Last updated on 2025-12-03 05:50:39 CET.
| Package | ERROR | OK |
|---|---|---|
| fwtraits | 13 | |
| specleanr | 1 | 11 |
Current CRAN status: OK: 13
Current CRAN status: ERROR: 1, OK: 11
Version: 1.0.0
Check: tests
Result: ERROR
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 ...
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.0.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘Plants.Rmd’ using rmarkdown
Quitting from Plants.Rmd:43-52 [get species occurences]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! error in evaluating the argument 'conn' in selecting a method for function 'dbGetQuery': Invalid Error: Invalid Input Error: Initialization function "spatial_duckdb_cpp_init" from file "/data/gannet/ripley/.local/share/R/duckdb/extensions/v1.4.2/linux_amd64/spatial.duckdb_extension" threw an exception: "Missing DB manager"
ℹ Context: rapi_execute
ℹ Error type: INVALID
ℹ Raw message: Invalid Input Error: Initialization function "spatial_duckdb_cpp_init" from file "/data/gannet/ripley/.local/share/R/duckdb/extensions/v1.4.2/linux_amd64/spatial.duckdb_extension" threw an exception: "Missing DB manager"
---
Backtrace:
▆
1. ├─specleanr::getdata(...)
2. │ └─base::sapply(...)
3. │ └─base::lapply(X = X, FUN = FUN, ...)
4. │ └─specleanr (local) FUN(X[[i]], ...)
5. │ └─specleanr::check_names(...)
6. │ └─specleanr:::fishbase(tables = "synonym")
7. │ ├─base::suppressMessages(rfishbase::synonyms())
8. │ │ └─base::withCallingHandlers(...)
9. │ └─rfishbase::synonyms()
10. │ ├─... %>% ...
11. │ └─rfishbase::fb_tbl("synonyms", server, version, db)
12. │ └─duckdbfs::open_dataset(urls[tbl])
13. │ └─duckdbfs:::parse_uri(sources, conn = conn, recursive = recursive)
14. │ └─duckdbfs:::load_httpfs(conn)
15. │ └─duckdbfs:::load_extension(...)
16. │ └─duckdbfs::duckdb_extensions()
17. │ ├─DBI::dbGetQuery(conn, query)
18. │ └─duckdbfs::cached_connection()
19. │ ├─DBI::dbExecute(conn, "LOAD spatial;")
20. │ └─DBI::dbExecute(conn, "LOAD spatial;")
21. │ ├─DBI::dbSendStatement(conn, statement, ...)
22. │ └─DBI::dbSendStatement(conn, statement, ...)
23. │ ├─DBI::dbSendQuery(conn, statement, ...)
24. │ └─duckdb::dbSendQuery(conn, statement, ...)
25. │ └─duckdb (local) .local(conn, statement, ...)
26. │ └─duckdb:::duckdb_result(...)
27. │ └─duckdb:::duckdb_execute(res)
28. │ └─duckdb:::rethrow_rapi_execute(...)
29. │ ├─rlang::try_fetch(...)
30. │ │ ├─base::tryCatch(...)
31. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
32. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
33. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
34. │ │ └─base::withCallingHandlers(...)
35. │ └─duckdb:::rapi_execute(stmt, convert_opts)
36. ├─dplyr::select(...)
37. ├─dplyr::mutate(., synonym = paste(SynGenus, SynSpecies))
38. ├─duckdb (local) `<fn>`(...)
