Running ‘spelling.R’
  Running ‘testthat.R’ [12s/37s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(taxadb)
  > 
  > ## Optionally we can select backend for testing: duckdb, MonetDBLite, or RSQLite
  > ## Sys.setenv("TAXADB_DRIVER"="MonetDBLite")
  > test_check("taxadb")
  [1] "Testing using backend duckdb_connection"
  [ FAIL 11 | WARN 0 | SKIP 4 | PASS 24 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (3)
  • testing all of COL is slow, using unit-test instead... (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-filter_by.R:11:3): filter_common ────────────────────────────────
  Error: Parser Error: syntax error at or near "2022"
  LINE 1: CREATE  TABLE 2022_common_itis_test AS SELECT #1,#2,#...
                        ^
  Backtrace:
       ▆
    1. └─taxadb::filter_common("Tufted Capuchin") at test-filter_by.R:11:2
    2.   └─taxadb::filter_by(...)
    3.     ├─dplyr::mutate(taxa_tbl(provider, schema, version, db), input = !!sym(by))
    4.     └─taxadb::taxa_tbl(provider, schema, version, db)
    5.       └─taxadb::td_create(...)
    6.         ├─taxadb:::suppress_msg(...)
    7.         │ └─base::withCallingHandlers(...)
    8.         └─arkdb::unark(...)
    9.           └─base::lapply(...)
   10.             └─arkdb (local) FUN(X[[i]], ...)
   11.               └─arkdb:::unark_file(...)
   12.                 └─arkdb::process_chunks(...)
   13.                   └─arkdb (local) process_fn(chunk)
   14.                     ├─DBI::dbWriteTable(db_con, tablename, chunk, append = TRUE)
   15.                     └─DBI::dbWriteTable(db_con, tablename, chunk, append = TRUE)
   16.                       └─duckdb (local) .local(conn, name, value, ...)
   17.                         ├─DBI::dbExecute(...)
   18.                         └─DBI::dbExecute(...)
   19.                           ├─DBI::dbSendStatement(conn, statement, ...)
   20.                           └─DBI::dbSendStatement(conn, statement, ...)
   21.                             ├─DBI::dbSendQuery(conn, statement, ...)
   22.                             └─duckdb::dbSendQuery(conn, statement, ...)
   23.                               └─duckdb (local) .local(conn, statement, ...)
   24.                                 └─duckdb:::rapi_prepare(conn@conn_ref, statement)
  ── Error (test-filter_by.R:23:4): filter_by ────────────────────────────────────
  Error: Parser Error: syntax error at or near "2022"
  LINE 1: CREATE  TABLE 2022_dwc_itis_test AS SELECT #1,#2,#3,#...
                        ^
  Backtrace:
       ▆
    1. └─taxadb::filter_by(sp, "scientificName", ignore_case = TRUE) at test-filter_by.R:23:3
    2.   ├─dplyr::mutate(taxa_tbl(provider, schema, version, db), input = !!sym(by))
    3.   └─taxadb::taxa_tbl(provider, schema, version, db)
    4.     └─taxadb::td_create(...)
    5.       ├─taxadb:::suppress_msg(...)
    6.       │ └─base::withCallingHandlers(...)
    7.       └─arkdb::unark(...)
    8.         └─base::lapply(...)
    9.           └─arkdb (local) FUN(X[[i]], ...)
   10.             └─arkdb:::unark_file(...)
   11.               └─arkdb::process_chunks(...)
   12.                 └─arkdb (local) process_fn(chunk)
   13.                   ├─DBI::dbWriteTable(db_con, tablename, chunk, append = TRUE)
   14.                   └─DBI::dbWriteTable(db_con, tablename, chunk, append = TRUE)
   15.                     └─duckdb (local) .local(conn, name, value, ...)
   16.                       ├─DBI::dbExecute(...)
   17.                       └─DBI::dbExecute(...)
   18.                         ├─DBI::dbSendStatement(conn, statement, ...)
   19.                         └─DBI::dbSendStatement(conn, statement, ...)
   20.                           ├─DBI::dbSendQuery(conn, statement, ...)
   21.                           └─duckdb::dbSendQuery(conn, statement, ...)
   22.                             └─duckdb (local) .local(conn, statement, ...)
