Error(s) in re-building vignettes:
--- re-building ‘aw_interpolation.qmd’ using html
[31m

processing file: aw_interpolation.qmd
[39m[31m[gannet:1982266:0:1982266] Caught signal 11 (Segmentation fault: Sent by the kernel at address (nil))
[39m[31m==== backtrace (tid:1982266) ====
 0  /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7fa217ce3df4]
 1  /lib64/libucs.so.0(+0x17aed) [0x7fa217ce5aed]
 2  /lib64/libucs.so.0(+0x17cbd) [0x7fa217ce5cbd]
 3  /lib64/libc.so.6(+0x1a040) [0x7fa22e928040]
 4  /tmp/RtmplhwcLW/working_dir/RtmpSUgDQG/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x1196b50) [0x7fa105ab4b50]
 5  /tmp/RtmplhwcLW/working_dir/RtmpSUgDQG/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x1168728) [0x7fa105a86728]
 6  /tmp/RtmplhwcLW/working_dir/RtmpSUgDQG/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x773544) [0x7fa105091544]
 7  /tmp/RtmplhwcLW/working_dir/RtmpSUgDQG/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x7718d9) [0x7fa10508f8d9]
 8  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper29LoadExternalExtensionInternalERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEERNS_19ExtensionActiveLoadE+0x18f) [0x7fa15107f85f]
 9  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper21LoadExternalExtensionERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEE+0x4a) [0x7fa15107f60a]
10  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZNK6duckdb12PhysicalLoad15GetDataInternalERNS_16ExecutionContextERNS_9DataChunkERNS_19OperatorSourceInputE+0x151) [0x7fa151e6d401]
11  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor15FetchFromSourceERNS_9DataChunkE+0x98) [0x7fa1526a10c8]
12  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor7ExecuteEm+0x146) [0x7fa15269dca6]
13  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12PipelineTask11ExecuteTaskENS_17TaskExecutionModeE+0x112) [0x7fa15269d8d2]
14  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12ExecutorTask7ExecuteENS_17TaskExecutionModeE+0xa0) [0x7fa152697570]
15  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb8Executor11ExecuteTaskEb+0x1c0) [0x7fa15269c8d0]
16  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb13ClientContext19ExecuteTaskInternalERNS_17ClientContextLockERNS_15BaseQueryResultEb+0x40) [0x7fa1524a8c60]
17  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb18PendingQueryResult15ExecuteInternalERNS_17ClientContextLockE+0x7a) [0x7fa1524ab3ba]
18  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb13ClientContext7ExecuteERKNSt3__112basic_stringIcNS1_11char_traitsIcEENS1_9allocatorIcEEEERNS_10shared_ptrINS_21PreparedStatementDataELb1EEERKNS_22PendingQueryParametersE+0xa0) [0x7fa1524ab100]
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) [0x7fa1524ce3a3]
20  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb17PreparedStatement7ExecuteERNS_6vectorINS_5ValueELb1ENSt3__19allocatorIS2_EEEEb+0x172) [0x7fa1524ce642]
21  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(+0x1087fc) [0x7fa150d087fc]
22  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_duckdb_rapi_execute+0x63) [0x7fa150d72f73]
23  /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8f5b4) [0x55642a5695b4]
24  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdae98) [0x55642a5b4e98]
25  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc921c) [0x55642a5a321c]
26  /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55642a5a29d5]
27  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9474) [0x55642a5a3474]
28  /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x26e) [0x55642a5a2a9e]
29  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9474) [0x55642a5a3474]
30  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdcfa0) [0x55642a5b6fa0]
31  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcd659) [0x55642a5a7659]
32  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc921c) [0x55642a5a321c]
33  /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55642a5a29d5]
34  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0b39) [0x55642a5bab39]
35  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe002b) [0x55642a5ba02b]
36  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc98f7) [0x55642a5a38f7]
37  /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f8) [0x55642a5a2e28]
38  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9474) [0x55642a5a3474]
39  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdcfa0) [0x55642a5b6fa0]
40  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcd659) [0x55642a5a7659]
41  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc921c) [0x55642a5a321c]
42  /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55642a5a29d5]
43  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0b39) [0x55642a5bab39]
44  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe002b) [0x55642a5ba02b]
45  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc98f7) [0x55642a5a38f7]
46  /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f8) [0x55642a5a2e28]
47  /data/gannet/ripley/R/test-clang/rlang/libs/rlang.so(+0x4993) [0x7fa22c2f2993]
48  /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8d703) [0x55642a567703]
49  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcfc54) [0x55642a5a9c54]
50  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc921c) [0x55642a5a321c]
51  /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55642a5a29d5]
52  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0b39) [0x55642a5bab39]
53  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe002b) [0x55642a5ba02b]
54  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc98f7) [0x55642a5a38f7]
55  /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f8) [0x55642a5a2e28]
56  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe5e98) [0x55642a5bfe98]
57  /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x55642a5a2c00]
58  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe518b) [0x55642a5bf18b]
59  /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x55642a5a2c00]
60  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0b39) [0x55642a5bab39]
61  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe002b) [0x55642a5ba02b]
=================================

