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

processing file: aw_interpolation.qmd
[39m[31mError in `duckdb_result()`:
! Invalid Error: Invalid Input Error: Initialization function "spatial_duckdb_cpp_init" from file "/[39m[31mdata/gannet/ripley/.local/share/R/duckdb/extensions/v1.5.2/linux_amd64/spatial.duckdb_extension" threw an exception: "Missing DB manager"
ℹ Context: rapi_execute
ℹ Error type: INVALID
Backtrace:
     ▆
  1. ├─duckspatial::ddbs_interpolate_aw(...)
  2. │ └─duckspatial:::resolve_spatial_connections(...)
  3. │   └─duckspatial:::ddbs_default_conn()
  4. │     └─duckspatial::ddbs_create_conn(dbdir = "memory", ...)
  5. │       └─duckspatial::ddbs_load(conn, quiet = TRUE)
  6. │         ├─base::suppressMessages(DBI::dbExecute(conn, glue::glue("LOAD {extension};")))
  7. │         │ └─base::withCallingHandlers(...)
  8. │         ├─DBI::dbExecute(conn, glue::glue("LOAD {extension};"))
  9. │         └─DBI::dbExecute(conn, glue::glue("LOAD {extension};"))
 10. │           ├─DBI::dbSendStatement(conn, statement, ...)
 11. │           └─DBI::dbSendStatement(conn, statement, ...)
 12. │             ├─DBI::dbSendQuery(conn, statement, ...)
 13. │             └─duckdb::dbSendQuery(conn, statement, ...)
 14. │               └─duckdb (local) .local(conn, statement, ...)
 15. │                 └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
 16. │                   └─duckdb:::duckdb_execute(res)
 17. │                     └─duckdb:::rethrow_rapi_execute(...)
 18. │                       ├─rlang::try_fetch(...)
 19. │                       │ ├─base::tryCatch(...)
 20. │                       │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 21. │                       │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 22. │                       │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 23. │                       │ └─base::withCallingHandlers(...)
 24. │                       └─duckdb:::rapi_execute(stmt, convert_opts)
 25. ├─duckdb (local) `<fn>`(...)
 26. │ └─rlang::abort(error_parts, class = "duckdb_error", !!!fields)
 27. │   └─rlang:::signal_abort(cnd, .file)
 28. │     └─base::signalCondition(cnd)
 29. └─rlang (local) `<fn>`(`<dckdb_rr>`)
 30.   └─handlers[[1L]](cnd)
 31.     └─duckdb:::rethrow_error_from_rapi(e, call)
 32.       └─rlang::abort(msg, call = call)