   23.                               └─duckdb:::rapi_prepare(conn@conn_ref, statement)
  ── Error (test-filter_by.R:47:3): filter_name ──────────────────────────────────
  Error: Parser Error: syntax error at or near "2022"
  LINE 1: CREATE  TABLE 2022_dwc_itis_test AS SELECT #1,#2,#3,#...
                        ^
  Backtrace:
       ▆
    1. └─taxadb::filter_name(sp, ignore_case = TRUE) at test-filter_by.R:47:2
    2.   └─taxadb::filter_by(...)
    3.     ├─dplyr::mutate(taxa_tbl(provider, schema, version, db), input = !!sym(by))
    4.     └─taxadb::taxa_tbl(provider, schema, version, db)
    5.       └─taxadb::td_create(...)
    6.         ├─taxadb:::suppress_msg(...)
    7.         │ └─base::withCallingHandlers(...)
    8.         └─arkdb::unark(...)
    9.           └─base::lapply(...)
   10.             └─arkdb (local) FUN(X[[i]], ...)
   11.               └─arkdb:::unark_file(...)
   12.                 └─arkdb::process_chunks(...)
   13.                   └─arkdb (local) process_fn(chunk)
   14.                     ├─DBI::dbWriteTable(db_con, tablename, chunk, append = TRUE)
   15.                     └─DBI::dbWriteTable(db_con, tablename, chunk, append = TRUE)
   16.                       └─duckdb (local) .local(conn, name, value, ...)
   17.                         ├─DBI::dbExecute(...)
   18.                         └─DBI::dbExecute(...)
   19.                           ├─DBI::dbSendStatement(conn, statement, ...)
   20.                           └─DBI::dbSendStatement(conn, statement, ...)
   21.                             ├─DBI::dbSendQuery(conn, statement, ...)
   22.                             └─duckdb::dbSendQuery(conn, statement, ...)
   23.                               └─duckdb (local) .local(conn, statement, ...)
   24.                                 └─duckdb:::rapi_prepare(conn@conn_ref, statement)
  ── Error (test-filter_by.R:54:3): filter_id ────────────────────────────────────
  Error: Parser Error: syntax error at or near "2022"
  LINE 1: CREATE  TABLE 2022_dwc_itis_test AS SELECT #1,#2,#3,#...
                        ^
  Backtrace:
       ▆
    1. └─taxadb::filter_id(c("ITIS:944156", "ITIS:944402")) at test-filter_by.R:54:2
    2.   └─taxadb::filter_by(...)
    3.     ├─dplyr::mutate(taxa_tbl(provider, schema, version, db), input = !!sym(by))
    4.     └─taxadb::taxa_tbl(provider, schema, version, db)
    5.       └─taxadb::td_create(...)
    6.         ├─taxadb:::suppress_msg(...)
    7.         │ └─base::withCallingHandlers(...)
    8.         └─arkdb::unark(...)
    9.           └─base::lapply(...)
   10.             └─arkdb (local) FUN(X[[i]], ...)
   11.               └─arkdb:::unark_file(...)
   12.                 └─arkdb::process_chunks(...)
   13.                   └─arkdb (local) process_fn(chunk)
   14.                     ├─DBI::dbWriteTable(db_con, tablename, chunk, append = TRUE)
   15.                     └─DBI::dbWriteTable(db_con, tablename, chunk, append = TRUE)
   16.                       └─duckdb (local) .local(conn, name, value, ...)
   17.                         ├─DBI::dbExecute(...)
   18.                         └─DBI::dbExecute(...)
   19.                           ├─DBI::dbSendStatement(conn, statement, ...)
   20.                           └─DBI::dbSendStatement(conn, statement, ...)
   21.                             ├─DBI::dbSendQuery(conn, statement, ...)
   22.                             └─duckdb::dbSendQuery(conn, statement, ...)
   23.                               └─duckdb (local) .local(conn, statement, ...)
   24.                                 └─duckdb:::rapi_prepare(conn@conn_ref, statement)
  ── Error (test-filter_by.R:64:3): filter_rank ──────────────────────────────────
  Error: Parser Error: syntax error at or near "2022"
  LINE 1: CREATE  TABLE 2022_dwc_itis_test AS SELECT #1,#2,#3,#...
