Running ‘testthat.R’ [53s/141s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > 
  > library(testthat)
  > library(specleanr)
  > 
  > test_check("specleanr")
  OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead.
  OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  [gannet:3215232:0:3215232] Caught signal 11 (Segmentation fault: Sent by the kernel at address (nil))
  ==== backtrace (tid:3215232) ====
   0  /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7f3ad23b2df4]
   1  /lib64/libucs.so.0(+0x17aed) [0x7f3ad23b4aed]
   2  /lib64/libucs.so.0(+0x17cbd) [0x7f3ad23b4cbd]
   3  /lib64/libc.so.6(+0x19c30) [0x7f3ae8627c30]
   4  /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.4.2/linux_amd64/spatial.duckdb_extension(+0xc042e8) [0x7f39a82042e8]
   5  /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.4.2/linux_amd64/spatial.duckdb_extension(+0xc07887) [0x7f39a8207887]
   6  /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.4.2/linux_amd64/spatial.duckdb_extension(+0xc07a04) [0x7f39a8207a04]
   7  /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.4.2/linux_amd64/spatial.duckdb_extension(+0x10c514a) [0x7f39a86c514a]
   8  /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.4.2/linux_amd64/spatial.duckdb_extension(+0x7d5b74) [0x7f39a7dd5b74]
   9  /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.4.2/linux_amd64/spatial.duckdb_extension(+0x7d4119) [0x7f39a7dd4119]
  10  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper29LoadExternalExtensionInternalERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEERNS_19ExtensionActiveLoadE+0x1b4) [0x7f39f95715f4]
  11  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper21LoadExternalExtensionERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEE+0x4a) [0x7f39f957137a]
  12  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZNK6duckdb12PhysicalLoad7GetDataERNS_16ExecutionContextERNS_9DataChunkERNS_19OperatorSourceInputE+0x151) [0x7f39fa3ab6b1]
  13  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor15FetchFromSourceERNS_9DataChunkE+0x9f) [0x7f39fab5d5df]
  14  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor7ExecuteEm+0x133) [0x7f39fab5a073]
  15  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12PipelineTask11ExecuteTaskENS_17TaskExecutionModeE+0x119) [0x7f39fab59ca9]
  16  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12ExecutorTask7ExecuteENS_17TaskExecutionModeE+0xa0) [0x7f39fab535c0]
  17  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb8Executor11ExecuteTaskEb+0x24a) [0x7f39fab58b8a]
  18  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb13ClientContext19ExecuteTaskInternalERNS_17ClientContextLockERNS_15BaseQueryResultEb+0x40) [0x7f39fa998280]
  19  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb18PendingQueryResult15ExecuteInternalERNS_17ClientContextLockE+0x7a) [0x7f39fa99a7ba]
  20  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb17PreparedStatement7ExecuteERNS_6vectorINS_5ValueELb1EEEb+0x5a) [0x7f39fa9bad1a]
  21  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_Z12rapi_executeN5cpp1116external_pointerIN6duckdb10RStatementEXadL_ZNS_15default_deleterIS2_EEvPT_EEEENS1_11ConvertOptsE+0x115) [0x7f39f9301b95]
  22  /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_duckdb_rapi_execute+0x63) [0x7f39f936a8f3]
  23  /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8e564) [0x55e092af8564]
  24  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdd470) [0x55e092b47470]
  25  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc62ac) [0x55e092b302ac]
  26  /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55e092b2fa35]
  27  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc6534) [0x55e092b30534]
  28  /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x26e) [0x55e092b2fafe]
  29  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc6534) [0x55e092b30534]
  30  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf5b0) [0x55e092b495b0]
  31  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcaf92) [0x55e092b34f92]
  32  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc62ac) [0x55e092b302ac]
  33  /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55e092b2fa35]
  34  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe2e29) [0x55e092b4ce29]
  35  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe232c) [0x55e092b4c32c]
  36  /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x55e092b2fe86]
  37  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc6534) [0x55e092b30534]
  38  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf5b0) [0x55e092b495b0]
  39  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcaf92) [0x55e092b34f92]
  40  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc62ac) [0x55e092b302ac]
  41  /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55e092b2fa35]
  42  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe2e29) [0x55e092b4ce29]
  43  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe232c) [0x55e092b4c32c]
  44  /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x55e092b2fe86]
  45  /data/gannet/ripley/R/test-clang/rlang/libs/rlang.so(+0x4603) [0x7f3ae60b8603]
  46  /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8c6b3) [0x55e092af66b3]
  47  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcdeab) [0x55e092b37eab]
  48  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc62ac) [0x55e092b302ac]
  49  /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55e092b2fa35]
  50  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe2e29) [0x55e092b4ce29]
  51  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe232c) [0x55e092b4c32c]
  52  /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x55e092b2fe86]
  53  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe83d8) [0x55e092b523d8]
  54  /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x55e092b2fc60]
  55  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe74eb) [0x55e092b514eb]
  56  /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x55e092b2fc60]
  57  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe2e29) [0x55e092b4ce29]
  58  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe232c) [0x55e092b4c32c]
  59  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcd6b3) [0x55e092b376b3]
  60  /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc62ac) [0x55e092b302ac]
  61  /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55e092b2fa35]
  =================================
  
   *** caught segfault ***
  address 0x4d200310f80, 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$ref, duckdb_convert_opts_impl(res@connection@convert_opts,     arrow = res@arrow))
   9: duckdb_execute(res)
  10: duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
  11: .local(conn, statement, ...)
  12: dbSendQuery(conn, statement, ...)
  13: dbSendQuery(conn, statement, ...)
  14: dbSendStatement(conn, statement, ...)
  15: dbSendStatement(conn, statement, ...)
  16: DBI::dbExecute(conn, "LOAD spatial;")
  17: DBI::dbExecute(conn, "LOAD spatial;")
  18: cached_connection()
  19: DBI::dbGetQuery(conn, query)
  20: duckdb_extensions()
  21: load_extension("httpfs", conn = conn, nightly = nightly, force = force)
  22: load_httpfs(conn)
  23: parse_uri(sources, conn = conn, recursive = recursive)
  24: duckdbfs::open_dataset(urls[tbl])
  25: fb_tbl("synonyms", server, version, db)
  26: mutate(., synonym = paste(SynGenus, SynSpecies))
  27: select(., dplyr::any_of(c("synonym", "Status", "SpecCode", "SynCode",     "CoL_ID", "TSN", "WoRMS_ID", "ZooBank_ID", "TaxonLevel")))
  28: fb_tbl("synonyms", server, version, db) %>% mutate(synonym = paste(SynGenus,     SynSpecies)) %>% select(dplyr::any_of(c("synonym", "Status",     "SpecCode", "SynCode", "CoL_ID", "TSN", "WoRMS_ID", "ZooBank_ID",     "TaxonLevel")))
  29: rfishbase::synonyms()
  30: withCallingHandlers(expr, message = function(c) if (inherits(c,     classes)) tryInvokeRestart("muffleMessage"))
  31: suppressMessages(rfishbase::synonyms())
  32: fishbase(tables = "synonym")
  33: check_names(mdf, colsp = "species", verbose = FALSE, merge = TRUE)
  34: eval(code, test_env)
  35: eval(code, test_env)
  36: withCallingHandlers({    eval(code, test_env)    new_expectations <- the$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("specleanr")
  An irrecoverable exception occurred. R is aborting now ...