Quitting from aw_interpolation.qmd:68-79 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `duckdb_result()`:
! Invalid Error: Invalid Input Error: Initialization function "spatial_duckdb_cpp_init" from file "/data/gannet/ripley/.local/share/R/duckdb/extensions/v1.5.2/linux_amd64/spatial.duckdb_extension" threw an exception: "Missing DB manager"
ℹ Context: rapi_execute
ℹ Error type: INVALID
---
Backtrace:
     ▆
  1. └─duckspatial::ddbs_interpolate_aw(...)
  2.   └─duckspatial:::resolve_spatial_connections(...)
  3.     └─duckspatial:::ddbs_default_conn()
  4.       └─duckspatial::ddbs_create_conn(dbdir = "memory", ...)
  5.         └─duckspatial::ddbs_load(conn, quiet = TRUE)
  6.           ├─base::suppressMessages(DBI::dbExecute(conn, glue::glue("LOAD {extension};")))
  7.           │ └─base::withCallingHandlers(...)
  8.           ├─DBI::dbExecute(conn, glue::glue("LOAD {extension};"))
  9.           └─DBI::dbExecute(conn, glue::glue("LOAD {extension};"))
 10.             ├─DBI::dbSendStatement(conn, statement, ...)
 11.             └─DBI::dbSendStatement(conn, statement, ...)
 12.               ├─DBI::dbSendQuery(conn, statement, ...)
 13.               └─duckdb::dbSendQuery(conn, statement, ...)
 14.                 └─duckdb (local) .local(conn, statement, ...)
 15.                   └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Execution halted
[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 evaluate cli `{}` expression: `extension`.
Caused by error:
! object 'extension' not found
--- 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 `duckdb_result()`:
! Invalid Error: Invalid Input Error: Initialization function "spatial_duckdb_cpp_init" from file "/[39m[31mdata/gannet/ripley/.local/share/R/duckdb/extensions/v1.5.2/linux_amd64/spatial.duckdb_extension" threw an exception: "Missing DB manager"
ℹ Context: rapi_execute
ℹ Error type: INVALID
Backtrace:
     ▆
  1. ├─duckspatial::ddbs_open_dataset(...)
  2. │ └─duckspatial:::ddbs_default_conn()
  3. │   └─duckspatial::ddbs_create_conn(dbdir = "memory", ...)
  4. │     └─duckspatial::ddbs_load(conn, quiet = TRUE)
  5. │       ├─base::suppressMessages(DBI::dbExecute(conn, glue::glue("LOAD {extension};")))
  6. │       │ └─base::withCallingHandlers(...)
  7. │       ├─DBI::dbExecute(conn, glue::glue("LOAD {extension};"))
  8. │       └─DBI::dbExecute(conn, glue::glue("LOAD {extension};"))
  9. │         ├─DBI::dbSendStatement(conn, statement, ...)
 10. │         └─DBI::dbSendStatement(conn, statement, ...)
 11. │           ├─DBI::dbSendQuery(conn, statement, ...)
 12. │           └─duckdb::dbSendQuery(conn, statement, ...)
 13. │             └─duckdb (local) .local(conn, statement, ...)
 14. │               └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
 15. │                 └─duckdb:::duckdb_execute(res)
 16. │                   └─duckdb:::rethrow_rapi_execute(...)
 17. │                     ├─rlang::try_fetch(...)
 18. │                     │ ├─base::tryCatch(...)
 19. │                     │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 20. │                     │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 21. │                     │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 22. │                     │ └─base::withCallingHandlers(...)
 23. │                     └─duckdb:::rapi_execute(stmt, convert_opts)
 24. ├─duckdb (local) `<fn>`(...)
 25. │ └─rlang::abort(error_parts, class = "duckdb_error", !!!fields)
 26. │   └─rlang:::signal_abort(cnd, .file)
 27. │     └─base::signalCondition(cnd)
 28. └─rlang (local) `<fn>`(`<dckdb_rr>`)
 29.   └─handlers[[1L]](cnd)
 30.     └─duckdb:::rethrow_error_from_rapi(e, call)
 31.       └─rlang::abort(msg, call = call)

Quitting from duckspatial.qmd:68-77 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `duckdb_result()`:
! Invalid Error: Invalid Input Error: Initialization function "spatial_duckdb_cpp_init" from file "/data/gannet/ripley/.local/share/R/duckdb/extensions/v1.5.2/linux_amd64/spatial.duckdb_extension" threw an exception: "Missing DB manager"
ℹ Context: rapi_execute
ℹ Error type: INVALID
---
Backtrace:
     ▆
  1. └─duckspatial::ddbs_open_dataset(...)
  2.   └─duckspatial:::ddbs_default_conn()
  3.     └─duckspatial::ddbs_create_conn(dbdir = "memory", ...)
  4.       └─duckspatial::ddbs_load(conn, quiet = TRUE)
  5.         ├─base::suppressMessages(DBI::dbExecute(conn, glue::glue("LOAD {extension};")))
  6.         │ └─base::withCallingHandlers(...)
  7.         ├─DBI::dbExecute(conn, glue::glue("LOAD {extension};"))
  8.         └─DBI::dbExecute(conn, glue::glue("LOAD {extension};"))
  9.           ├─DBI::dbSendStatement(conn, statement, ...)
 10.           └─DBI::dbSendStatement(conn, statement, ...)
 11.             ├─DBI::dbSendQuery(conn, statement, ...)
 12.             └─duckdb::dbSendQuery(conn, statement, ...)
 13.               └─duckdb (local) .local(conn, statement, ...)
 14.                 └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Execution halted
[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:
! Could not evaluate cli `{}` expression: `extension`.
Caused by error:
! object 'extension' not found
--- failed re-building ‘duckspatial.qmd’