 *** caught segfault ***
address 0x4d2001e3f3a, 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$ref, duckdb_convert_opts_impl(res@connection@convert_opts,     arrow = res@arrow))
 9: duckdb_execute(res)
10: duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
11: .local(conn, statement, ...)
12: dbSendQuery(conn, statement, ...)
13: dbSendQuery(conn, statement, ...)
14: dbSendStatement(conn, statement, ...)
15: dbSendStatement(conn, statement, ...)
16: DBI::dbExecute(conn, glue::glue("LOAD {extension};"))
17: DBI::dbExecute(conn, glue::glue("LOAD {extension};"))
18: withCallingHandlers(expr, message = function(c) if (inherits(c,     classes)) tryInvokeRestart("muffleMessage"))
19: suppressMessages(DBI::dbExecute(conn, glue::glue("LOAD {extension};")))
20: doTryCatch(return(expr), name, parentenv, handler)
21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
22: tryCatchList(expr, classes, parentenv, handlers)
23: tryCatch({    suppressMessages(DBI::dbExecute(conn, glue::glue("LOAD {extension};")))}, error = function(e) {    cli::cli_abort(c("Failed to load the {extension} extension.",         x = conditionMessage(e), i = "The binary may be corrupt or incompatible with this platform/DuckDB version.",         i = "Try reinstalling with {.code ddbs_install(extension = '{extension}', upgrade = TRUE)}"))})
24: ddbs_load(conn, quiet = TRUE)
25: ddbs_create_conn(dbdir = "memory", ...)
26: ddbs_default_conn()
27: resolve_spatial_connections(target, source, conn, quiet = quiet)
28: ddbs_interpolate_aw(target = grid, source = nc, tid = "target_id",     sid = "source_id", extensive = "BIR74", weight = "total",     mode = "sf")
29: eval(expr, envir)
30: eval(expr, envir)
31: withVisible(eval(expr, envir))
32: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) {    watcher$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$push(cnd)    switch(on_error, continue = invokeRestart("eval_continue"),         stop = invokeRestart("eval_stop"), error = NULL)})
33: eval(call)
34: eval(call)
35: with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers)
36: doWithOneRestart(return(expr), restart)
37: withOneRestart(expr, restarts[[1L]])
38: withRestartList(expr, restarts[-nr])
39: doWithOneRestart(return(expr), restart)
40: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
41: withRestartList(expr, restarts)
42: withRestarts(with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
43: evaluate::evaluate(...)
44: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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))
45: in_dir(input_dir(), expr)
46: 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$render, options)))
47: eng_r(options)
48: block_exec(params)
49: call_block(x)
50: process_group(group)
51: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    })
52: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    }), list(rlang_trace_top_env = knit_global()))
53: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    }), list(rlang_trace_top_env = knit_global())), function(loc) {    setwd(wd)    write_utf8(res, output %n% stdout())    paste0("\nQuitting from ", loc, if (!is.null(error))         paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
54: process_file(text, output)
55: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
56: rmarkdown::render(input = input, output_format = output_format,     knit_root_dir = knit_root_dir, params = params, run_pandoc = FALSE,     envir = env)
57: execute(params$input, params$format, params$tempDir, params$libDir,     params$dependencies, params$cwd, params$params, params$resourceDir,     params$handledLanguages, params$markdown)
58: .main()
An irrecoverable exception occurred. R is aborting now ...
[39m[33mWARN: Error encountered when rendering files[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
[31m

