Last updated on 2026-08-03 23:50:35 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 | 9.76 | 132.51 | 142.27 | 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 | 14.52 | 181.90 | 196.42 | 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 | 19.00 | 203.00 | 222.00 | 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 | 26.00 | 252.00 | 278.00 | OK |
Version: 1.2.1
Check: for new files in some other directories
Result: NOTE
Found the following files/directories:
‘~/tmp/scratch/Rtmp06GJNM’ ‘~/tmp/scratch/Rtmp0RP6uU’
‘~/tmp/scratch/Rtmp15PsCu’ ‘~/tmp/scratch/Rtmp1CJ0gv’
‘~/tmp/scratch/Rtmp1Hk05M’ ‘~/tmp/scratch/Rtmp1o5J2l’
‘~/tmp/scratch/Rtmp1pKz6n’ ‘~/tmp/scratch/Rtmp1wGOlJ’
‘~/tmp/scratch/Rtmp1wMSaB’ ‘~/tmp/scratch/Rtmp217IMs’
‘~/tmp/scratch/Rtmp2DdusW’ ‘~/tmp/scratch/Rtmp2G4pOo’
‘~/tmp/scratch/Rtmp2MwNzd’ ‘~/tmp/scratch/Rtmp2OSaaG’
‘~/tmp/scratch/Rtmp2P0NZT’ ‘~/tmp/scratch/Rtmp2SfoxQ’
‘~/tmp/scratch/Rtmp2eApbY’ ‘~/tmp/scratch/Rtmp3IPHWz’
‘~/tmp/scratch/Rtmp3Mo0rU’ ‘~/tmp/scratch/Rtmp3RMaIc’
‘~/tmp/scratch/Rtmp3dglbr’ ‘~/tmp/scratch/Rtmp49KSz8’
‘~/tmp/scratch/Rtmp4FWZz9’ ‘~/tmp/scratch/Rtmp4lF2Z7’
‘~/tmp/scratch/Rtmp55NER7’ ‘~/tmp/scratch/Rtmp5E4JEk’
‘~/tmp/scratch/Rtmp62FxCL’ ‘~/tmp/scratch/Rtmp6zfYK8’
‘~/tmp/scratch/Rtmp7UN9sK’ ‘~/tmp/scratch/Rtmp7VNUtX’
‘~/tmp/scratch/Rtmp8653nb’ ‘~/tmp/scratch/Rtmp9DPADm’
‘~/tmp/scratch/Rtmp9czaTx’ ‘~/tmp/scratch/RtmpAK7M0W’
‘~/tmp/scratch/RtmpAMhAvX’ ‘~/tmp/scratch/RtmpAU65VN’
‘~/tmp/scratch/RtmpAYwsS8’ ‘~/tmp/scratch/RtmpAZ9T4l’
‘~/tmp/scratch/RtmpBSEJXk’ ‘~/tmp/scratch/RtmpCn8MSM’
‘~/tmp/scratch/RtmpDU65UA’ ‘~/tmp/scratch/RtmpDXomhy’
‘~/tmp/scratch/RtmpEinq8b’ ‘~/tmp/scratch/RtmpF2x7lp’
‘~/tmp/scratch/RtmpF9aNDK’ ‘~/tmp/scratch/RtmpFCWvZd’
‘~/tmp/scratch/RtmpFZvllT’ ‘~/tmp/scratch/RtmpFqKmY6’
‘~/tmp/scratch/RtmpG8qhN2’ ‘~/tmp/scratch/RtmpGGA1GK’
‘~/tmp/scratch/RtmpGVWWDH’ ‘~/tmp/scratch/RtmpGWJsQK’
‘~/tmp/scratch/RtmpGlFXjr’ ‘~/tmp/scratch/RtmpHPmwah’
‘~/tmp/scratch/RtmpHUU5Zk’ ‘~/tmp/scratch/RtmpHcDZDt’
‘~/tmp/scratch/RtmpJGNWws’ ‘~/tmp/scratch/RtmpK0XViw’
‘~/tmp/scratch/RtmpKdyjep’ ‘~/tmp/scratch/RtmpKklopd’
‘~/tmp/scratch/RtmpKqlcPU’ ‘~/tmp/scratch/RtmpKsJUbu’
‘~/tmp/scratch/RtmpKszkaf’ ‘~/tmp/scratch/RtmpLcD288’
‘~/tmp/scratch/RtmpMUZUj5’ ‘~/tmp/scratch/RtmpPQ5ki9’
‘~/tmp/scratch/RtmpPRpr3g’ ‘~/tmp/scratch/RtmpPzaTib’
‘~/tmp/scratch/RtmpR5r79u’ ‘~/tmp/scratch/RtmpRb78YX’