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

processing file: spatial_joins.qmd
[39m[31m[gannet:1047240:0:1048346] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x6d3662)
[39m[31m==== backtrace (tid:1048346) ====
 0  /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7f7ca71b7df4]
 1  /lib64/libucs.so.0(+0x17aed) [0x7f7ca71b9aed]
 2  /lib64/libucs.so.0(+0x17cbd) [0x7f7ca71b9cbd]
 3  /lib64/libc.so.6(+0x1a040) [0x7f7cbd728040]
 4  /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.5.2/linux_amd64/spatial.duckdb_extension(+0xc26268) [0x7f7b7c826268]
 5  /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.5.2/linux_amd64/spatial.duckdb_extension(+0xc29927) [0x7f7b7c829927]
 6  /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.5.2/linux_amd64/spatial.duckdb_extension(+0xc29aa4) [0x7f7b7c829aa4]
 7  /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.5.2/linux_amd64/spatial.duckdb_extension(+0x1152a6a) [0x7f7b7cd52a6a]
 8  /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.5.2/linux_amd64/spatial.duckdb_extension(+0x75c104) [0x7f7b7c35c104]
 9  /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.5.2/linux_amd64/spatial.duckdb_extension(+0x75a499) [0x7f7b7c35a499]
10  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper29LoadExternalExtensionInternalERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEERNS_19ExtensionActiveLoadE+0x18f) [0x7f7bdfe79e3f]
11  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper21LoadExternalExtensionERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEE+0x4a) [0x7f7bdfe79bea]
12  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZNK6duckdb12PhysicalLoad15GetDataInternalERNS_16ExecutionContextERNS_9DataChunkERNS_19OperatorSourceInputE+0x151) [0x7f7be0c5e831]
13  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor15FetchFromSourceERNS_9DataChunkE+0x9b) [0x7f7be148d8eb]
14  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor7ExecuteEm+0x146) [0x7f7be148a4c6]
15  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12PipelineTask11ExecuteTaskENS_17TaskExecutionModeE+0x154) [0x7f7be148a134]
16  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12ExecutorTask7ExecuteENS_17TaskExecutionModeE+0xa0) [0x7f7be1483d90]
17  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb13TaskScheduler14ExecuteForeverEPNSt3__16atomicIbEE+0x39a) [0x7f7be1490b1a]
18  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(+0x1a9c68c) [0x7f7be149c68c]
19  /lib64/libc.so.6(+0x71f14) [0x7f7cbd77ff14]
20  /lib64/libc.so.6(+0xf532c) [0x7f7cbd80332c]
=================================