processing file: benchmark.qmd
[39m[31moutput file: benchmark.knit.md

[39m[1mpandoc [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: {}
  
[1mmetadata[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
[31m

processing file: duckspatial.qmd
[39m[31mError in `value[[3L]]()`:
! Failed to load the spatial extension.
✖ Invalid Error: Invalid Input Error: Initialization functio[39m[31mn
  "spatial_duckdb_cpp_init" from file
  "/tmp/RtmplhwcLW/working_dir/Rtmpeh5GLW/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension"
  threw an exception: "Missing DB manager" ℹ Context: rapi_execute ℹ Error
  type: INVALID
ℹ The binary may be corrupt or incompatible with this platform/DuckDB version.
ℹ Try reinstalling with `ddbs_install(extension = 'spatial', upgrade = TRUE)`
Backtrace:
     ▆
  1. └─duckspatial::ddbs_open_dataset(...)
  2.   └─duckspatial:::ddbs_default_conn()
  3.     └─duckspatial::ddbs_create_conn(dbdir = "memory", ...)
  4.       └─duckspatial::ddbs_load(conn, quiet = TRUE)
  5.         └─base::tryCatch(...)
  6.           └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  7.             └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  8.               └─value[[3L]](cond)
  9.                 └─cli::cli_abort(...)
 10.                   └─rlang::abort(...)
[39m[31m
Quitting from duckspatial.qmd:78-87 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `value[[3L]]()`:
! Failed to load the spatial extension.
✖ Invalid Error: Invalid Input Error: Initialization function
  "spatial_duckdb_cpp_init" from file
  "/tmp/RtmplhwcLW/working_dir/Rtmpeh5GLW/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension"
  threw an exception: "Missing DB manager" ℹ Context: rapi_execute ℹ Error
  type: INVALID
ℹ The binary may be corrupt or incompatible with this platform/DuckDB version.
ℹ Try reinstalling with `ddbs_install(extension = 'spatial', upgrade = TRUE)`
---
Backtrace:
    ▆
 1. └─duckspatial::ddbs_open_dataset(...)
 2.   └─duckspatial:::ddbs_default_conn()
 3.     └─duckspatial::ddbs_create_conn(dbdir = "memory", ...)
 4.       └─duckspatial::ddbs_load(conn, quiet = TRUE)
 5.         └─base::tryCatch(...)
 6.           └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 7.             └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 8.               └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

[39m[31mExecution halted
[39m[33mWARN: Error encountered when rendering files[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
  [31mError in `value[[3L]]()`:[39m
  ! Failed to load the spatial extension.
  ✖ Invalid Error: Invalid Input Error: Initialization functio[31mn[39m
  "spatial_duckdb_cpp_init" from file
  "/tmp/RtmplhwcLW/working_dir/Rtmpeh5GLW/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension"
  threw an exception: "Missing DB manager" ℹ Context: rapi_execute ℹ Error
  type: INVALID
  ℹ The binary may be corrupt or incompatible with this platform/DuckDB
  version.
  ℹ Try reinstalling with `ddbs_install(extension = 'spatial', upgrade = TRUE)`
  Backtrace:
  ▆
  1. └─duckspatial::ddbs_open_dataset(...)
  2.  └─duckspatial:::ddbs_default_conn()
  3.  └─duckspatial::ddbs_create_conn(dbdir = "memory", ...)
  4.  └─duckspatial::ddbs_load(conn, quiet = TRUE)
  5.  └─base::tryCatch(...)
  6.  └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  7.  └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  8.  └─value[[3L]](cond)
  9.  └─cli::cli_abort(...)
  10.  └─rlang::abort(...)
  