                        ^
  Backtrace:
       ▆
    1. └─taxadb::filter_rank("Sapajus", "genus") at test-filter_by.R:64:2
    2.   └─taxadb::filter_by(...)
    3.     ├─dplyr::mutate(taxa_tbl(provider, schema, version, db), input = !!sym(by))
    4.     └─taxadb::taxa_tbl(provider, schema, version, db)
    5.       └─taxadb::td_create(...)
    6.         ├─taxadb:::suppress_msg(...)
    7.         │ └─base::withCallingHandlers(...)
    8.         └─arkdb::unark(...)
    9.           └─base::lapply(...)
   10.             └─arkdb (local) FUN(X[[i]], ...)
   11.               └─arkdb:::unark_file(...)
   12.                 └─arkdb::process_chunks(...)
   13.                   └─arkdb (local) process_fn(chunk)
   14.                     ├─DBI::dbWriteTable(db_con, tablename, chunk, append = TRUE)
   15.                     └─DBI::dbWriteTable(db_con, tablename, chunk, append = TRUE)
   16.                       └─duckdb (local) .local(conn, name, value, ...)
   17.                         ├─DBI::dbExecute(...)
   18.                         └─DBI::dbExecute(...)
   19.                           ├─DBI::dbSendStatement(conn, statement, ...)
   20.                           └─DBI::dbSendStatement(conn, statement, ...)
   21.                             ├─DBI::dbSendQuery(conn, statement, ...)
   22.                             └─duckdb::dbSendQuery(conn, statement, ...)
   23.                               └─duckdb (local) .local(conn, statement, ...)
   24.                                 └─duckdb:::rapi_prepare(conn@conn_ref, statement)
  ── Error (test-filter_by.R:71:3): filter_common ────────────────────────────────
  Error: Parser Error: syntax error at or near "2022"
  LINE 1: CREATE  TABLE 2022_common_itis_test AS SELECT #1,#2,#...
                        ^
  Backtrace:
       ▆
    1. └─taxadb::filter_common("man", "itis_test") at test-filter_by.R:71:2
    2.   └─taxadb::filter_by(...)
    3.     ├─dplyr::mutate(taxa_tbl(provider, schema, version, db), input = !!sym(by))
    4.     └─taxadb::taxa_tbl(provider, schema, version, db)
    5.       └─taxadb::td_create(...)
    6.         ├─taxadb:::suppress_msg(...)
    7.         │ └─base::withCallingHandlers(...)
    8.         └─arkdb::unark(...)
    9.           └─base::lapply(...)
   10.             └─arkdb (local) FUN(X[[i]], ...)
   11.               └─arkdb:::unark_file(...)
   12.                 └─arkdb::process_chunks(...)
   13.                   └─arkdb (local) process_fn(chunk)
   14.                     ├─DBI::dbWriteTable(db_con, tablename, chunk, append = TRUE)
   15.                     └─DBI::dbWriteTable(db_con, tablename, chunk, append = TRUE)
   16.                       └─duckdb (local) .local(conn, name, value, ...)
   17.                         ├─DBI::dbExecute(...)
   18.                         └─DBI::dbExecute(...)
   19.                           ├─DBI::dbSendStatement(conn, statement, ...)
   20.                           └─DBI::dbSendStatement(conn, statement, ...)
   21.                             ├─DBI::dbSendQuery(conn, statement, ...)
   22.                             └─duckdb::dbSendQuery(conn, statement, ...)
   23.                               └─duckdb (local) .local(conn, statement, ...)
   24.                                 └─duckdb:::rapi_prepare(conn@conn_ref, statement)
  ── Error (test-fuzzy_filter.R:6:3): we can fuzzy match scientific and common names ──
  Error: Parser Error: syntax error at or near "2022"
  LINE 1: CREATE  TABLE 2022_dwc_itis_test AS SELECT #1,#2,#3,#...
                        ^
  Backtrace:
       ▆
    1. └─taxadb::fuzzy_filter(name, "vernacularName", "itis_test") at test-fuzzy_filter.R:6:2
    2.   ├─dplyr::mutate(taxa_tbl(provider, "dwc", version, db), input = !!sym(by))
    3.   └─taxadb::taxa_tbl(provider, "dwc", version, db)
    4.     └─taxadb::td_create(...)
    5.       ├─taxadb:::suppress_msg(...)