39. │ └─rlang::abort(error_parts, class = "duckdb_error", !!!fields)
40. │ └─rlang:::signal_abort(cnd, .file)
41. │ └─base::signalCondition(cnd)
42. ├─rlang (local) `<fn>`(`<dckdb_rr>`)
43. │ └─handlers[[1L]](cnd)
44. │ └─duckdb:::rethrow_error_from_rapi(e, call)
45. │ └─rlang::abort(msg, call = call)
46. │ └─rlang:::signal_abort(cnd, .file)
47. │ └─base::signalCondition(cnd)
48. └─base (local) `<fn>`(`<rlng_rrr>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Plants.Rmd' failed with diagnostics:
error in evaluating the argument 'conn' in selecting a method for function 'dbGetQuery': Invalid Error: Invalid Input Error: Initialization function "spatial_duckdb_cpp_init" from file "/data/gannet/ripley/.local/share/R/duckdb/extensions/v1.4.2/linux_amd64/spatial.duckdb_extension" threw an exception: "Missing DB manager"
ℹ Context: rapi_execute
ℹ Error type: INVALID
ℹ Raw message: Invalid Input Error: Initialization function "spatial_duckdb_cpp_init" from file "/data/gannet/ripley/.local/share/R/duckdb/extensions/v1.4.2/linux_amd64/spatial.duckdb_extension" threw an exception: "Missing DB manager"
--- failed re-building ‘Plants.Rmd’
--- re-building ‘addspeciesecologicalranges.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘addspeciesecologicalranges.Rmd’
--- re-building ‘eOutlier.Rmd’ using rmarkdown
[gannet:3239695:0:3239695] Caught signal 11 (Segmentation fault: Sent by the kernel at address (nil))
==== backtrace (tid:3239695) ====
0 /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7f8bcffb2df4]
1 /lib64/libucs.so.0(+0x17aed) [0x7f8bcffb4aed]
2 /lib64/libucs.so.0(+0x17cbd) [0x7f8bcffb4cbd]
3 /lib64/libc.so.6(+0x19c30) [0x7f8be7027c30]
4 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.4.2/linux_amd64/spatial.duckdb_extension(+0x10e4500) [0x7f8ab46e4500]
5 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.4.2/linux_amd64/spatial.duckdb_extension(+0x10c5108) [0x7f8ab46c5108]
6 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.4.2/linux_amd64/spatial.duckdb_extension(+0x7d5b74) [0x7f8ab3dd5b74]
7 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.4.2/linux_amd64/spatial.duckdb_extension(+0x7d4119) [0x7f8ab3dd4119]
8 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper29LoadExternalExtensionInternalERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEERNS_19ExtensionActiveLoadE+0x1b4) [0x7f8b06d715f4]
9 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper21LoadExternalExtensionERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEE+0x4a) [0x7f8b06d7137a]
10 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZNK6duckdb12PhysicalLoad7GetDataERNS_16ExecutionContextERNS_9DataChunkERNS_19OperatorSourceInputE+0x151) [0x7f8b07bab6b1]
11 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor15FetchFromSourceERNS_9DataChunkE+0x9f) [0x7f8b0835d5df]
12 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor7ExecuteEm+0x133) [0x7f8b0835a073]
13 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12PipelineTask11ExecuteTaskENS_17TaskExecutionModeE+0x119) [0x7f8b08359ca9]
14 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12ExecutorTask7ExecuteENS_17TaskExecutionModeE+0xa0) [0x7f8b083535c0]
15 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb8Executor11ExecuteTaskEb+0x24a) [0x7f8b08358b8a]
16 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb13ClientContext19ExecuteTaskInternalERNS_17ClientContextLockERNS_15BaseQueryResultEb+0x40) [0x7f8b08198280]
17 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb18PendingQueryResult15ExecuteInternalERNS_17ClientContextLockE+0x7a) [0x7f8b0819a7ba]
18 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb17PreparedStatement7ExecuteERNS_6vectorINS_5ValueELb1EEEb+0x5a) [0x7f8b081bad1a]
19 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_Z12rapi_executeN5cpp1116external_pointerIN6duckdb10RStatementEXadL_ZNS_15default_deleterIS2_EEvPT_EEEENS1_11ConvertOptsE+0x115) [0x7f8b06b01b95]
20 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_duckdb_rapi_execute+0x63) [0x7f8b06b6a8f3]
21 /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8e564) [0x5624ba3e6564]
