Running 'spelling.R' [0s]
  Running 'testthat.R' [14s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(taxadb)
  > 
  > #Sys.setenv(TAXADB_DRIVER="MonetDBLite")
  > test_check("taxadb")
  driver not specified, trying duckdb
  [1] "Testing using backend duckdb_connection"
  == Skipped tests ===============================================================
  * On CRAN (3)
  * testing all of COL is slow, using unit-test instead... (1)
  
  == Failed tests ================================================================
  -- Error (test-filter_by.R:23:4): filter_by ------------------------------------
  Error: duckdb_startup_R: Failed to open database
  Backtrace:
       x
    1. \-taxadb::filter_by(sp, "scientificName", ignore_case = TRUE) 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_connect()
    5.     \-arkdb::local_db(dbdir = dbdir, driver = driver, readonly = read_only)
    6.       \-arkdb:::db_driver(dbname, driver = driver, read_only = read_only)
    7.         +-DBI::dbConnect(duckdb(), file.path(dbname, driver), read_only = read_only)
    8.         \-DBI::dbConnect(duckdb(), file.path(dbname, driver), read_only = read_only)
    9.           \-duckdb:::.local(drv, ...)
   10.             \-duckdb::duckdb(dbdir, read_only)
   11.               \-methods::new(...)
   12.                 +-methods::initialize(value, ...)
   13.                 \-methods::initialize(value, ...)
  -- Error (test-filter_by.R:47:3): filter_name ----------------------------------
  Error: duckdb_startup_R: Failed to open database
  Backtrace:
       x
    1. \-taxadb::filter_name(sp, ignore_case = TRUE) 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_connect()
    6.     \-arkdb::local_db(dbdir = dbdir, driver = driver, readonly = read_only)
    7.       \-arkdb:::db_driver(dbname, driver = driver, read_only = read_only)
    8.         +-DBI::dbConnect(duckdb(), file.path(dbname, driver), read_only = read_only)
    9.         \-DBI::dbConnect(duckdb(), file.path(dbname, driver), read_only = read_only)
   10.           \-duckdb:::.local(drv, ...)
   11.             \-duckdb::duckdb(dbdir, read_only)
   12.               \-methods::new(...)
   13.                 +-methods::initialize(value, ...)
   14.                 \-methods::initialize(value, ...)
  -- Error (test-filter_by.R:54:3): filter_id ------------------------------------
  Error: duckdb_startup_R: Failed to open database
  Backtrace:
       x
    1. \-taxadb::filter_id(c("ITIS:944156", "ITIS:944402")) 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_connect()
    6.     \-arkdb::local_db(dbdir = dbdir, driver = driver, readonly = read_only)
    7.       \-arkdb:::db_driver(dbname, driver = driver, read_only = read_only)
    8.         +-DBI::dbConnect(duckdb(), file.path(dbname, driver), read_only = read_only)
    9.         \-DBI::dbConnect(duckdb(), file.path(dbname, driver), read_only = read_only)
   10.           \-duckdb:::.local(drv, ...)
   11.             \-duckdb::duckdb(dbdir, read_only)
   12.               \-methods::new(...)
   13.                 +-methods::initialize(value, ...)
   14.                 \-methods::initialize(value, ...)
  -- Error (test-filter_by.R:64:3): filter_rank ----------------------------------
  Error: duckdb_startup_R: Failed to open database
  Backtrace:
       x
    1. \-taxadb::filter_rank("Sapajus", "genus") 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_connect()
    6.     \-arkdb::local_db(dbdir = dbdir, driver = driver, readonly = read_only)
    7.       \-arkdb:::db_driver(dbname, driver = driver, read_only = read_only)
    8.         +-DBI::dbConnect(duckdb(), file.path(dbname, driver), read_only = read_only)
    9.         \-DBI::dbConnect(duckdb(), file.path(dbname, driver), read_only = read_only)
   10.           \-duckdb:::.local(drv, ...)
   11.             \-duckdb::duckdb(dbdir, read_only)
   12.               \-methods::new(...)
   13.                 +-methods::initialize(value, ...)
   14.                 \-methods::initialize(value, ...)
  -- Error (test-filter_by.R:71:3): filter_common --------------------------------
  Error: duckdb_startup_R: Failed to open database
  Backtrace:
       x
    1. \-taxadb::filter_common("man", "itis") 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_connect()
    6.     \-arkdb::local_db(dbdir = dbdir, driver = driver, readonly = read_only)
    7.       \-arkdb:::db_driver(dbname, driver = driver, read_only = read_only)
    8.         +-DBI::dbConnect(duckdb(), file.path(dbname, driver), read_only = read_only)
    9.         \-DBI::dbConnect(duckdb(), file.path(dbname, driver), read_only = read_only)
   10.           \-duckdb:::.local(drv, ...)
   11.             \-duckdb::duckdb(dbdir, read_only)
   12.               \-methods::new(...)
   13.                 +-methods::initialize(value, ...)
   14.                 \-methods::initialize(value, ...)
