disabled for this
driver.
ℹ Recreate the driver with duckdb(allow_extensions = TRUE) to enable it (this
may crash R on a Linux build not compiled with libstdc++; see
https://github.com/duckdb/duckdb-r/issues/1107). ℹ See ?duckdb for details. ℹ
Context: load_extension
✖ community: DuckDB extension loading (INSTALL / LOAD) is disabled for this
driver. ℹ Recreate the driver with duckdb(allow_extensions = TRUE) to enable
it (this may crash R on a Linux build not compiled with libstdc++; see
https://github.com/duckdb/duckdb-r/issues/1107). ℹ See ?duckdb for details. ℹ
Context: load_extension
ℹ It might not be available for this version of DuckDB, or the install
location
may not be writable.
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-fedora-clang