Last updated on 2026-01-11 07:49:52 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.2.0 | 2.21 | 24.70 | 26.91 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.2.0 | 1.54 | 19.27 | 20.81 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.9.0 | 8.00 | 114.55 | 122.55 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 0.9.0 | 153.76 | OK | |||
| r-devel-windows-x86_64 | 0.2.0 | 4.00 | 44.00 | 48.00 | OK | |
| r-patched-linux-x86_64 | 0.2.0 | 2.22 | 20.74 | 22.96 | OK | |
| r-release-linux-x86_64 | 0.2.0 | 1.49 | 20.40 | 21.89 | OK | |
| r-release-macos-arm64 | 0.9.0 | 1.00 | 31.00 | 32.00 | OK | |
| r-release-macos-x86_64 | 0.9.0 | 3.00 | 106.00 | 109.00 | OK | |
| r-release-windows-x86_64 | 0.2.0 | 4.00 | 44.00 | 48.00 | OK | |
| r-oldrel-macos-arm64 | 0.9.0 | 1.00 | 39.00 | 40.00 | OK | |
| r-oldrel-macos-x86_64 | 0.9.0 | 14.00 | ERROR | |||
| r-oldrel-windows-x86_64 | 0.2.0 | 5.00 | 51.00 | 56.00 | OK |
Version: 0.9.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [9s/57s]
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)
Important: 'crs_column' and 'crs' arguments are deprecated and will be removed in the next version.
If possible, use the default values of these arguments to avoid future issues.
> 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
Reading layer `rivers' from data source
`/data/gannet/ripley/R/packages/tests-clang/duckspatial.Rcheck/duckspatial/spatial/rivers.geojson'
using driver `GeoJSON'
Simple feature collection with 100 features and 1 field
Geometry type: LINESTRING
Dimension: XY
Bounding box: xmin: 2766878 ymin: 2222357 xmax: 3578648 ymax: 2459939
Projected CRS: ETRS89-extended / LAEA Europe
Saving _problems/test-compatibility-5.R
[gannet:2953564:0:2954733] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x7e7e2106)
==== backtrace (tid:2954733) ====
0 /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7f88c53e7df4]
1 /lib64/libucs.so.0(+0x17aed) [0x7f88c53e9aed]
2 /lib64/libucs.so.0(+0x17cbd) [0x7f88c53e9cbd]
3 /lib64/libc.so.6(+0x19c30) [0x7f88de027c30]
4 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.4.3/linux_amd64/spatial.duckdb_extension(+0x10e9860) [0x7f87b04e9860]
5 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.4.3/linux_amd64/spatial.duckdb_extension(+0x10c8508) [0x7f87b04c8508]
6 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.4.3/linux_amd64/spatial.duckdb_extension(+0x7d6434) [0x7f87afbd6434]
7 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.4.3/linux_amd64/spatial.duckdb_extension(+0x7d49d9) [0x7f87afbd49d9]
8 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper29LoadExternalExtensionInternalERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEERNS_19ExtensionActiveLoadE+0x1b4) [0x7f88ca171a54]
9 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper21LoadExternalExtensionERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEE+0x4a) [0x7f88ca1717da]
10 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZNK6duckdb12PhysicalLoad7GetDataERNS_16ExecutionContextERNS_9DataChunkERNS_19OperatorSourceInputE+0x151) [0x7f88cafac941]
11 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor15FetchFromSourceERNS_9DataChunkE+0x9f) [0x7f88cb75f55f]
12 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor7ExecuteEm+0x133) [0x7f88cb75bff3]
13 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12PipelineTask11ExecuteTaskENS_17TaskExecutionModeE+0x15b) [0x7f88cb75bc6b]
14 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12ExecutorTask7ExecuteENS_17TaskExecutionModeE+0xa0) [0x7f88cb755540]
15 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb13TaskScheduler14ExecuteForeverEPNSt3__16atomicIbEE+0x379) [0x7f88cb762849]
16 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(+0x196d7bc) [0x7f88cb76d7bc]
17 /lib64/libc.so.6(+0x711d4) [0x7f88de07f1d4]
18 /lib64/libc.so.6(+0xf3cec) [0x7f88de101cec]
=================================
*** caught segfault ***
address 0x4d2002d115c, 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$ref, duckdb_convert_opts_impl(res@connection@convert_opts, arrow = res@arrow))
9: duckdb_execute(res)
10: duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
11: .local(conn, statement, ...)
12: dbSendQuery(conn, statement, ...)
13: dbSendQuery(conn, statement, ...)
14: dbSendStatement(conn, statement, ...)
15: dbSendStatement(conn, statement, ...)
16: DBI::dbExecute(conn, "LOAD spatial;")
17: DBI::dbExecute(conn, "LOAD spatial;")
18: withCallingHandlers(expr, message = function(c) if (inherits(c, classes)) tryInvokeRestart("muffleMessage"))
19: suppressMessages(DBI::dbExecute(conn, "LOAD spatial;"))
20: duckspatial::ddbs_load(conn, quiet = TRUE)
21: ddbs_create_conn("memory")
22: eval(code, test_env)
23: eval(code, test_env)
24: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
25: doTryCatch(return(expr), name, parentenv, handler)
26: tryCatchOne(expr, names, parentenv, handlers[[1L]])
27: tryCatchList(expr, classes, parentenv, handlers)
28: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
29: doWithOneRestart(return(expr), restart)
30: withOneRestart(expr, restarts[[1L]])
31: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
32: test_code(code, parent.frame())
33: test_that("Round trip: write -> read for various geometry types", { skip_if_not_installed("duckdb") conn <- ddbs_create_conn("memory") on.exit(ddbs_stop_conn(conn), add = TRUE) line <- sf::st_sf(id = 1, geom = sf::st_as_sfc("LINESTRING(0 0, 1 1)"), crs = 4326) polygon <- sf::st_sf(id = 1, geom = sf::st_as_sfc("POLYGON((0 0, 1 0, 1 1, 0 1, 0 0))"), crs = 4326) multipoint <- sf::st_sf(id = 1, geom = sf::st_as_sfc("MULTIPOINT(0 0, 1 1)"), crs = 4326) datasets <- list(line = line, polygon = polygon, multipoint = multipoint) for (name in names(datasets)) { data <- datasets[[name]] table_name <- paste0("rt_write_", name) ddbs_write_vector(conn, data, table_name, overwrite = TRUE) result <- ddbs_read_vector(conn, table_name) expect_s3_class(result, "sf") expect_equal(nrow(result), 1) expect_equal(sf::st_crs(result), sf::st_crs(data)) expect_true(all.equal(sf::st_geometry(result), sf::st_geometry(data), check.attributes = FALSE)) } })
34: eval(code, test_env)
35: eval(code, test_env)
36: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
37: doTryCatch(return(expr), name, parentenv, handler)
38: tryCatchOne(expr, names, parentenv, handlers[[1L]])
39: tryCatchList(expr, classes, parentenv, handlers)
40: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
41: doWithOneRestart(return(expr), restart)
42: withOneRestart(expr, restarts[[1L]])
43: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
44: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
45: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
46: FUN(X[[i]], ...)