  -- Error (test-fuzzy_filter.R:6:3): we can fuzzy match scientific and common names --
  Error: duckdb_startup_R: Failed to open database
  Backtrace:
       x
    1. \-taxadb::fuzzy_filter(name, "vernacularName", "itis") 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_connect()
    5.     \-arkdb::local_db(dbdir = dbdir, driver = driver, readonly = read_only)
    6.       \-arkdb:::db_driver(dbname, driver = driver, read_only = read_only)
    7.         +-DBI::dbConnect(duckdb(), file.path(dbname, driver), read_only = read_only)
    8.         \-DBI::dbConnect(duckdb(), file.path(dbname, driver), read_only = read_only)
    9.           \-duckdb:::.local(drv, ...)
   10.             \-duckdb::duckdb(dbdir, read_only)
   11.               \-methods::new(...)
   12.                 +-methods::initialize(value, ...)
   13.                 \-methods::initialize(value, ...)
  -- Error (test-fuzzy_filter.R:23:3): we can fuzzy match scientific and common names --
  Error: duckdb_startup_R: Failed to open database
  Backtrace:
       x
    1. \-taxadb::common_contains(name, "itis") 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_connect()
    6.     \-arkdb::local_db(dbdir = dbdir, driver = driver, readonly = read_only)
    7.       \-arkdb:::db_driver(dbname, driver = driver, read_only = read_only)
    8.         +-DBI::dbConnect(duckdb(), file.path(dbname, driver), read_only = read_only)
    9.         \-DBI::dbConnect(duckdb(), file.path(dbname, driver), read_only = read_only)
   10.           \-duckdb:::.local(drv, ...)
   11.             \-duckdb::duckdb(dbdir, read_only)
   12.               \-methods::new(...)
   13.                 +-methods::initialize(value, ...)
   14.                 \-methods::initialize(value, ...)
  -- Error (test-get_ids.R:6:3): we can use get_ids options ----------------------
  Error: duckdb_startup_R: Failed to open database
  Backtrace:
       x
    1. +-taxadb::get_ids("Homo sapiens", format = "bare", db = "itis") test-get_ids.R:6:2
    2. | +-`%>%`(...)
    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_connect()
    8. |   \-arkdb::local_db(dbdir = dbdir, driver = driver, readonly = read_only)
    9. |     \-arkdb:::db_driver(dbname, driver = driver, read_only = read_only)
   10. |       +-DBI::dbConnect(duckdb(), file.path(dbname, driver), read_only = read_only)
   11. |       \-DBI::dbConnect(duckdb(), file.path(dbname, driver), read_only = read_only)
   12. |         \-duckdb:::.local(drv, ...)
   13. |           \-duckdb::duckdb(dbdir, read_only)
   14. |             \-methods::new(...)
   15. |               +-methods::initialize(value, ...)
   16. |               \-methods::initialize(value, ...)
   17. \-dplyr::arrange(., sort)
  -- Error (test-get_names.R:68:3): we can handle more intensive comparisons: ITIS test --
  Error: duckdb_startup_R: Failed to open database
  Backtrace:
       x
    1. +-taxa_tbl() %>% pull(taxonID) test-get_names.R:68:2
    2. +-dplyr::pull(., taxonID)
    3. \-taxadb::taxa_tbl()
    4.   \-taxadb::td_connect()
    5.     \-arkdb::local_db(dbdir = dbdir, driver = driver, readonly = read_only)
    6.       \-arkdb:::db_driver(dbname, driver = driver, read_only = read_only)
    7.         +-DBI::dbConnect(duckdb(), file.path(dbname, driver), read_only = read_only)
    8.         \-DBI::dbConnect(duckdb(), file.path(dbname, driver), read_only = read_only)
    9.           \-duckdb:::.local(drv, ...)
   10.             \-duckdb::duckdb(dbdir, read_only)
   11.               \-methods::new(...)
   12.                 +-methods::initialize(value, ...)
   13.                 \-methods::initialize(value, ...)
  -- Error (test-taxadb.R:9:3): we can set up a db and call basic functions ------
  Error: duckdb_startup_R: Failed to open database
  Backtrace:
       x
    1. \-taxadb::td_connect() test-taxadb.R:9:2
    2.   \-arkdb::local_db(dbdir = dbdir, driver = driver, readonly = read_only)
    3.     \-arkdb:::db_driver(dbname, driver = driver, read_only = read_only)
    4.       +-DBI::dbConnect(duckdb(), file.path(dbname, driver), read_only = read_only)
    5.       \-DBI::dbConnect(duckdb(), file.path(dbname, driver), read_only = read_only)
    6.         \-duckdb:::.local(drv, ...)
    7.           \-duckdb::duckdb(dbdir, read_only)
    8.             \-methods::new(...)
    9.               +-methods::initialize(value, ...)
   10.               \-methods::initialize(value, ...)
  
  [ FAIL 10 | WARN 0 | SKIP 4 | PASS 26 ]
  Error: Test failures
  In addition: Warning messages:
  1: In for (v in vnames) { :
    duckdb_finalize_connection_R: Connection is garbage-collected, use dbDisconnect() to avoid this.
  2: In for (v in vnames) { :
    duckdb_finalize_database_R: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this.
  driver not specified, trying duckdb
  Error in initialize(value, ...) : 
    duckdb_startup_R: Failed to open database
  Calls: test_check ... test_dir -> test_files -> test_files -> <Anonymous>
  Execution halted