22 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdd470) [0x5624ba435470]
23 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc62ac) [0x5624ba41e2ac]
24 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x5624ba41da35]
25 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc6534) [0x5624ba41e534]
26 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x26e) [0x5624ba41dafe]
27 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc6534) [0x5624ba41e534]
28 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf5b0) [0x5624ba4375b0]
29 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcaf92) [0x5624ba422f92]
30 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc62ac) [0x5624ba41e2ac]
31 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x5624ba41da35]
32 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe2e29) [0x5624ba43ae29]
33 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe232c) [0x5624ba43a32c]
34 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x5624ba41de86]
35 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc6534) [0x5624ba41e534]
36 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf5b0) [0x5624ba4375b0]
37 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcaf92) [0x5624ba422f92]
38 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc62ac) [0x5624ba41e2ac]
39 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x5624ba41da35]
40 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe2e29) [0x5624ba43ae29]
41 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe232c) [0x5624ba43a32c]
42 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x5624ba41de86]
43 /data/gannet/ripley/R/test-clang/rlang/libs/rlang.so(+0x4603) [0x7f8be4433603]
44 /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8c6b3) [0x5624ba3e46b3]
45 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcdeab) [0x5624ba425eab]
46 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc62ac) [0x5624ba41e2ac]
47 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x5624ba41da35]
48 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe2e29) [0x5624ba43ae29]
49 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe232c) [0x5624ba43a32c]
50 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x5624ba41de86]
51 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe83d8) [0x5624ba4403d8]
52 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x5624ba41dc60]
53 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe74eb) [0x5624ba43f4eb]
54 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x5624ba41dc60]
55 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe2e29) [0x5624ba43ae29]
56 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe232c) [0x5624ba43a32c]
57 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcd6b3) [0x5624ba4256b3]
58 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc62ac) [0x5624ba41e2ac]
59 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x5624ba41da35]
60 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe2e29) [0x5624ba43ae29]
61 /data/gannet/ripley/R/R-clang/bin/exec/R(R_execMethod+0x2cb) [0x5624ba43dc5b]
=================================
*** caught segfault ***
address 0x4d200316f0f, 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(data = spp, verbose = verbose, pct = pct, sn = sn)
34: FUN(X[[i]], ...)
35: lapply(X = X, FUN = FUN, ...)
36: sapply(data, function(spp) { checkFB <- check_names(data = spp, verbose = verbose, pct = pct, sn = sn) if (is.na(checkFB)) { checksppx <- spp } else { checksppx <- checkFB } sapply(db, FUN = function(xdb) { if (xdb == "gbif") { ndata <- tryCatch(expr = rgbif::occ_count(scientificName = checksppx), error = function(e) { if (grepl(" HTTP2 framing layer", e$message) == TRUE) { if (isTRUE(warn)) warning("GBIF webpage is misbehvaing and return HTTP2 frame layer message", call. = FALSE) return(NULL) } }) if (!is.null(ndata)) { if (ndata == 0) { if (isTRUE(verbose)) message("No records found for ", checksppx, " in GBIF") gbifx <- NULL } else if (ndata <= 50000 & is.null(extent)) { if (gbiflim <= 50000) { gbifsp <- rgbif::occ_data(scientificName = checksppx, limit = gbiflim) if (isTRUE(verbose)) message(nrow(gbifsp$data), " records for ", checksppx, " in GBIF were downloaded based on the gbiflimit of ", gbiflim) gbifx <- gbifsp$data } else { gbifsp <- rgbif::occ_data(scientificName = checksppx, limit = ndata) if (isTRUE(verbose)) message(nrow(gbifsp$data), " records for ", checksppx, " in GBIF were download as they were the maximum records found.") gbifx <- gbifsp$data } } else if (!is.null(extent)) { extval <- extentvalues(extent, xdb) if (gbiflim <= 50000) { gbifsp <- rgbif::occ_data(scientificName = checksppx, limit = gbiflim, decimalLongitude = paste0(extval[1], ",", extval[3]), decimalLatitude = paste0(extval[2], ",", extval[4]), ...) if (isTRUE(verbose)) message(nrow(gbifsp$data), " records for ", checksppx, " in GBIF were downloaded based on the gbif limit of ", gbiflim) } else { gbifsp <- rgbif::occ_data(scientificName = checksppx, limit = gbiflim, decimalLongitude = paste0(extval[1], ",", extval[3]), decimalLatitude = paste0(extval[2], ",", extval[4]), ...) if (isTRUE(verbose)) message("All ", nrow(gbifsp$data), " records for ", checksppx, " in GBIF were downloaded") } gbifx <- gbifsp$data } else if (ndata > 50000 && is.null(extent)) { if (isTRUE(verbose)) message("Only ", gbiflim, " records will be downloaded.") gbifsp <- rgbif::occ_data(scientificName = checksppx, limit = gbiflim, ...) gbifx <- gbifsp$data } else { gbifx = NULL } if (is(gbifx, "data.frame")) { if ("decimalLatitude" %in% colnames(gbifx) == TRUE) { gbifx } else { if (isTRUE(warn)) warning("The data for ", checksppx, " will be removed since no cordinates were found in GBIF database.", call. = FALSE) gbifx <- NULL } } else { gbifx = NULL } } else { gbifx <- NULL } } else if (xdb == "vertnet") { sptx <- scan(text = checksppx, what = " ", quiet = TRUE) if (!is.null(extent)) vbbox <- extentvalues(extent, xdb) else vbbox <- NULL vertx <- tryCatch(rvertnet::searchbyterm(genus = tolower(sptx[1]), specificepithet = tolower(sptx[2]), limit = vertlim, messages = FALSE, bbox = vbbox), error = function(e) { if (grepl("Internal Server Error \\(HTTP 500\\)", e$message) == TRUE | grepl("Service Unavailable \\(HTTP 503\\)", e$message) == TRUE) { if (isTRUE(warn)) warning("The VertNet database has returned 500 or 503 error message and will be skipped for ", checksppx, ".", call. = FALSE) return(NULL) } else { return(NULL) } }) if (is.null(vertx)) { if (isTRUE(verbose)) message("No records for ", checksppx, " in vertnet were found") vertxdf <- NULL } else { vertxdf <- vertx$data if (isTRUE(verbose)) message(nrow(vertxdf), " records for ", checksppx, " in vertnet downloaded.") vertxdf } } else if (xdb == "inat") { if (!is.null(extent)) vbbox <- extentvalues(extent, xdb) else vbbox <- NULL inatx <- tryCatch(expr = { sx <- rinat::get_inat_obs(taxon_name = checksppx, maxresults = inatlim, bounds = vbbox) }, error = function(e) { if (isTRUE(verbose)) message("No data exist for species ", checksppx, " in inaturalist were found.") return(0) }) if (length(inatx) > 1) { inatx <- sx if (isTRUE(verbose)) message(nrow(inatx), " records for ", checksppx, " in inaturalist downloaded.") inatx } else { inatx <- NULL } } else { stop("Database name not acceptable. Use only gbif, vertnet, or inat") } }, simplify = FALSE)}, simplify = FALSE)
37: getdata(data = c("Squalius cephalus", "Salmo trutta", "Thymallus thymallus", "Anguilla anguilla"), extent = danube, gbiflim = 50, inatlim = 50, vertlim = 50, verbose = FALSE)
38: eval(expr, envir)
39: eval(expr, envir)
40: withVisible(eval(expr, envir))
41: withCallingHandlers(code, 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)})
42: eval(call)
43: eval(call)
44: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
45: doWithOneRestart(return(expr), restart)
46: withOneRestart(expr, restarts[[1L]])
47: withRestartList(expr, restarts[-nr])
48: doWithOneRestart(return(expr), restart)
49: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
50: withRestartList(expr, restarts)
51: withRestarts(with_handlers({ for (expr in tle$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)
52: evaluate::evaluate(...)