    6.       │ └─base::withCallingHandlers(...)
    7.       └─arkdb::unark(...)
    8.         └─base::lapply(...)
    9.           └─arkdb (local) FUN(X[[i]], ...)
   10.             └─arkdb:::unark_file(...)
   11.               └─arkdb::process_chunks(...)
   12.                 └─arkdb (local) process_fn(chunk)
   13.                   ├─DBI::dbWriteTable(db_con, tablename, chunk, append = TRUE)
   14.                   └─DBI::dbWriteTable(db_con, tablename, chunk, append = TRUE)
   15.                     └─duckdb (local) .local(conn, name, value, ...)
   16.                       ├─DBI::dbExecute(...)
   17.                       └─DBI::dbExecute(...)
   18.                         ├─DBI::dbSendStatement(conn, statement, ...)
   19.                         └─DBI::dbSendStatement(conn, statement, ...)
   20.                           ├─DBI::dbSendQuery(conn, statement, ...)
   21.                           └─duckdb::dbSendQuery(conn, statement, ...)
   22.                             └─duckdb (local) .local(conn, statement, ...)
   23.                               └─duckdb:::rapi_prepare(conn@conn_ref, statement)
  ── Error (test-fuzzy_filter.R:23:3): we can fuzzy match scientific and common names ──
  Error: Parser Error: syntax error at or near "2022"
  LINE 1: CREATE  TABLE 2022_dwc_itis_test AS SELECT #1,#2,#3,#...
                        ^
  Backtrace:
       ▆
    1. └─taxadb::common_contains(name, "itis_test") at test-fuzzy_filter.R:23:2
    2.   └─taxadb::fuzzy_filter(...)
    3.     ├─dplyr::mutate(taxa_tbl(provider, "dwc", version, db), input = !!sym(by))
    4.     └─taxadb::taxa_tbl(provider, "dwc", version, db)
    5.       └─taxadb::td_create(...)
    6.         ├─taxadb:::suppress_msg(...)
    7.         │ └─base::withCallingHandlers(...)
    8.         └─arkdb::unark(...)
    9.           └─base::lapply(...)
   10.             └─arkdb (local) FUN(X[[i]], ...)
   11.               └─arkdb:::unark_file(...)
   12.                 └─arkdb::process_chunks(...)
   13.                   └─arkdb (local) process_fn(chunk)
   14.                     ├─DBI::dbWriteTable(db_con, tablename, chunk, append = TRUE)
   15.                     └─DBI::dbWriteTable(db_con, tablename, chunk, append = TRUE)
   16.                       └─duckdb (local) .local(conn, name, value, ...)
   17.                         ├─DBI::dbExecute(...)
   18.                         └─DBI::dbExecute(...)
   19.                           ├─DBI::dbSendStatement(conn, statement, ...)
   20.                           └─DBI::dbSendStatement(conn, statement, ...)
   21.                             ├─DBI::dbSendQuery(conn, statement, ...)
   22.                             └─duckdb::dbSendQuery(conn, statement, ...)
   23.                               └─duckdb (local) .local(conn, statement, ...)
   24.                                 └─duckdb:::rapi_prepare(conn@conn_ref, statement)
  ── Error (test-get_ids.R:5:3): we can use get_ids options ──────────────────────
  Error: Parser Error: syntax error at or near "2022"
  LINE 1: CREATE  TABLE 2022_dwc_itis_test AS SELECT #1,#2,#3,#...
                        ^
  Backtrace:
       ▆
    1. ├─taxadb::get_ids("Homo sapiens", format = "bare", db = "itis_test") at test-get_ids.R:5:2
    2. │ ├─... %>% arrange(sort)
    3. │ └─taxadb::filter_name(...)
    4. │   └─taxadb::filter_by(...)
    5. │     ├─dplyr::mutate(taxa_tbl(provider, schema, version, db), input = !!sym(by))
    6. │     └─taxadb::taxa_tbl(provider, schema, version, db)
    7. │       └─taxadb::td_create(...)
    8. │         ├─taxadb:::suppress_msg(...)
    9. │         │ └─base::withCallingHandlers(...)
   10. │         └─arkdb::unark(...)
   11. │           └─base::lapply(...)
   12. │             └─arkdb (local) FUN(X[[i]], ...)
   13. │               └─arkdb:::unark_file(...)
