Last updated on 2025-12-01 03:54:51 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.0 | 35.42 | 628.59 | 664.01 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.0.0 | 24.41 | 418.31 | 442.72 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.0.0 | 88.00 | 744.91 | 832.91 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 1.0.0 | 155.00 | 919.66 | 1074.66 | OK | |
| r-patched-linux-x86_64 | 1.0.0 | 37.69 | 610.89 | 648.58 | OK | |
| r-release-linux-x86_64 | 1.0.0 | 35.79 | 611.42 | 647.21 | OK | |
| r-release-macos-arm64 | 1.0.0 | 15.00 | 305.00 | 320.00 | OK | |
| r-release-macos-x86_64 | 1.0.0 | 64.00 | 868.00 | 932.00 | OK | |
| r-oldrel-macos-arm64 | 1.0.0 | 12.00 | 302.00 | 314.00 | OK | |
| r-oldrel-macos-x86_64 | 1.0.0 | 65.00 | 1233.00 | 1298.00 | OK | |
| r-oldrel-windows-x86_64 | 1.0.0 | 46.00 | 575.00 | 621.00 | OK |
Version: 1.0.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [136s/121s]
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).
Saving _problems/test-methods-12.R
Non numeric columns Species were removed from data.
mixediqr was implemented successfully for species .
logboxplot was implemented successfully for species .
iqr was implemented successfully for species .
[ FAIL 1 | WARN 0 | SKIP 8 | PASS 157 ]
══ Skipped tests (8) ═══════════════════════════════════════════════════════════
• On CRAN (8): 'test-checknames.R:10:13', 'test-checknames.R:19:13',
'test-checknames.R:33:13', 'test-checknames.R:40:13', 'test-getdata.R:5:13',
'test-getdata.R:20:13', 'test-getdata.R:29:13', 'test-multidetect.R:543:13'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-methods.R:12:1'): (code run outside of `test_that()`) ──────────
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "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\"\ni Context: rapi_execute\ni Error type: INVALID\ni 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\"", trace = structure(list(call = list(check_names(mdf, colsp = "species", verbose = FALSE, merge = TRUE), fishbase(tables = "synonym"), suppressMessages(rfishbase::synonyms()), withCallingHandlers(expr, message = function(c) if (inherits(c, classes)) tryInvokeRestart("muffleMessage")), rfishbase::synonyms(), 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"))), select(., dplyr::any_of(c("synonym", "Status", "SpecCode", "SynCode", "CoL_ID", "TSN", "WoRMS_ID", "ZooBank_ID", "TaxonLevel"))), mutate(., synonym = paste(SynGenus, SynSpecies)), fb_tbl("synonyms", server, version, db), duckdbfs::open_dataset(urls[tbl]), parse_uri(sources, conn = conn, recursive = recursive), load_httpfs(conn), load_extension("httpfs", conn = conn, nightly = nightly, force = force), duckdb_extensions(), DBI::dbGetQuery(conn, query), cached_connection(), DBI::dbExecute(conn, "LOAD spatial;"), DBI::dbExecute(conn, "LOAD spatial;"), dbSendStatement(conn, statement, ...), dbSendStatement(conn, statement, ...), dbSendQuery(conn, statement, ...), dbSendQuery(conn, statement, ...), .local(conn, statement, ...), duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow), duckdb_execute(res), rethrow_rapi_execute(res@stmt_lst$ref, duckdb_convert_opts_impl(res@connection@convert_opts, arrow = res@arrow)), rlang::try_fetch(rapi_execute(stmt, convert_opts), error = function(e) { rethrow_error_from_rapi(e, call) }), 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]]), tryCatchList(expr, classes, parentenv, handlers), tryCatchOne(expr, names, parentenv, handlers[[1L]]), doTryCatch(return(expr), name, parentenv, handler), 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") } }), rapi_execute(stmt, convert_opts), `<fn>`("rapi_execute", "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\"", "INVALID", "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\"", `<list>`), rlang::abort(error_parts, class = "duckdb_error", !!!fields), signal_abort(cnd, .file), signalCondition(cnd), `<fn>`(`<dckdb_rr>`), handlers[[1L]](cnd), rethrow_error_from_rapi(e, call), rlang::abort(msg, call = call)), parent = c(0L, 1L, 2L, 3L, 2L, 5L, 0L, 0L, 5L, 9L, 10L, 11L, 12L, 13L, 14L, 14L, 16L, 16L, 18L, 18L, 20L, 20L, 22L, 23L, 24L, 25L, 26L, 27L, 28L, 29L, 30L, 27L, 26L, 0L, 34L, 35L, 36L, 0L, 38L, 39L, 40L), visible = c(TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE), namespace = c("specleanr", "specleanr", "base", "base", "rfishbase", NA, "dplyr", "dplyr", "rfishbase", "duckdbfs", "duckdbfs", "duckdbfs", "duckdbfs", "duckdbfs", "DBI", "duckdbfs", "DBI", "DBI", "DBI", "DBI", "DBI", "duckdb", "duckdb", "duckdb", "duckdb", "duckdb", "rlang", "base", "base", "base", "base", "base", "duckdb", "duckdb", "rlang", "rlang", "base", "rlang", NA, "duckdb", "rlang"), scope = c("::", ":::", "::", "::", "::", NA, "::", "::", "::", "::", ":::", ":::", ":::", "::", "::", "::", "::", "::", "::", "::", "::", "::", "local", ":::", ":::", ":::", "::", "::", "local", "local", "local", "::", ":::", "local", "::", ":::", "::", "local", NA, ":::", "::"), error_frame = c(FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE)), row.names = c(NA, -41L), version = 2L, class = c("rlang_trace", "rlib_trace", "tbl", "data.frame")), parent = NULL, rlang = list(inherit = TRUE), call = duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)), class = c("rlang_error", "error", "condition")))`: 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::check_names(...) at test-methods.R:12:1
2. │ └─specleanr:::fishbase(tables = "synonym")
3. │ ├─base::suppressMessages(rfishbase::synonyms())
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rfishbase::synonyms()
6. │ ├─... %>% ...
7. │ └─rfishbase::fb_tbl("synonyms", server, version, db)
8. │ └─duckdbfs::open_dataset(urls[tbl])
9. │ └─duckdbfs:::parse_uri(sources, conn = conn, recursive = recursive)
10. │ └─duckdbfs:::load_httpfs(conn)
11. │ └─duckdbfs:::load_extension(...)
12. │ └─duckdbfs::duckdb_extensions()
13. │ ├─DBI::dbGetQuery(conn, query)
14. │ └─duckdbfs::cached_connection()
15. │ ├─DBI::dbExecute(conn, "LOAD spatial;")
16. │ └─DBI::dbExecute(conn, "LOAD spatial;")
17. │ ├─DBI::dbSendStatement(conn, statement, ...)
18. │ └─DBI::dbSendStatement(conn, statement, ...)
19. │ ├─DBI::dbSendQuery(conn, statement, ...)
20. │ └─duckdb::dbSendQuery(conn, statement, ...)
21. │ └─duckdb (local) .local(conn, statement, ...)
22. │ └─duckdb:::duckdb_result(...)
23. │ └─duckdb:::duckdb_execute(res)
24. │ └─duckdb:::rethrow_rapi_execute(...)
25. │ ├─rlang::try_fetch(...)
26. │ │ ├─base::tryCatch(...)
27. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
28. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
29. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
30. │ │ └─base::withCallingHandlers(...)
31. │ └─duckdb:::rapi_execute(stmt, convert_opts)
32. ├─dplyr::select(...)
33. ├─dplyr::mutate(., synonym = paste(SynGenus, SynSpecies))
34. ├─duckdb (local) `<fn>`(...)
35. │ └─rlang::abort(error_parts, class = "duckdb_error", !!!fields)
36. │ └─rlang:::signal_abort(cnd, .file)
37. │ └─base::signalCondition(cnd)
38. ├─rlang (local) `<fn>`(`<dckdb_rr>`)
39. │ └─handlers[[1L]](cnd)
40. │ └─duckdb:::rethrow_error_from_rapi(e, call)
41. │ └─rlang::abort(msg, call = call)
42. │ └─rlang:::signal_abort(cnd, .file)
43. │ └─base::signalCondition(cnd)
44. └─base (local) `<fn>`(`<rlng_rrr>`)
[ FAIL 1 | WARN 0 | SKIP 8 | PASS 157 ]
Error:
! Test failures.