53: 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$render, options))
54: in_dir(input_dir(), expr)
55: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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)))
56: eng_r(options)
57: block_exec(params)
58: call_block(x)
59: process_group(group)
60: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (xfun::pkg_available("rlang", "1.0.0")) { if (is_R_CMD_build() || is_R_CMD_check()) { cnd = tryCatch(rlang::entrace(e), error = identity) error <<- format(cnd) } else { rlang::entrace(e) } } })
61: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (xfun::pkg_available("rlang", "1.0.0")) { if (is_R_CMD_build() || is_R_CMD_check()) { cnd = tryCatch(rlang::entrace(e), error = identity) error <<- format(cnd) } else { rlang::entrace(e) } } }), 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)
62: process_file(text, output)
63: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
64: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
65: vweave_rmarkdown(...)
66: engine$weave(file, quiet = quiet, encoding = enc)
67: doTryCatch(return(expr), name, parentenv, handler)
68: tryCatchOne(expr, names, parentenv, handlers[[1L]])
69: tryCatchList(expr, classes, parentenv, handlers)
70: tryCatch({ engine$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)))})
71: tools:::.buildOneVignette("eOutlier.Rmd", "/data/gannet/ripley/R/packages/tests-clang/specleanr.Rcheck/vign_test/specleanr", TRUE, FALSE, "eOutlier", "UTF-8", "/tmp/Rtmpj0fi5j/working_dir/RtmpaAEPGU/file3155dd4bd7db89.rds")
An irrecoverable exception occurred. R is aborting now ...
--- re-building ‘generaloutlier.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘generaloutlier.Rmd’
--- re-building ‘loessmethodoptimisation.Rmd’ using rmarkdown
[gannet:3248903:0:3248903] Caught signal 11 (Segmentation fault: Sent by the kernel at address (nil))
==== backtrace (tid:3248903) ====
0 /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7f7aa304ddf4]
1 /lib64/libucs.so.0(+0x17aed) [0x7f7aa304faed]
2 /lib64/libucs.so.0(+0x17cbd) [0x7f7aa304fcbd]
3 /lib64/libc.so.6(+0x19c30) [0x7f7ab9929c30]
4 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.4.2/linux_amd64/spatial.duckdb_extension(+0x10e6460) [0x7f79444e6460]
5 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.4.2/linux_amd64/spatial.duckdb_extension(+0x10c5108) [0x7f79444c5108]
6 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.4.2/linux_amd64/spatial.duckdb_extension(+0x7d5b74) [0x7f7943bd5b74]
7 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.4.2/linux_amd64/spatial.duckdb_extension(+0x7d4119) [0x7f7943bd4119]
8 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper29LoadExternalExtensionInternalERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEERNS_19ExtensionActiveLoadE+0x1b4) [0x7f79d95715f4]
9 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper21LoadExternalExtensionERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEE+0x4a) [0x7f79d957137a]
10 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZNK6duckdb12PhysicalLoad7GetDataERNS_16ExecutionContextERNS_9DataChunkERNS_19OperatorSourceInputE+0x151) [0x7f79da3ab6b1]
11 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor15FetchFromSourceERNS_9DataChunkE+0x9f) [0x7f79dab5d5df]
12 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor7ExecuteEm+0x133) [0x7f79dab5a073]
13 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12PipelineTask11ExecuteTaskENS_17TaskExecutionModeE+0x119) [0x7f79dab59ca9]
14 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12ExecutorTask7ExecuteENS_17TaskExecutionModeE+0xa0) [0x7f79dab535c0]
15 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb8Executor11ExecuteTaskEb+0x24a) [0x7f79dab58b8a]
16 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb13ClientContext19ExecuteTaskInternalERNS_17ClientContextLockERNS_15BaseQueryResultEb+0x40) [0x7f79da998280]
17 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb18PendingQueryResult15ExecuteInternalERNS_17ClientContextLockE+0x7a) [0x7f79da99a7ba]
18 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb17PreparedStatement7ExecuteERNS_6vectorINS_5ValueELb1EEEb+0x5a) [0x7f79da9bad1a]
19 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_Z12rapi_executeN5cpp1116external_pointerIN6duckdb10RStatementEXadL_ZNS_15default_deleterIS2_EEvPT_EEEENS1_11ConvertOptsE+0x115) [0x7f79d9301b95]
20 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_duckdb_rapi_execute+0x63) [0x7f79d936a8f3]
21 /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8e564) [0x55a4a6a03564]
22 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdd470) [0x55a4a6a52470]
