Last updated on 2026-06-18 08:52:46 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.1 | 30.13 | 322.42 | 352.55 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.1.1 | 24.72 | 207.78 | 232.50 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.1.1 | 60.00 | 496.21 | 556.21 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 0.1.1 | 61.00 | 567.81 | 628.81 | OK | |
| r-devel-windows-x86_64 | 0.1.1 | 36.00 | 270.00 | 306.00 | OK | |
| r-patched-linux-x86_64 | 0.1.1 | 32.59 | 302.36 | 334.95 | OK | |
| r-release-linux-x86_64 | 0.1.1 | 29.55 | 303.08 | 332.63 | OK | |
| r-release-macos-arm64 | 0.1.1 | 8.00 | 73.00 | 81.00 | OK | |
| r-release-macos-x86_64 | 0.1.1 | 24.00 | 385.00 | 409.00 | OK | |
| r-release-windows-x86_64 | 0.1.1 | 31.00 | 271.00 | 302.00 | OK | |
| r-oldrel-macos-arm64 | 0.1.1 | 7.00 | 80.00 | 87.00 | OK | |
| r-oldrel-macos-x86_64 | 0.1.1 | 23.00 | 413.00 | 436.00 | OK | |
| r-oldrel-windows-x86_64 | 0.1.1 | 48.00 | 384.00 | 432.00 | OK |
Version: 0.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [29s/49s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(dbSpatial)
>
> test_check("dbSpatial")
Saving _problems/test-extract-15.R
Saving _problems/test-spatial-functions-15.R
Saving _problems/test-spatial-functions-35.R
Saving _problems/test-spatial-functions-70.R
[gannet:4105076:0:4105076] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x14)
==== backtrace (tid:4105076) ====
0 /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7f552cd8cdf4]
1 /lib64/libucs.so.0(+0x17aed) [0x7f552cd8eaed]
2 /lib64/libucs.so.0(+0x17cbd) [0x7f552cd8ecbd]
3 /lib64/libc.so.6(+0x1a040) [0x7f5541c29040]
4 /tmp/Rtmp7f4MUY/working_dir/RtmpPiUdOB/file3ea3742075c1cd/R/duckdb/extensions/v1.5.2/linux_amd64/spatial.duckdb_extension(+0x1181e00) [0x7f541833ce00]
5 /tmp/Rtmp7f4MUY/working_dir/RtmpPiUdOB/file3ea3742075c1cd/R/duckdb/extensions/v1.5.2/linux_amd64/spatial.duckdb_extension(+0x1152a28) [0x7f541830da28]
6 /tmp/Rtmp7f4MUY/working_dir/RtmpPiUdOB/file3ea3742075c1cd/R/duckdb/extensions/v1.5.2/linux_amd64/spatial.duckdb_extension(+0x75c104) [0x7f5417917104]
7 /tmp/Rtmp7f4MUY/working_dir/RtmpPiUdOB/file3ea3742075c1cd/R/duckdb/extensions/v1.5.2/linux_amd64/spatial.duckdb_extension(+0x75a499) [0x7f5417915499]
8 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper29LoadExternalExtensionInternalERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEERNS_19ExtensionActiveLoadE+0x18f) [0x7f5463679e3f]
9 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper21LoadExternalExtensionERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEE+0x4a) [0x7f5463679bea]
10 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZNK6duckdb12PhysicalLoad15GetDataInternalERNS_16ExecutionContextERNS_9DataChunkERNS_19OperatorSourceInputE+0x151) [0x7f546445e831]
11 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor15FetchFromSourceERNS_9DataChunkE+0x9b) [0x7f5464c8d8eb]
12 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor7ExecuteEm+0x146) [0x7f5464c8a4c6]
13 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12PipelineTask11ExecuteTaskENS_17TaskExecutionModeE+0x112) [0x7f5464c8a0f2]
14 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12ExecutorTask7ExecuteENS_17TaskExecutionModeE+0xa0) [0x7f5464c83d90]
15 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb8Executor11ExecuteTaskEb+0x1c0) [0x7f5464c890f0]
16 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb13ClientContext19ExecuteTaskInternalERNS_17ClientContextLockERNS_15BaseQueryResultEb+0x40) [0x7f5464a981f0]
17 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb18PendingQueryResult15ExecuteInternalERNS_17ClientContextLockE+0x7a) [0x7f5464a9a97a]
18 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb13ClientContext7ExecuteERKNSt3__112basic_stringIcNS1_11char_traitsIcEENS1_9allocatorIcEEEERNS_10shared_ptrINS_21PreparedStatementDataELb1EEERKNS_22PendingQueryParametersE+0xa0) [0x7f5464a9a6c0]
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) [0x7f5464abd473]