 *** caught segfault ***
address 0x4d2000ffac8, cause 'unknown'

Traceback:
 1: rapi_execute(stmt, convert_opts)
 2: withCallingHandlers(expr, condition = function(cnd) {    {        .__handler_frame__. <- TRUE        .__setup_frame__. <- frame        if (inherits(cnd, "message")) {            except <- c("warning", "error")        }        else if (inherits(cnd, "warning")) {            except <- "error"        }        else {            except <- ""        }    }    while (!is_null(cnd)) {        if (inherits(cnd, "error")) {            out <- handlers[[1L]](cnd)            if (!inherits(out, "rlang_zap"))                 throw(out)        }        inherit <- .subset2(.subset2(cnd, "rlang"), "inherit")        if (is_false(inherit)) {            return()        }        cnd <- .subset2(cnd, "parent")    }})
 3: doTryCatch(return(expr), name, parentenv, handler)
 4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 5: tryCatchList(expr, classes, parentenv, handlers)
 6: tryCatch(withCallingHandlers(expr, condition = function(cnd) {    {        .__handler_frame__. <- TRUE        .__setup_frame__. <- frame        if (inherits(cnd, "message")) {            except <- c("warning", "error")        }        else if (inherits(cnd, "warning")) {            except <- "error"        }        else {            except <- ""        }    }    while (!is_null(cnd)) {        if (inherits(cnd, "error")) {            out <- handlers[[1L]](cnd)            if (!inherits(out, "rlang_zap"))                 throw(out)        }        inherit <- .subset2(.subset2(cnd, "rlang"), "inherit")        if (is_false(inherit)) {            return()        }        cnd <- .subset2(cnd, "parent")    }}), stackOverflowError = handlers[[1L]])
 7: rlang::try_fetch(rapi_execute(stmt, convert_opts), error = function(e) {    rethrow_error_from_rapi(e, call)})
 8: rethrow_rapi_execute(res@stmt_lst$ref, duckdb_convert_opts_impl(res@connection@convert_opts,     arrow = res@arrow))
 9: duckdb_execute(res)
10: duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
11: .local(conn, statement, ...)
12: dbSendQuery(conn, statement, ...)
13: dbSendQuery(conn, statement, ...)
14: dbSendStatement(conn, statement, ...)
15: dbSendStatement(conn, statement, ...)
16: DBI::dbExecute(conn, glue::glue("LOAD {extension};"))
17: DBI::dbExecute(conn, glue::glue("LOAD {extension};"))
18: withCallingHandlers(expr, message = function(c) if (inherits(c,     classes)) tryInvokeRestart("muffleMessage"))
19: suppressMessages(DBI::dbExecute(conn, glue::glue("LOAD {extension};")))
20: ddbs_load(conn, quiet = TRUE)
21: ddbs_create_conn(dbdir = "memory", ...)
22: ddbs_default_conn()
23: resolve_spatial_connections(x, y, conn, conn_x, conn_y, quiet = quiet)
24: ddbs_join(x = points_sf, y = countries_sf, join = "within")
25: eval(expr, envir)
26: eval(expr, envir)
27: withVisible(eval(expr, envir))
28: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) {    watcher$capture_plot_and_output()    if (on_message$capture) {        watcher$push(cnd)    }    if (on_message$silence) {        invokeRestart("muffleMessage")    }}, warning = function (cnd) {    if (getOption("warn") >= 2 || getOption("warn") < 0) {        return()    }    watcher$capture_plot_and_output()    if (on_warning$capture) {        cnd <- sanitize_call(cnd)        watcher$push(cnd)    }    if (on_warning$silence) {        invokeRestart("muffleWarning")    }}, error = function (cnd) {    watcher$capture_plot_and_output()    cnd <- sanitize_call(cnd)    watcher$push(cnd)    switch(on_error, continue = invokeRestart("eval_continue"),         stop = invokeRestart("eval_stop"), error = NULL)})
29: eval(call)
30: eval(call)
31: with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers)
32: doWithOneRestart(return(expr), restart)
33: withOneRestart(expr, restarts[[1L]])
34: withRestartList(expr, restarts[-nr])
35: doWithOneRestart(return(expr), restart)
36: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
37: withRestartList(expr, restarts)
38: withRestarts(with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
39: evaluate::evaluate(...)
40: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,     keep_message = if (is.numeric(options$message)) TRUE else options$message,     stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0L        else 2L    }, output_handler = knit_handlers(options$render, options))
41: in_dir(input_dir(), expr)
42: in_input_dir(evaluate(code, envir = env, new_device = FALSE,     keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,     keep_message = if (is.numeric(options$message)) TRUE else options$message,     stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0L        else 2L    }, output_handler = knit_handlers(options$render, options)))
43: eng_r(options)
44: block_exec(params)
45: call_block(x)
46: process_group(group)
47: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    })
48: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    }), list(rlang_trace_top_env = knit_global()))
49: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    }), list(rlang_trace_top_env = knit_global())), function(loc) {    setwd(wd)    write_utf8(res, output %n% stdout())    paste0("\nQuitting from ", loc, if (!is.null(error))         paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
50: process_file(text, output)
51: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
52: rmarkdown::render(input = input, output_format = output_format,     knit_root_dir = knit_root_dir, params = params, run_pandoc = FALSE,     envir = env)
53: execute(params$input, params$format, params$tempDir, params$libDir,     params$dependencies, params$cwd, params$params, params$resourceDir,     params$handledLanguages, params$markdown)
54: .main()
An irrecoverable exception occurred. R is aborting now ...
[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