23 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc62ac) [0x55a4a6a3b2ac]
24 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55a4a6a3aa35]
25 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc6534) [0x55a4a6a3b534]
26 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x26e) [0x55a4a6a3aafe]
27 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc6534) [0x55a4a6a3b534]
28 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf5b0) [0x55a4a6a545b0]
29 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcaf92) [0x55a4a6a3ff92]
30 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc62ac) [0x55a4a6a3b2ac]
31 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55a4a6a3aa35]
32 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe2e29) [0x55a4a6a57e29]
33 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe232c) [0x55a4a6a5732c]
34 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x55a4a6a3ae86]
35 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc6534) [0x55a4a6a3b534]
36 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf5b0) [0x55a4a6a545b0]
37 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcaf92) [0x55a4a6a3ff92]
38 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc62ac) [0x55a4a6a3b2ac]
39 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55a4a6a3aa35]
40 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe2e29) [0x55a4a6a57e29]
41 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe232c) [0x55a4a6a5732c]
42 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x55a4a6a3ae86]
43 /data/gannet/ripley/R/test-clang/rlang/libs/rlang.so(+0x4603) [0x7f7aafabb603]
44 /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8c6b3) [0x55a4a6a016b3]
45 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcdeab) [0x55a4a6a42eab]
46 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc62ac) [0x55a4a6a3b2ac]
47 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55a4a6a3aa35]
48 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe2e29) [0x55a4a6a57e29]
49 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe232c) [0x55a4a6a5732c]
50 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x55a4a6a3ae86]
51 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe83d8) [0x55a4a6a5d3d8]
52 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x55a4a6a3ac60]
53 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe74eb) [0x55a4a6a5c4eb]
54 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x55a4a6a3ac60]
55 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe2e29) [0x55a4a6a57e29]
56 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe232c) [0x55a4a6a5732c]
57 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcd6b3) [0x55a4a6a426b3]
58 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc62ac) [0x55a4a6a3b2ac]
59 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x55a4a6a3aa35]
60 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe2e29) [0x55a4a6a57e29]
61 /data/gannet/ripley/R/R-clang/bin/exec/R(R_execMethod+0x2cb) [0x55a4a6a5ac5b]
=================================
*** caught segfault ***
address 0x4d200319307, 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$ref, duckdb_convert_opts_impl(res@connection@convert_opts, arrow = res@arrow))
9: duckdb_execute(res)
10: duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
11: .local(conn, statement, ...)
12: dbSendQuery(conn, statement, ...)
13: dbSendQuery(conn, statement, ...)
14: dbSendStatement(conn, statement, ...)
15: dbSendStatement(conn, statement, ...)
16: DBI::dbExecute(conn, "LOAD spatial;")
17: DBI::dbExecute(conn, "LOAD spatial;")
18: cached_connection()
19: DBI::dbGetQuery(conn, query)
20: duckdb_extensions()
21: load_extension("httpfs", conn = conn, nightly = nightly, force = force)
22: load_httpfs(conn)
23: parse_uri(sources, conn = conn, recursive = recursive)
24: duckdbfs::open_dataset(urls[tbl])
25: fb_tbl("synonyms", server, version, db)
26: mutate(., synonym = paste(SynGenus, SynSpecies))
27: select(., dplyr::any_of(c("synonym", "Status", "SpecCode", "SynCode", "CoL_ID", "TSN", "WoRMS_ID", "ZooBank_ID", "TaxonLevel")))
28: fb_tbl("synonyms", server, version, db) %>% mutate(synonym = paste(SynGenus, SynSpecies)) %>% select(dplyr::any_of(c("synonym", "Status", "SpecCode", "SynCode", "CoL_ID", "TSN", "WoRMS_ID", "ZooBank_ID", "TaxonLevel")))
29: rfishbase::synonyms()
30: withCallingHandlers(expr, message = function(c) if (inherits(c, classes)) tryInvokeRestart("muffleMessage"))
31: suppressMessages(rfishbase::synonyms())
32: fishbase(tables = "synonym")
33: check_names(data = spp, verbose = verbose, pct = pct, sn = sn)
34: FUN(X[[i]], ...)
