Running ‘testthat.R’ [27s/78s]
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:333632:0:336190] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x6d3662)
  ==== backtrace (tid: 336190) ====
   0  /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7f66f0f9bdf4]
   1  /lib64/libucs.so.0(+0x17aed) [0x7f66f0f9daed]
   2  /lib64/libucs.so.0(+0x17cbd) [0x7f66f0f9dcbd]
   3  /lib64/libc.so.6(+0x1a040) [0x7f6706429040]
   4  /data/gannet/ripley/R/test-clang/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0xc3adc8) [0x7f65d063adc8]
   5  /data/gannet/ripley/R/test-clang/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0xc3e487) [0x7f65d063e487]
   6  /data/gannet/ripley/R/test-clang/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0xc3e604) [0x7f65d063e604]
   7  /data/gannet/ripley/R/test-clang/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x11685aa) [0x7f65d0b685aa]
   8  /data/gannet/ripley/R/test-clang/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x773384) [0x7f65d0173384]
   9  /data/gannet/ripley/R/test-clang/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension(+0x771719) [0x7f65d0171719]
  10  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper29LoadExternalExtensionInternalERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEERNS_19ExtensionActiveLoadE+0x18f) [0x7f6627e7f85f]
  11  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper21LoadExternalExtensionERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEE+0x4a) [0x7f6627e7f60a]
  12  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZNK6duckdb12PhysicalLoad15GetDataInternalERNS_16ExecutionContextERNS_9DataChunkERNS_19OperatorSourceInputE+0x151) [0x7f6628c6d401]
  13  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor15FetchFromSourceERNS_9DataChunkE+0x98) [0x7f66294a10c8]
  14  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor7ExecuteEm+0x146) [0x7f662949dca6]
  15  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12PipelineTask11ExecuteTaskENS_17TaskExecutionModeE+0x154) [0x7f662949d914]
  16  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12ExecutorTask7ExecuteENS_17TaskExecutionModeE+0xa0) [0x7f6629497570]
  17  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb13TaskScheduler14ExecuteForeverEPNSt3__16atomicIbEE+0x39a) [0x7f66294a432a]
  18  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(+0x1aafe9c) [0x7f66294afe9c]
  19  /lib64/libc.so.6(+0x71f14) [0x7f6706480f14]
  20  /lib64/libc.so.6(+0xf532c) [0x7f670650432c]
  =================================
  
   *** caught segfault ***
  address 0x4d200051740, 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 ...