   14. │                 └─arkdb::process_chunks(...)
   15. │                   └─arkdb (local) process_fn(chunk)
   16. │                     ├─DBI::dbWriteTable(db_con, tablename, chunk, append = TRUE)
   17. │                     └─DBI::dbWriteTable(db_con, tablename, chunk, append = TRUE)
   18. │                       └─duckdb (local) .local(conn, name, value, ...)
   19. │                         ├─DBI::dbExecute(...)
   20. │                         └─DBI::dbExecute(...)
   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:::rapi_prepare(conn@conn_ref, statement)
   27. └─dplyr::arrange(., sort)
  ── Error (test-get_names.R:68:3): we can handle more intensive comparisons: ITIS test ──
  Error: Parser Error: syntax error at or near "2022"
  LINE 1: CREATE  TABLE 2022_dwc_itis_test AS SELECT #1,#2,#3,#...
                        ^
  Backtrace:
       ▆
    1. ├─taxa_tbl() %>% pull(taxonID) at test-get_names.R:68:2
    2. ├─dplyr::pull(., taxonID)
    3. └─taxadb::taxa_tbl()
    4.   └─taxadb::td_create(...)
    5.     ├─taxadb:::suppress_msg(...)
    6.     │ └─base::withCallingHandlers(...)
    7.     └─arkdb::unark(...)
    8.       └─base::lapply(...)
    9.         └─arkdb (local) FUN(X[[i]], ...)
   10.           └─arkdb:::unark_file(...)
   11.             └─arkdb::process_chunks(...)
   12.               └─arkdb (local) process_fn(chunk)
   13.                 ├─DBI::dbWriteTable(db_con, tablename, chunk, append = TRUE)
   14.                 └─DBI::dbWriteTable(db_con, tablename, chunk, append = TRUE)
   15.                   └─duckdb (local) .local(conn, name, value, ...)
   16.                     ├─DBI::dbExecute(...)
   17.                     └─DBI::dbExecute(...)
   18.                       ├─DBI::dbSendStatement(conn, statement, ...)
   19.                       └─DBI::dbSendStatement(conn, statement, ...)
   20.                         ├─DBI::dbSendQuery(conn, statement, ...)
   21.                         └─duckdb::dbSendQuery(conn, statement, ...)
   22.                           └─duckdb (local) .local(conn, statement, ...)
   23.                             └─duckdb:::rapi_prepare(conn@conn_ref, statement)
  ── Error (test-taxadb.R:10:3): we can set up a db and call basic functions ─────
  Error: Parser Error: syntax error at or near "2022"
  LINE 1: CREATE  TABLE 2022_dwc_itis_test AS SELECT #1,#2,#3,#...
                        ^
  Backtrace:
       ▆
    1. └─taxadb::taxa_tbl(db = db, provider = "itis_test") at test-taxadb.R:10:2
    2.   └─taxadb::td_create(...)
    3.     ├─taxadb:::suppress_msg(...)
    4.     │ └─base::withCallingHandlers(...)
    5.     └─arkdb::unark(...)
    6.       └─base::lapply(...)
    7.         └─arkdb (local) FUN(X[[i]], ...)
    8.           └─arkdb:::unark_file(...)
    9.             └─arkdb::process_chunks(...)
   10.               └─arkdb (local) process_fn(chunk)
   11.                 ├─DBI::dbWriteTable(db_con, tablename, chunk, append = TRUE)
   12.                 └─DBI::dbWriteTable(db_con, tablename, chunk, append = TRUE)
   13.                   └─duckdb (local) .local(conn, name, value, ...)
   14.                     ├─DBI::dbExecute(...)
   15.                     └─DBI::dbExecute(...)
   16.                       ├─DBI::dbSendStatement(conn, statement, ...)
   17.                       └─DBI::dbSendStatement(conn, statement, ...)
   18.                         ├─DBI::dbSendQuery(conn, statement, ...)
   19.                         └─duckdb::dbSendQuery(conn, statement, ...)
   20.                           └─duckdb (local) .local(conn, statement, ...)
   21.                             └─duckdb:::rapi_prepare(conn@conn_ref, statement)
  
  [ FAIL 11 | WARN 0 | SKIP 4 | PASS 24 ]
  Error: Test failures
  Execution halted