35: lapply(X = X, FUN = FUN, ...)
36: sapply(data, function(spp) { checkFB <- check_names(data = spp, verbose = verbose, pct = pct, sn = sn) if (is.na(checkFB)) { checksppx <- spp } else { checksppx <- checkFB } sapply(db, FUN = function(xdb) { if (xdb == "gbif") { ndata <- tryCatch(expr = rgbif::occ_count(scientificName = checksppx), error = function(e) { if (grepl(" HTTP2 framing layer", e$message) == TRUE) { if (isTRUE(warn)) warning("GBIF webpage is misbehvaing and return HTTP2 frame layer message", call. = FALSE) return(NULL) } }) if (!is.null(ndata)) { if (ndata == 0) { if (isTRUE(verbose)) message("No records found for ", checksppx, " in GBIF") gbifx <- NULL } else if (ndata <= 50000 & is.null(extent)) { if (gbiflim <= 50000) { gbifsp <- rgbif::occ_data(scientificName = checksppx, limit = gbiflim) if (isTRUE(verbose)) message(nrow(gbifsp$data), " records for ", checksppx, " in GBIF were downloaded based on the gbiflimit of ", gbiflim) gbifx <- gbifsp$data } else { gbifsp <- rgbif::occ_data(scientificName = checksppx, limit = ndata) if (isTRUE(verbose)) message(nrow(gbifsp$data), " records for ", checksppx, " in GBIF were download as they were the maximum records found.") gbifx <- gbifsp$data } } else if (!is.null(extent)) { extval <- extentvalues(extent, xdb) if (gbiflim <= 50000) { gbifsp <- rgbif::occ_data(scientificName = checksppx, limit = gbiflim, decimalLongitude = paste0(extval[1], ",", extval[3]), decimalLatitude = paste0(extval[2], ",", extval[4]), ...) if (isTRUE(verbose)) message(nrow(gbifsp$data), " records for ", checksppx, " in GBIF were downloaded based on the gbif limit of ", gbiflim) } else { gbifsp <- rgbif::occ_data(scientificName = checksppx, limit = gbiflim, decimalLongitude = paste0(extval[1], ",", extval[3]), decimalLatitude = paste0(extval[2], ",", extval[4]), ...) if (isTRUE(verbose)) message("All ", nrow(gbifsp$data), " records for ", checksppx, " in GBIF were downloaded") } gbifx <- gbifsp$data } else if (ndata > 50000 && is.null(extent)) { if (isTRUE(verbose)) message("Only ", gbiflim, " records will be downloaded.") gbifsp <- rgbif::occ_data(scientificName = checksppx, limit = gbiflim, ...) gbifx <- gbifsp$data } else { gbifx = NULL } if (is(gbifx, "data.frame")) { if ("decimalLatitude" %in% colnames(gbifx) == TRUE) { gbifx } else { if (isTRUE(warn)) warning("The data for ", checksppx, " will be removed since no cordinates were found in GBIF database.", call. = FALSE) gbifx <- NULL } } else { gbifx = NULL } } else { gbifx <- NULL } } else if (xdb == "vertnet") { sptx <- scan(text = checksppx, what = " ", quiet = TRUE) if (!is.null(extent)) vbbox <- extentvalues(extent, xdb) else vbbox <- NULL vertx <- tryCatch(rvertnet::searchbyterm(genus = tolower(sptx[1]), specificepithet = tolower(sptx[2]), limit = vertlim, messages = FALSE, bbox = vbbox), error = function(e) { if (grepl("Internal Server Error \\(HTTP 500\\)", e$message) == TRUE | grepl("Service Unavailable \\(HTTP 503\\)", e$message) == TRUE) { if (isTRUE(warn)) warning("The VertNet database has returned 500 or 503 error message and will be skipped for ", checksppx, ".", call. = FALSE) return(NULL) } else { return(NULL) } }) if (is.null(vertx)) { if (isTRUE(verbose)) message("No records for ", checksppx, " in vertnet were found") vertxdf <- NULL } else { vertxdf <- vertx$data if (isTRUE(verbose)) message(nrow(vertxdf), " records