  Quitting from duckspatial.qmd:78-87 [unnamed-chunk-2]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error in `value[[3L]]()`:
  ! Failed to load the spatial extension.
  ✖ Invalid Error: Invalid Input Error: Initialization function
  "spatial_duckdb_cpp_init" from file
  "/tmp/RtmplhwcLW/working_dir/Rtmpeh5GLW/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension"
  threw an exception: "Missing DB manager" ℹ Context: rapi_execute ℹ Error
  type: INVALID
  ℹ The binary may be corrupt or incompatible with this platform/DuckDB
  version.
  ℹ Try reinstalling with `ddbs_install(extension = 'spatial', upgrade = TRUE)`
  ---
  Backtrace:
  ▆
  1. └─duckspatial::ddbs_open_dataset(...)
  2.  └─duckspatial:::ddbs_default_conn()
  3.  └─duckspatial::ddbs_create_conn(dbdir = "memory", ...)
  4.  └─duckspatial::ddbs_load(conn, quiet = TRUE)
  5.  └─base::tryCatch(...)
  6.  └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  7.  └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  8.  └─value[[3L]](cond)
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  [31mExecution halted[39m
  [33mWARN: Error encountered when rendering files[39m
  
Caused by error in `processx::run()`:
! System command 'quarto' failed
--- failed re-building ‘duckspatial.qmd’

--- re-building ‘spatial_joins.qmd’ using html
[31m

processing file: spatial_joins.qmd
[39m[31m[gannet:1988211:0:1988603] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x6d3662)
[39m[31m==== backtrace (tid:1988603) ====
 0  /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7f09519e4df4]
 1  /lib64/libucs.so.0(+0x17aed) [0x7f09519e6aed]
 2  /lib64/libucs.so.0(+0x17cbd) [0x7f09519e6cbd]
 3  /lib64/libc.so.6(+0x1a040) [0x7f0968029040]
 4  /tmp/RtmplhwcLW/working_dir/RtmpLGNJRH/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0xc3af88) [0x7f083076ff88]
 5  /tmp/RtmplhwcLW/working_dir/RtmpLGNJRH/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0xc3e647) [0x7f0830773647]
 6  /tmp/RtmplhwcLW/working_dir/RtmpLGNJRH/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0xc3e7c4) [0x7f08307737c4]
 7  /tmp/RtmplhwcLW/working_dir/RtmpLGNJRH/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x116876a) [0x7f0830c9d76a]
 8  /tmp/RtmplhwcLW/working_dir/RtmpLGNJRH/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x773544) [0x7f08302a8544]
 9  /tmp/RtmplhwcLW/working_dir/RtmpLGNJRH/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x7718d9) [0x7f08302a68d9]
10  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper29LoadExternalExtensionInternalERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEERNS_19ExtensionActiveLoadE+0x18f) [0x7f088a67f85f]
11  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper21LoadExternalExtensionERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEE+0x4a) [0x7f088a67f60a]
12  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZNK6duckdb12PhysicalLoad15GetDataInternalERNS_16ExecutionContextERNS_9DataChunkERNS_19OperatorSourceInputE+0x151) [0x7f088b46d401]
13  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor15FetchFromSourceERNS_9DataChunkE+0x98) [0x7f088bca10c8]
14  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor7ExecuteEm+0x146) [0x7f088bc9dca6]
15  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12PipelineTask11ExecuteTaskENS_17TaskExecutionModeE+0x154) [0x7f088bc9d914]
16  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12ExecutorTask7ExecuteENS_17TaskExecutionModeE+0xa0) [0x7f088bc97570]
17  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb13TaskScheduler14ExecuteForeverEPNSt3__16atomicIbEE+0x39a) [0x7f088bca432a]
18  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(+0x1aafe9c) [0x7f088bcafe9c]
19  /lib64/libc.so.6(+0x71f14) [0x7f0968080f14]
20  /lib64/libc.so.6(+0xf532c) [0x7f096810432c]
=================================