‘~/tmp/scratch/RtmpRqotb3’ ‘~/tmp/scratch/RtmpS9LkRT’
‘~/tmp/scratch/RtmpSY5Suj’ ‘~/tmp/scratch/RtmpSfEpGD’
‘~/tmp/scratch/RtmpSx3KvD’ ‘~/tmp/scratch/RtmpTAyo8m’
‘~/tmp/scratch/RtmpTOJouR’ ‘~/tmp/scratch/RtmpTSXdmG’
‘~/tmp/scratch/RtmpTWIWBW’ ‘~/tmp/scratch/RtmpTacjqD’
‘~/tmp/scratch/RtmpTsHj2q’ ‘~/tmp/scratch/RtmpTyjvOk’
‘~/tmp/scratch/RtmpU1vTGJ’ ‘~/tmp/scratch/RtmpU7Sc0Y’
‘~/tmp/scratch/RtmpURrrZ6’ ‘~/tmp/scratch/RtmpUXb2f8’
‘~/tmp/scratch/RtmpUnOa8A’ ‘~/tmp/scratch/RtmpV0tGMQ’
‘~/tmp/scratch/RtmpVlV0fN’ ‘~/tmp/scratch/RtmpX92fZT’
‘~/tmp/scratch/RtmpXyZlCp’ ‘~/tmp/scratch/RtmpYLLGxH’
‘~/tmp/scratch/RtmpYPtxEP’ ‘~/tmp/scratch/RtmpYgrwFF’
‘~/tmp/scratch/RtmpZ98lF3’ ‘~/tmp/scratch/RtmpZLgj3l’
‘~/tmp/scratch/RtmpZST1YZ’ ‘~/tmp/scratch/RtmpalW03y’
‘~/tmp/scratch/Rtmpan67WL’ ‘~/tmp/scratch/RtmpatKryc’
‘~/tmp/scratch/RtmpbEQReH’ ‘~/tmp/scratch/RtmpbVz2hC’
‘~/tmp/scratch/Rtmpbpetwr’ ‘~/tmp/scratch/Rtmpbw3UgM’
‘~/tmp/scratch/RtmpceIj6T’ ‘~/tmp/scratch/Rtmpd8papx’
‘~/tmp/scratch/RtmpdffNOd’ ‘~/tmp/scratch/RtmpeDwCGe’
‘~/tmp/scratch/RtmpePKYjN’ ‘~/tmp/scratch/RtmpeeFlQK’
‘~/tmp/scratch/RtmpeiCtCA’ ‘~/tmp/scratch/Rtmpf2h8BF’
‘~/tmp/scratch/RtmpfPET15’ ‘~/tmp/scratch/RtmpfUpDPg’
‘~/tmp/scratch/RtmpgaDgND’ ‘~/tmp/scratch/RtmpgfvxvI’
‘~/tmp/scratch/RtmphKz5RD’ ‘~/tmp/scratch/RtmpiRDrRQ’
‘~/tmp/scratch/Rtmpje5JDY’ ‘~/tmp/scratch/RtmpkBas4P’
‘~/tmp/scratch/RtmpkEurff’ ‘~/tmp/scratch/Rtmpkiazta’
‘~/tmp/scratch/RtmpkqKI26’ ‘~/tmp/scratch/RtmpkwGFXq’
‘~/tmp/scratch/RtmpkzqswO’ ‘~/tmp/scratch/RtmplCaBlf’
‘~/tmp/scratch/Rtmpm33MPO’ ‘~/tmp/scratch/Rtmpm8ZZ5H’
‘~/tmp/scratch/RtmpmELG3N’ ‘~/tmp/scratch/RtmpmQdRwP’
‘~/tmp/scratch/RtmpmozLk1’ ‘~/tmp/scratch/RtmpnXwtLi’
‘~/tmp/scratch/RtmpnsmPBN’ ‘~/tmp/scratch/Rtmpo6vWSx’
‘~/tmp/scratch/Rtmpoa8io8’ ‘~/tmp/scratch/RtmpofKdax’
‘~/tmp/scratch/RtmppNeiFJ’ ‘~/tmp/scratch/Rtmppdkswv’
‘~/tmp/scratch/Rtmpq4uhxo’ ‘~/tmp/scratch/RtmpqDFu91’
‘~/tmp/scratch/RtmpqKd58n’ ‘~/tmp/scratch/Rtmpqhxm9z’
‘~/tmp/scratch/Rtmpqtz5IP’ ‘~/tmp/scratch/RtmprHcwlU’
‘~/tmp/scratch/RtmprfhGWD’ ‘~/tmp/scratch/RtmprraUaS’
‘~/tmp/scratch/RtmprutMA3’ ‘~/tmp/scratch/RtmpsFDmEv’
‘~/tmp/scratch/RtmpsVpSaf’ ‘~/tmp/scratch/RtmptSdavW’
‘~/tmp/scratch/RtmpuGLvg2’ ‘~/tmp/scratch/RtmpvUvfeQ’
‘~/tmp/scratch/RtmpvXQjgE’ ‘~/tmp/scratch/Rtmpvd4TDn’
‘~/tmp/scratch/RtmpwP47hq’ ‘~/tmp/scratch/RtmpwYzXgH’
‘~/tmp/scratch/Rtmpy1vgPP’ ‘~/tmp/scratch/Rtmpy55QHd’