for ", checksppx, " in vertnet downloaded.") vertxdf } } else if (xdb == "inat") { if (!is.null(extent)) vbbox <- extentvalues(extent, xdb) else vbbox <- NULL inatx <- tryCatch(expr = { sx <- rinat::get_inat_obs(taxon_name = checksppx, maxresults = inatlim, bounds = vbbox) }, error = function(e) { if (isTRUE(verbose)) message("No data exist for species ", checksppx, " in inaturalist were found.") return(0) }) if (length(inatx) > 1) { inatx <- sx if (isTRUE(verbose)) message(nrow(inatx), " records for ", checksppx, " in inaturalist downloaded.") inatx } else { inatx <- NULL } } else { stop("Database name not acceptable. Use only gbif, vertnet, or inat") } }, simplify = FALSE)}, simplify = FALSE)
37: getdata(data = c("Squalius cephalus", "Salmo trutta", "Thymallus thymallus"), extent = danube, gbiflim = 50, inatlim = 50, vertlim = 50, verbose = FALSE)
38: eval(expr, envir)
39: eval(expr, envir)
40: withVisible(eval(expr, envir))
41: withCallingHandlers(code, message = function (cnd) { watcher$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$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
42: eval(call)
43: eval(call)
44: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
45: doWithOneRestart(return(expr), restart)
46: withOneRestart(expr, restarts[[1L]])
47: withRestartList(expr, restarts[-nr])
48: doWithOneRestart(return(expr), restart)
49: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
50: withRestartList(expr, restarts)
51: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
52: evaluate::evaluate(...)
53: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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))
54: in_dir(input_dir(), expr)
55: 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$render, options)))
56: eng_r(options)
57: block_exec(params)
58: call_block(x)
59: process_group(group)
60: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (xfun::pkg_available("rlang", "1.0.0")) { if (is_R_CMD_build() || is_R_CMD_check()) { cnd = tryCatch(rlang::entrace(e), error = identity) error <<- format(cnd) } else { rlang::entrace(e) } } })
61: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (xfun::pkg_available("rlang", "1.0.0")) { if (is_R_CMD_build() || is_R_CMD_check()) { cnd = tryCatch(rlang::entrace(e), error = identity) error <<- format(cnd) } else { rlang::entrace(e) } } }), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
62: process_file(text, output)
63: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
64: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
65: vweave_rmarkdown(...)
66: engine$weave(file, quiet = quiet, encoding = enc)
67: doTryCatch(return(expr), name, parentenv, handler)
68: tryCatchOne(expr, names, parentenv, handlers[[1L]])
69: tryCatchList(expr, classes, parentenv, handlers)
70: 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)))})
71: tools:::.buildOneVignette("loessmethodoptimisation.Rmd", "/data/gannet/ripley/R/packages/tests-clang/specleanr.Rcheck/vign_test/specleanr", TRUE, FALSE, "loessmethodoptimisation", "UTF-8", "/tmp/Rtmpj0fi5j/working_dir/RtmpaAEPGU/file3155dd313058b3.rds")
An irrecoverable exception occurred. R is aborting now ...
SUMMARY: processing the following files failed:
‘Plants.Rmd’ ‘eOutlier.Rmd’ ‘loessmethodoptimisation.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang