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