20 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb17PreparedStatement7ExecuteERNS_6vectorINS_5ValueELb1ENSt3__19allocatorIS2_EEEEb+0x172) [0x7f5464abd712]
21 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_Z12rapi_executeN5cpp1116external_pointerIN6duckdb10RStatementEXadL_ZNS_15default_deleterIS2_EEvPT_EEEENS1_11ConvertOptsE+0x115) [0x7f5463307f75]
22 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_duckdb_rapi_execute+0x66) [0x7f54633704a6]
23 /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8f524) [0x5643a429b524]
24 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdae08) [0x5643a42e6e08]
25 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc918c) [0x5643a42d518c]
26 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x5643a42d4945]
27 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc93e4) [0x5643a42d53e4]
28 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x26e) [0x5643a42d4a0e]
29 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc93e4) [0x5643a42d53e4]
30 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdcf10) [0x5643a42e8f10]
31 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcd5c9) [0x5643a42d95c9]
32 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc918c) [0x5643a42d518c]
33 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x5643a42d4945]
34 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0aa9) [0x5643a42ecaa9]
35 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdff9b) [0x5643a42ebf9b]
36 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9867) [0x5643a42d5867]
37 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f8) [0x5643a42d4d98]
38 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc93e4) [0x5643a42d53e4]
39 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdcf10) [0x5643a42e8f10]
40 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcd5c9) [0x5643a42d95c9]
41 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc918c) [0x5643a42d518c]
42 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x5643a42d4945]
43 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0aa9) [0x5643a42ecaa9]
44 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdff9b) [0x5643a42ebf9b]
45 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9867) [0x5643a42d5867]
46 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f8) [0x5643a42d4d98]
47 /data/gannet/ripley/R/test-clang/rlang/libs/rlang.so(+0x4983) [0x7f553f6b7983]
48 /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8d673) [0x5643a4299673]
49 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcfbc4) [0x5643a42dbbc4]
50 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc918c) [0x5643a42d518c]
51 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x5643a42d4945]
52 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0aa9) [0x5643a42ecaa9]
53 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdff9b) [0x5643a42ebf9b]
54 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9867) [0x5643a42d5867]
55 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f8) [0x5643a42d4d98]
56 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe5e08) [0x5643a42f1e08]
57 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x5643a42d4b70]
58 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe50fb) [0x5643a42f10fb]
59 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x5643a42d4b70]
60 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0aa9) [0x5643a42ecaa9]
61 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdff9b) [0x5643a42ebf9b]
=================================
*** caught segfault ***
address 0x4d2003ea374, 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$ref, duckdb_convert_opts_impl(res@connection@convert_opts, arrow = res@arrow))
9: duckdb_execute(res)
10: duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
11: .local(conn, statement, ...)
12: dbSendQuery(conn, statement, ...)
13: dbSendQuery(conn, statement, ...)
14: dbSendStatement(conn, statement, ...)
15: dbSendStatement(conn, statement, ...)