47: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
48: doTryCatch(return(expr), name, parentenv, handler)
49: tryCatchOne(expr, names, parentenv, handlers[[1L]])
50: tryCatchList(expr, classes, parentenv, handlers)
51: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
52: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
53: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call)
54: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle)
55: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
56: test_check("duckspatial")
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.9.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘aw_interpolation.Rmd’ using rmarkdown
[gannet:2961082:0:2962363] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x9d71006221)
==== backtrace (tid:2962363) ====
0 /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7f8d6f77ddf4]
1 /lib64/libucs.so.0(+0x17aed) [0x7f8d6f77faed]
2 /lib64/libucs.so.0(+0x17cbd) [0x7f8d6f77fcbd]
3 /lib64/libc.so.6(+0x19c30) [0x7f8d85f29c30]
4 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.4.3/linux_amd64/spatial.duckdb_extension(+0x10e7900) [0x7f8c484e7900]
5 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.4.3/linux_amd64/spatial.duckdb_extension(+0x10c8508) [0x7f8c484c8508]
6 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.4.3/linux_amd64/spatial.duckdb_extension(+0x7d6434) [0x7f8c47bd6434]
7 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.4.3/linux_amd64/spatial.duckdb_extension(+0x7d49d9) [0x7f8c47bd49d9]
8 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper29LoadExternalExtensionInternalERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEERNS_19ExtensionActiveLoadE+0x1b4) [0x7f8ca8571a54]
9 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper21LoadExternalExtensionERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEE+0x4a) [0x7f8ca85717da]
10 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZNK6duckdb12PhysicalLoad7GetDataERNS_16ExecutionContextERNS_9DataChunkERNS_19OperatorSourceInputE+0x151) [0x7f8ca93ac941]
11 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor15FetchFromSourceERNS_9DataChunkE+0x9f) [0x7f8ca9b5f55f]
12 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor7ExecuteEm+0x133) [0x7f8ca9b5bff3]
13 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12PipelineTask11ExecuteTaskENS_17TaskExecutionModeE+0x15b) [0x7f8ca9b5bc6b]
14 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12ExecutorTask7ExecuteENS_17TaskExecutionModeE+0xa0) [0x7f8ca9b55540]
15 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb13TaskScheduler14ExecuteForeverEPNSt3__16atomicIbEE+0x379) [0x7f8ca9b62849]
16 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(+0x196d7bc) [0x7f8ca9b6d7bc]
17 /lib64/libc.so.6(+0x711d4) [0x7f8d85f811d4]
18 /lib64/libc.so.6(+0xf3cec) [0x7f8d86003cec]
=================================
*** caught segfault ***
address 0x4d2002d2eba, 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, "LOAD spatial;")
17: DBI::dbExecute(conn, "LOAD spatial;")
18: withCallingHandlers(expr, message = function(c) if (inherits(c, classes)) tryInvokeRestart("muffleMessage"))
19: suppressMessages(DBI::dbExecute(conn, "LOAD spatial;"))
20: duckspatial::ddbs_load(conn, quiet = TRUE)
21: ddbs_create_conn()
22: ddbs_interpolate_aw(target = grid, source = nc, tid = "target_id", sid = "source_id", extensive = "BIR74", weight = "total", output = "sf")
23: eval(expr, envir)
24: eval(expr, envir)
25: withVisible(eval(expr, envir))
26: 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)})
27: eval(call)
28: eval(call)
29: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
30: doWithOneRestart(return(expr), restart)
31: withOneRestart(expr, restarts[[1L]])
32: withRestartList(expr, restarts[-nr])
33: doWithOneRestart(return(expr), restart)
34: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
35: withRestartList(expr, restarts)
36: withRestarts(with_handlers({ for (expr in tle$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)
37: evaluate::evaluate(...)
38: 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$render, options))
39: in_dir(input_dir(), expr)
40: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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)))
41: eng_r(options)
42: block_exec(params)
43: call_block(x)
44: process_group(group)
45: 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) })
46: 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()))
47: 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)
48: process_file(text, output)
49: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
50: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
51: vweave_rmarkdown(...)
52: engine$weave(file, quiet = quiet, encoding = enc)
53: doTryCatch(return(expr), name, parentenv, handler)
54: tryCatchOne(expr, names, parentenv, handlers[[1L]])
55: tryCatchList(expr, classes, parentenv, handlers)
56: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
57: tools:::.buildOneVignette("aw_interpolation.Rmd", "/data/gannet/ripley/R/packages/tests-clang/duckspatial.Rcheck/vign_test/duckspatial", TRUE, FALSE, "aw_interpolation", "UTF-8", "/tmp/Rtmpu3u2ac/working_dir/RtmpsiXpF1/file2d2e0e564c59fa.rds")
An irrecoverable exception occurred. R is aborting now ...
--- re-building ‘benchmark.Rmd’ using rmarkdown
--- finished re-building ‘benchmark.Rmd’
--- re-building ‘duckspatial.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘duckspatial.Rmd’
--- re-building ‘spatial_joins.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘spatial_joins.Rmd’
SUMMARY: processing the following file failed:
‘aw_interpolation.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.9.0
Check: package dependencies
Result: ERROR
Package required but not available: ‘arrow’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-oldrel-macos-x86_64