Last updated on 2026-02-12 10:50:26 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-fedora-clang | 0.2.0 | 75.44 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.2.0 | 72.21 | OK | |||
| r-devel-macos-arm64 | 0.2.0 | 1.00 | 17.00 | 18.00 | OK | |
| r-release-macos-arm64 | 0.2.0 | OK | ||||
| r-release-macos-x86_64 | 0.2.0 | 4.00 | 65.00 | 69.00 | OK | |
| r-oldrel-macos-arm64 | 0.2.0 | 1.00 | 25.00 | 26.00 | OK | |
| r-oldrel-macos-x86_64 | 0.2.0 | 13.00 | ERROR |
Version: 0.2.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [14s/29s]
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(cnefetools)
>
> test_check("cnefetools")
v All 6 CNEFE points were captured within the provided polygon.
Assuming columns 1 and 2 contain x, y coordinates in EPSG:4326
v All 5 CNEFE points were captured within the provided polygon.
[gannet:3528491:0:3529667] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x5)
==== backtrace (tid:3529667) ====
0 /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7fe5e0db2df4]
1 /lib64/libucs.so.0(+0x17aed) [0x7fe5e0db4aed]
2 /lib64/libucs.so.0(+0x17cbd) [0x7fe5e0db4cbd]
3 /lib64/libc.so.6(+0x19c30) [0x7fe60d227c30]
4 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.4.4/linux_amd64/spatial.duckdb_extension(+0x10ecf30) [0x7fe3b84ecf30]
5 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.4.4/linux_amd64/spatial.duckdb_extension(+0x10cbeb8) [0x7fe3b84cbeb8]
6 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.4.4/linux_amd64/spatial.duckdb_extension(+0x7d8bb4) [0x7fe3b7bd8bb4]
7 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.4.4/linux_amd64/spatial.duckdb_extension(+0x7d7159) [0x7fe3b7bd7159]
8 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper29LoadExternalExtensionInternalERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEERNS_19ExtensionActiveLoadE+0x1b4) [0x7fe4115734a4]
9 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper21LoadExternalExtensionERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEE+0x4a) [0x7fe41157322a]
10 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZNK6duckdb12PhysicalLoad7GetDataERNS_16ExecutionContextERNS_9DataChunkERNS_19OperatorSourceInputE+0x151) [0x7fe4123a9511]
11 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor15FetchFromSourceERNS_9DataChunkE+0x9f) [0x7fe412b5e6cf]
12 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor7ExecuteEm+0x133) [0x7fe412b5b163]
13 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12PipelineTask11ExecuteTaskENS_17TaskExecutionModeE+0x15b) [0x7fe412b5addb]
14 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12ExecutorTask7ExecuteENS_17TaskExecutionModeE+0xa0) [0x7fe412b546b0]
15 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb13TaskScheduler14ExecuteForeverEPNSt3__16atomicIbEE+0x379) [0x7fe412b619b9]
16 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(+0x196c87c) [0x7fe412b6c87c]
17 /lib64/libc.so.6(+0x711d4) [0x7fe60d27f1d4]
18 /lib64/libc.so.6(+0xf3cec) [0x7fe60d301cec]
=================================
*** caught segfault ***
address 0x4d20035d72b, 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$ref, duckdb_convert_opts_impl(res@connection@convert_opts, arrow = res@arrow))
9: duckdb_execute(res)
10: duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
11: .local(conn, statement, ...)
12: dbSendQuery(conn, statement, ...)
13: dbSendQuery(conn, statement, ...)
14: dbSendStatement(conn, statement, ...)
15: dbSendStatement(conn, statement, ...)
16: DBI::dbExecute(con_check, "LOAD spatial;")
17: DBI::dbExecute(con_check, "LOAD spatial;")
18: doTryCatch(return(expr), name, parentenv, handler)
19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
20: tryCatchList(expr, classes, parentenv, handlers)
21: tryCatch({ DBI::dbExecute(con_check, "LOAD spatial;") TRUE}, error = function(e) { tryCatch({ DBI::dbExecute(con_check, "INSTALL spatial; LOAD spatial;") TRUE }, error = function(e2) FALSE)})
22: eval(code, test_env)
23: eval(code, test_env)
24: withCallingHandlers({ eval(code, test_env) new_expectations <- the$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: testthat::test_that("tracts_to_h3 returns an sf object with requested variables", { testthat::skip_if_not_installed("duckdb") testthat::skip_if_not_installed("duckspatial") testthat::skip_if_not_installed("h3jsr") con_check <- DBI::dbConnect(duckdb::duckdb(), dbdir = ":memory:") on.exit(DBI::dbDisconnect(con_check, shutdown = TRUE), add = TRUE) ok_zipfs <- tryCatch({ DBI::dbExecute(con_check, "LOAD zipfs;") TRUE }, error = function(e) { tryCatch({ DBI::dbExecute(con_check, "INSTALL zipfs; LOAD zipfs;") TRUE }, error = function(e2) FALSE) }) ok_h3 <- tryCatch({ DBI::dbExecute(con_check, "LOAD h3;") TRUE }, error = function(e) { tryCatch({ DBI::dbExecute(con_check, "INSTALL h3; LOAD h3;") TRUE }, error = function(e2) FALSE) }) ok_spatial <- tryCatch({ DBI::dbExecute(con_check, "LOAD spatial;") TRUE }, error = function(e) { tryCatch({ DBI::dbExecute(con_check, "INSTALL spatial; LOAD spatial;") TRUE }, error = function(e2) FALSE) }) if (!ok_zipfs) { testthat::skip("DuckDB zipfs extension not available.") } if (!ok_h3) { testthat::skip("DuckDB h3 extension not available.") } if (!ok_spatial) { testthat::skip("DuckDB spatial extension not available.") } res <- NULL testthat::with_mocked_bindings({ testthat::expect_message(res <- cnefetools::tracts_to_h3(code_muni = 2927408, h3_resolution = 9, vars = c("pop_ph", "avg_inc_resp", "n_resp", "female", "age_70m"), cache = TRUE, verbose = FALSE), "Dasymetric interpolation diagnostics", fixed = TRUE) testthat::expect_s3_class(res, "sf") needed <- c("id_hex", "pop_ph", "avg_inc_resp", "n_resp", "female", "age_70m") testthat::expect_true(all(needed %in% names(res))) timing <- attr(res, "timing", exact = TRUE) testthat::expect_true(is.list(timing) || is.null(timing)) testthat::expect_true(is.numeric(res$pop_ph)) testthat::expect_gt(sum(res$pop_ph, na.rm = TRUE), 0) testthat::expect_equal(round(sum(res$pop_ph, na.rm = TRUE)), 100) testthat::expect_true(is.numeric(res$avg_inc_resp) || all(is.na(res$avg_inc_resp))) }, .sc_create_views_in_duckdb = function(con, code_muni, cache, verbose) { DBI::dbExecute(con, "\n CREATE OR REPLACE VIEW sc_muni AS\n SELECT\n '292740800000001' AS code_tract,\n 100::INTEGER AS pop_ph,\n 60::INTEGER AS female,\n 5::INTEGER AS age_70m,\n 40::INTEGER AS n_resp,\n 2000.0::DOUBLE AS avg_inc_resp,\n ST_GeomFromText('POLYGON((0 0, 1 0, 1 1, 0 1, 0 0))') AS geom\n UNION ALL\n SELECT\n '292740800000002' AS code_tract,\n 50::INTEGER AS pop_ph,\n 20::INTEGER AS female,\n 2::INTEGER AS age_70m,\n 10::INTEGER AS n_resp,\n 3000.0::DOUBLE AS avg_inc_resp,\n ST_GeomFromText('POLYGON((2 0, 3 0, 3 1, 2 1, 2 0))') AS geom\n ") }, .cnefe_create_points_view_in_duckdb = function(con, code_muni, index, cache, verbose) { DBI::dbExecute(con, "\n CREATE OR REPLACE VIEW cnefe_pts AS\n SELECT\n 1::BIGINT AS COD_UNICO_ENDERECO,\n 1::INTEGER AS COD_ESPECIE,\n 0.2::DOUBLE AS lon,\n 0.2::DOUBLE AS lat,\n ST_Point(0.2, 0.2) AS geom\n UNION ALL\n SELECT 2, 1, 0.2, 0.8, ST_Point(0.2, 0.8)\n UNION ALL\n SELECT 3, 1, 0.8, 0.2, ST_Point(0.8, 0.2)\n UNION ALL\n SELECT 4, 1, 0.8, 0.8, ST_Point(0.8, 0.8)\n UNION ALL\n SELECT 5, 1, 10.0, 10.0, ST_Point(10.0, 10.0)\n ") }) })
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("cnefetools")
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.2.0
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