‘~/tmp/scratch/RtmpzZoz7u’ ‘~/tmp/scratch/Rtmpzny30C’
‘~/tmp/scratch/RtmpzsqPFp’
‘~/tmp/scratch/quarto-sessione63f4c73484d8da’
‘~/tmp/scratch/xvfb-run.2JkOQA’ ‘~/tmp/scratch/xvfb-run.2ORve7’
‘~/tmp/scratch/xvfb-run.4Fh8vt’ ‘~/tmp/scratch/xvfb-run.5ZbFHm’
‘~/tmp/scratch/xvfb-run.5lRZ3t’ ‘~/tmp/scratch/xvfb-run.6HRy6X’
‘~/tmp/scratch/xvfb-run.6MOuYc’ ‘~/tmp/scratch/xvfb-run.6PNM4S’
‘~/tmp/scratch/xvfb-run.6ejrjG’ ‘~/tmp/scratch/xvfb-run.6jtk6R’
‘~/tmp/scratch/xvfb-run.6lfwFo’ ‘~/tmp/scratch/xvfb-run.79FQ8x’
‘~/tmp/scratch/xvfb-run.7lcbmL’ ‘~/tmp/scratch/xvfb-run.A7ftrn’
‘~/tmp/scratch/xvfb-run.B40UCT’ ‘~/tmp/scratch/xvfb-run.DZgS2D’
‘~/tmp/scratch/xvfb-run.DnzfYT’ ‘~/tmp/scratch/xvfb-run.DsSc2Z’
‘~/tmp/scratch/xvfb-run.EblXVC’ ‘~/tmp/scratch/xvfb-run.FBZKgd’
‘~/tmp/scratch/xvfb-run.FSVJ5s’ ‘~/tmp/scratch/xvfb-run.GxZOis’
‘~/tmp/scratch/xvfb-run.Hx75rI’ ‘~/tmp/scratch/xvfb-run.I9HdBC’
‘~/tmp/scratch/xvfb-run.IP2t2k’ ‘~/tmp/scratch/xvfb-run.JJttc0’
‘~/tmp/scratch/xvfb-run.NLVkxD’ ‘~/tmp/scratch/xvfb-run.NT3Ueb’
‘~/tmp/scratch/xvfb-run.QoZInW’ ‘~/tmp/scratch/xvfb-run.TCGRC7’
‘~/tmp/scratch/xvfb-run.WTf1tC’ ‘~/tmp/scratch/xvfb-run.Z9jXTs’
‘~/tmp/scratch/xvfb-run.ZCMaGB’ ‘~/tmp/scratch/xvfb-run.ZIYdVX’
‘~/tmp/scratch/xvfb-run.ZVUM6N’ ‘~/tmp/scratch/xvfb-run.as7dGr’
‘~/tmp/scratch/xvfb-run.bbTTLb’ ‘~/tmp/scratch/xvfb-run.bvuifo’
‘~/tmp/scratch/xvfb-run.c6EfEd’ ‘~/tmp/scratch/xvfb-run.dbTVP2’
‘~/tmp/scratch/xvfb-run.e9QU4x’ ‘~/tmp/scratch/xvfb-run.fdW6aY’
‘~/tmp/scratch/xvfb-run.ghHoj8’ ‘~/tmp/scratch/xvfb-run.h2mUEk’
‘~/tmp/scratch/xvfb-run.ixIJvf’ ‘~/tmp/scratch/xvfb-run.jZnZx8’
‘~/tmp/scratch/xvfb-run.kUayBM’ ‘~/tmp/scratch/xvfb-run.l2Lh9Y’
‘~/tmp/scratch/xvfb-run.lPWI6F’ ‘~/tmp/scratch/xvfb-run.lt5Z4y’
‘~/tmp/scratch/xvfb-run.mPk2aw’ ‘~/tmp/scratch/xvfb-run.oatuUG’
‘~/tmp/scratch/xvfb-run.ogcdmz’ ‘~/tmp/scratch/xvfb-run.omQFau’
‘~/tmp/scratch/xvfb-run.p3oDYX’ ‘~/tmp/scratch/xvfb-run.rQTj7l’
‘~/tmp/scratch/xvfb-run.sHmdrX’ ‘~/tmp/scratch/xvfb-run.tMM5lL’
‘~/tmp/scratch/xvfb-run.tN14Qm’ ‘~/tmp/scratch/xvfb-run.tO6Bc8’
‘~/tmp/scratch/xvfb-run.uqZyzL’ ‘~/tmp/scratch/xvfb-run.uuxNno’
‘~/tmp/scratch/xvfb-run.vFiXb1’ ‘~/tmp/scratch/xvfb-run.vsJjzW’
‘~/tmp/scratch/xvfb-run.vxqL5F’ ‘~/tmp/scratch/xvfb-run.wQ5WOa’
‘~/tmp/scratch/xvfb-run.yBhzfz’ ‘~/tmp/scratch/xvfb-run.yTi4OY’
‘~/tmp/scratch/xvfb-run.yn2G6q’
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