 *** caught segfault ***
address 0x4d2001e5673, 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$ref, duckdb_convert_opts_impl(res@connection@convert_opts,     arrow = res@arrow))
 9: duckdb_execute(res)
10: duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
11: .local(conn, statement, ...)
12: dbSendQuery(conn, statement, ...)
13: dbSendQuery(conn, statement, ...)
14: dbSendStatement(conn, statement, ...)
15: dbSendStatement(conn, statement, ...)
16: DBI::dbExecute(conn, glue::glue("LOAD {extension};"))
17: DBI::dbExecute(conn, glue::glue("LOAD {extension};"))
18: withCallingHandlers(expr, message = function(c) if (inherits(c,     classes)) tryInvokeRestart("muffleMessage"))
19: suppressMessages(DBI::dbExecute(conn, glue::glue("LOAD {extension};")))
20: doTryCatch(return(expr), name, parentenv, handler)
21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
22: tryCatchList(expr, classes, parentenv, handlers)
23: tryCatch({    suppressMessages(DBI::dbExecute(conn, glue::glue("LOAD {extension};")))}, error = function(e) {    cli::cli_abort(c("Failed to load the {extension} extension.",         x = conditionMessage(e), i = "The binary may be corrupt or incompatible with this platform/DuckDB version.",         i = "Try reinstalling with {.code ddbs_install(extension = '{extension}', upgrade = TRUE)}"))})
24: ddbs_load(conn, quiet = TRUE)
25: ddbs_create_conn(dbdir = "memory", ...)
26: ddbs_default_conn()
27: resolve_spatial_connections(x, y, conn, conn_x, conn_y, quiet = quiet)
28: ddbs_join(x = points_sf, y = countries_sf, join = "within")
29: eval(expr, envir)
30: eval(expr, envir)
31: withVisible(eval(expr, envir))
32: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) {    watcher$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$push(cnd)    switch(on_error, continue = invokeRestart("eval_continue"),         stop = invokeRestart("eval_stop"), error = NULL)})
33: eval(call)
34: eval(call)
35: with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers)
36: doWithOneRestart(return(expr), restart)
37: withOneRestart(expr, restarts[[1L]])
38: withRestartList(expr, restarts[-nr])
39: doWithOneRestart(return(expr), restart)
40: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
41: withRestartList(expr, restarts)
42: withRestarts(with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
43: evaluate::evaluate(...)
44: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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))
45: in_dir(input_dir(), expr)
46: 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$render, options)))
47: eng_r(options)
48: block_exec(params)
49: call_block(x)
50: process_group(group)
51: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    })
52: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    }), list(rlang_trace_top_env = knit_global()))
53: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    }), list(rlang_trace_top_env = knit_global())), function(loc) {    setwd(wd)    write_utf8(res, output %n% stdout())    paste0("\nQuitting from ", loc, if (!is.null(error))         paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
54: process_file(text, output)
55: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
56: rmarkdown::render(input = input, output_format = output_format,     knit_root_dir = knit_root_dir, params = params, run_pandoc = FALSE,     envir = env)
57: execute(params$input, params$format, params$tempDir, params$libDir,     params$dependencies, params$cwd, params$params, params$resourceDir,     params$handledLanguages, params$markdown)
58: .main()
An irrecoverable exception occurred. R is aborting now ...
[39m[33mWARN: Error encountered when rendering files[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