Execution halted
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
Quitting from eOutlier.Rmd:40-66 [datasoruces]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<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 'eOutlier.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 ‘eOutlier.Rmd’
--- 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:2370219:0:2370219] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x2)
==== backtrace (tid:2370219) ====
0 /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7f6a087b2df4]
1 /lib64/libucs.so.0(+0x17aed) [0x7f6a087b4aed]
2 /lib64/libucs.so.0(+0x17cbd) [0x7f6a087b4cbd]
3 /lib64/libc.so.6(+0x19c30) [0x7f6a1fd29c30]
4 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.4.2/linux_amd64/spatial.duckdb_extension(+0x10e6460) [0x7f68e84e6460]
5 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.4.2/linux_amd64/spatial.duckdb_extension(+0x10c5108) [0x7f68e84c5108]
6 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.4.2/linux_amd64/spatial.duckdb_extension(+0x7d5b74) [0x7f68e7bd5b74]
7 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.4.2/linux_amd64/spatial.duckdb_extension(+0x7d4119) [0x7f68e7bd4119]
8 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper29LoadExternalExtensionInternalERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEERNS_19ExtensionActiveLoadE+0x1b4) [0x7f693f9715f4]
9 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper21LoadExternalExtensionERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEE+0x4a) [0x7f693f97137a]
10 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZNK6duckdb12PhysicalLoad7GetDataERNS_16ExecutionContextERNS_9DataChunkERNS_19OperatorSourceInputE+0x151) [0x7f69407ab6b1]
11 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor15FetchFromSourceERNS_9DataChunkE+0x9f) [0x7f6940f5d5df]
12 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor7ExecuteEm+0x133) [0x7f6940f5a073]
13 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12PipelineTask11ExecuteTaskENS_17TaskExecutionModeE+0x119) [0x7f6940f59ca9]
14 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12ExecutorTask7ExecuteENS_17TaskExecutionModeE+0xa0) [0x7f6940f535c0]
15 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb8Executor11ExecuteTaskEb+0x24a) [0x7f6940f58b8a]
16 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb13ClientContext19ExecuteTaskInternalERNS_17ClientContextLockERNS_15BaseQueryResultEb+0x40) [0x7f6940d98280]
17 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb18PendingQueryResult15ExecuteInternalERNS_17ClientContextLockE+0x7a) [0x7f6940d9a7ba]
18 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb17PreparedStatement7ExecuteERNS_6vectorINS_5ValueELb1EEEb+0x5a) [0x7f6940dbad1a]
19 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_Z12rapi_executeN5cpp1116external_pointerIN6duckdb10RStatementEXadL_ZNS_15default_deleterIS2_EEvPT_EEEENS1_11ConvertOptsE+0x115) [0x7f693f701b95]
20 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_duckdb_rapi_execute+0x63) [0x7f693f76a8f3]
21 /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8e564) [0x5583ba637564]
22 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdd470) [0x5583ba686470]
23 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc62ac) [0x5583ba66f2ac]
24 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x5583ba66ea35]
25 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc6534) [0x5583ba66f534]
26 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x26e) [0x5583ba66eafe]
27 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc6534) [0x5583ba66f534]
28 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf5b0) [0x5583ba6885b0]
29 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcaf92) [0x5583ba673f92]
30 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc62ac) [0x5583ba66f2ac]
31 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x5583ba66ea35]
32 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe2e29) [0x5583ba68be29]
33 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe232c) [0x5583ba68b32c]
34 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x5583ba66ee86]
35 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc6534) [0x5583ba66f534]
36 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdf5b0) [0x5583ba6885b0]
37 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcaf92) [0x5583ba673f92]
38 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc62ac) [0x5583ba66f2ac]
39 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x5583ba66ea35]
40 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe2e29) [0x5583ba68be29]
41 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe232c) [0x5583ba68b32c]
42 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x5583ba66ee86]
43 /data/gannet/ripley/R/test-clang/rlang/libs/rlang.so(+0x4603) [0x7f6a16130603]
44 /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8c6b3) [0x5583ba6356b3]
45 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcdeab) [0x5583ba676eab]
46 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc62ac) [0x5583ba66f2ac]
47 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x5583ba66ea35]
48 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe2e29) [0x5583ba68be29]
49 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe232c) [0x5583ba68b32c]
50 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x5583ba66ee86]
51 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe83d8) [0x5583ba6913d8]
52 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x5583ba66ec60]
53 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe74eb) [0x5583ba6904eb]
54 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x5583ba66ec60]
55 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe2e29) [0x5583ba68be29]
56 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe232c) [0x5583ba68b32c]
57 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcd6b3) [0x5583ba6766b3]
58 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc62ac) [0x5583ba66f2ac]
59 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x5583ba66ea35]
60 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe2e29) [0x5583ba68be29]
61 /data/gannet/ripley/R/R-clang/bin/exec/R(R_execMethod+0x2cb) [0x5583ba68ec5b]
=================================
*** caught segfault ***
address 0x4d200242aab, 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/RtmpXkO4ee/working_dir/RtmpSuPjXp/file23f86c58e4d1f.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
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.