16: DBI::dbExecute(conn, query)
17: DBI::dbExecute(conn, query)
18: loadSpatial(conn = conn)
19: withCallingHandlers(expr, message = function(c) if (inherits(c, classes)) tryInvokeRestart("muffleMessage"))
20: suppressMessages(loadSpatial(conn = conn))
21: dbSpatial(conn = con, name = "test_pts", value = df, x_colName = "x", y_colName = "y", overwrite = TRUE)
22: eval(code, test_env)
23: eval(code, test_env)
24: withCallingHandlers({ eval(code, test_env) new_expectations <- the$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$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
32: test_code(code, parent.frame())
33: test_that("st_join works with different predicates", { skip_if_not_installed("duckdb") con <- DBI::dbConnect(duckdb::duckdb()) on.exit(DBI::dbDisconnect(con, shutdown = TRUE)) df <- data.frame(id = 1:3, x = c(0, 10, 20), y = c(0, 10, 20)) pts <- dbSpatial(conn = con, name = "test_pts", value = df, x_colName = "x", y_colName = "y", overwrite = TRUE) res <- st_join(pts, pts, join = sf::st_intersects) expect_s4_class(res, "dbSpatial") expect_equal(nrow(dplyr::collect(res[])), 3)})
34: eval(code, test_env)
35: eval(code, test_env)
36: withCallingHandlers({ eval(code, test_env) new_expectations <- the$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("dbSpatial")
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.1.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘class_structure.Rmd’ using rmarkdown
[gannet:4110255:0:4110255] Caught signal 11 (Segmentation fault: address not mapped to object at address 0xc6)
==== backtrace (tid:4110255) ====
0 /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7fb7981b7df4]
1 /lib64/libucs.so.0(+0x17aed) [0x7fb7981b9aed]
2 /lib64/libucs.so.0(+0x17cbd) [0x7fb7981b9cbd]
3 /lib64/libc.so.6(+0x1a040) [0x7fb7b1928040]
4 /tmp/Rtmp7f4MUY/working_dir/RtmpSQFULG/file3eb7af4241b17b/R/duckdb/extensions/v1.5.2/linux_amd64/spatial.duckdb_extension(+0x1181e00) [0x7fb6cf949e00]
5 /tmp/Rtmp7f4MUY/working_dir/RtmpSQFULG/file3eb7af4241b17b/R/duckdb/extensions/v1.5.2/linux_amd64/spatial.duckdb_extension(+0x1152a28) [0x7fb6cf91aa28]
6 /tmp/Rtmp7f4MUY/working_dir/RtmpSQFULG/file3eb7af4241b17b/R/duckdb/extensions/v1.5.2/linux_amd64/spatial.duckdb_extension(+0x75c104) [0x7fb6cef24104]
7 /tmp/Rtmp7f4MUY/working_dir/RtmpSQFULG/file3eb7af4241b17b/R/duckdb/extensions/v1.5.2/linux_amd64/spatial.duckdb_extension(+0x75a499) [0x7fb6cef22499]
8 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper29LoadExternalExtensionInternalERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEERNS_19ExtensionActiveLoadE+0x18f) [0x7fb79ca79e3f]
9 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper21LoadExternalExtensionERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEE+0x4a) [0x7fb79ca79bea]
10 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZNK6duckdb12PhysicalLoad15GetDataInternalERNS_16ExecutionContextERNS_9DataChunkERNS_19OperatorSourceInputE+0x151) [0x7fb79d85e831]
11 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor15FetchFromSourceERNS_9DataChunkE+0x9b) [0x7fb79e08d8eb]
12 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor7ExecuteEm+0x146) [0x7fb79e08a4c6]
13 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12PipelineTask11ExecuteTaskENS_17TaskExecutionModeE+0x112) [0x7fb79e08a0f2]
14 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12ExecutorTask7ExecuteENS_17TaskExecutionModeE+0xa0) [0x7fb79e083d90]
15 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb8Executor11ExecuteTaskEb+0x1c0) [0x7fb79e0890f0]
16 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb13ClientContext19ExecuteTaskInternalERNS_17ClientContextLockERNS_15BaseQueryResultEb+0x40) [0x7fb79de981f0]
17 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb18PendingQueryResult15ExecuteInternalERNS_17ClientContextLockE+0x7a) [0x7fb79de9a97a]
18 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb13ClientContext7ExecuteERKNSt3__112basic_stringIcNS1_11char_traitsIcEENS1_9allocatorIcEEEERNS_10shared_ptrINS_21PreparedStatementDataELb1EEERKNS_22PendingQueryParametersE+0xa0) [0x7fb79de9a6c0]
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) [0x7fb79debd473]
20 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb17PreparedStatement7ExecuteERNS_6vectorINS_5ValueELb1ENSt3__19allocatorIS2_EEEEb+0x172) [0x7fb79debd712]
21 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_Z12rapi_executeN5cpp1116external_pointerIN6duckdb10RStatementEXadL_ZNS_15default_deleterIS2_EEvPT_EEEENS1_11ConvertOptsE+0x115) [0x7fb79c707f75]
22 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_duckdb_rapi_execute+0x66) [0x7fb79c7704a6]
23 /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8f524) [0x564ff4463524]
24 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdae08) [0x564ff44aee08]
25 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc918c) [0x564ff449d18c]
26 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x564ff449c945]
27 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc93e4) [0x564ff449d3e4]
28 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x26e) [0x564ff449ca0e]
29 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc93e4) [0x564ff449d3e4]
30 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdcf10) [0x564ff44b0f10]
31 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcd5c9) [0x564ff44a15c9]
32 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc918c) [0x564ff449d18c]
33 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x564ff449c945]
34 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0aa9) [0x564ff44b4aa9]
35 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdff9b) [0x564ff44b3f9b]
36 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9867) [0x564ff449d867]
37 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f8) [0x564ff449cd98]
38 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc93e4) [0x564ff449d3e4]
39 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdcf10) [0x564ff44b0f10]
40 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcd5c9) [0x564ff44a15c9]
41 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc918c) [0x564ff449d18c]
42 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x564ff449c945]
43 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0aa9) [0x564ff44b4aa9]
44 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdff9b) [0x564ff44b3f9b]
45 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9867) [0x564ff449d867]
46 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f8) [0x564ff449cd98]
47 /data/gannet/ripley/R/test-clang/rlang/libs/rlang.so(+0x4983) [0x7fb7af33c983]
48 /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8d673) [0x564ff4461673]
49 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcfbc4) [0x564ff44a3bc4]
50 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc918c) [0x564ff449d18c]
51 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x564ff449c945]
52 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0aa9) [0x564ff44b4aa9]
53 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdff9b) [0x564ff44b3f9b]
54 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc9867) [0x564ff449d867]
55 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f8) [0x564ff449cd98]
56 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe5e08) [0x564ff44b9e08]
57 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x564ff449cb70]
58 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe50fb) [0x564ff44b90fb]
59 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x564ff449cb70]
60 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0aa9) [0x564ff44b4aa9]
61 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdff9b) [0x564ff44b3f9b]
=================================
*** caught segfault ***
address 0x4d2003eb7af, 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, query)
17: DBI::dbExecute(conn, query)
18: loadSpatial(conn = conn)
19: withCallingHandlers(expr, message = function(c) if (inherits(c, classes)) tryInvokeRestart("muffleMessage"))
20: suppressMessages(loadSpatial(conn = conn))
21: dbSpatial(conn = con, name = "class_structure_points", value = coords, x_colName = "x", y_colName = "y", overwrite = TRUE)
22: eval(expr, envir)
23: eval(expr, envir)
24: withVisible(eval(expr, envir))
25: 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)})
26: eval(call)
27: eval(call)
28: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
29: doWithOneRestart(return(expr), restart)
30: withOneRestart(expr, restarts[[1L]])
31: withRestartList(expr, restarts[-nr])
32: doWithOneRestart(return(expr), restart)
33: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
34: withRestartList(expr, restarts)
35: withRestarts(with_handlers({ for (expr in tle$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)
36: evaluate::evaluate(...)
37: 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$render, options))
38: in_dir(input_dir(), expr)
39: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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)))
40: eng_r(options)
41: block_exec(params)
42: call_block(x)
43: process_group(group)
44: 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) })
45: 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()))
46: 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)
47: process_file(text, output)
48: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
49: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
50: vweave_rmarkdown(...)
51: engine$weave(file, quiet = quiet, encoding = enc)
52: doTryCatch(return(expr), name, parentenv, handler)
53: tryCatchOne(expr, names, parentenv, handlers[[1L]])
54: tryCatchList(expr, classes, parentenv, handlers)
55: tryCatch({ engine$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)), domain = NA)})
56: tools:::.buildOneVignette("class_structure.Rmd", "/data/gannet/ripley/R/packages/tests-clang/dbSpatial.Rcheck/vign_test/dbSpatial", TRUE, FALSE, "class_structure", "UTF-8", "/tmp/Rtmp7f4MUY/working_dir/Rtmp0uGl5t/file3eb7255fd0a0be.rds")
An irrecoverable exception occurred. R is aborting now ...
--- re-building ‘getting_started.Rmd’ using rmarkdown
Quitting from getting_started.Rmd:40-53 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `duckdb_result()`:
! Invalid Error: Invalid Input Error: Initialization function "spatial_duckdb_cpp_init" from file "/tmp/Rtmp7f4MUY/working_dir/RtmplxshMl/file3ede017f8610d1/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. └─dbSpatial::dbSpatial(...)
2. ├─base::suppressMessages(loadSpatial(conn = conn))
3. │ └─base::withCallingHandlers(...)
4. └─dbSpatial::loadSpatial(conn = conn)
5. ├─DBI::dbExecute(conn, query)
6. └─DBI::dbExecute(conn, query)
7. ├─DBI::dbSendStatement(conn, statement, ...)
8. └─DBI::dbSendStatement(conn, statement, ...)
9. ├─DBI::dbSendQuery(conn, statement, ...)
10. └─duckdb::dbSendQuery(conn, statement, ...)
11. └─duckdb (local) .local(conn, statement, ...)
12. └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'getting_started.Rmd' failed with diagnostics:
Invalid Error: Invalid Input Error: Initialization function "spatial_duckdb_cpp_init" from file "/tmp/Rtmp7f4MUY/working_dir/RtmplxshMl/file3ede017f8610d1/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
--- failed re-building ‘getting_started.Rmd’
--- re-building ‘spatial_operations.Rmd’ using rmarkdown
Quitting from spatial_operations.Rmd:24-35 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `duckdb_result()`:
! Invalid Error: Invalid Input Error: Initialization function "spatial_duckdb_cpp_init" from file "/tmp/Rtmp7f4MUY/working_dir/RtmpQeiPfj/file3ee8963eec7456/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. └─dbSpatial::dbSpatial(...)
2. ├─base::suppressMessages(loadSpatial(conn = conn))
3. │ └─base::withCallingHandlers(...)
4. └─dbSpatial::loadSpatial(conn = conn)
5. ├─DBI::dbExecute(conn, query)
6. └─DBI::dbExecute(conn, query)
7. ├─DBI::dbSendStatement(conn, statement, ...)
8. └─DBI::dbSendStatement(conn, statement, ...)
9. ├─DBI::dbSendQuery(conn, statement, ...)
10. └─duckdb::dbSendQuery(conn, statement, ...)
11. └─duckdb (local) .local(conn, statement, ...)
12. └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'spatial_operations.Rmd' failed with diagnostics:
Invalid Error: Invalid Input Error: Initialization function "spatial_duckdb_cpp_init" from file "/tmp/Rtmp7f4MUY/working_dir/RtmpQeiPfj/file3ee8963eec7456/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
--- failed re-building ‘spatial_operations.Rmd’
SUMMARY: processing the following files failed:
‘class_structure.Rmd’ ‘getting_started.Rmd’ ‘spatial_operations.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang