CRAN Package Check Results for Package taxadb

Last updated on 2022-09-11 12:56:30 CEST.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-clang	0.1.5	8.40	82.63	91.03	ERROR
r-devel-linux-x86_64-debian-gcc	0.1.5	6.37	61.36	67.73	ERROR
r-devel-linux-x86_64-fedora-clang	0.1.5			122.60	ERROR
r-devel-linux-x86_64-fedora-gcc	0.1.5			120.92	ERROR
r-devel-windows-x86_64	0.1.5	28.00	126.00	154.00	ERROR
r-patched-linux-x86_64	0.1.5	8.93	77.31	86.24	ERROR
r-release-linux-x86_64	0.1.5	8.25	76.25	84.50	ERROR
r-release-macos-arm64	0.1.5			40.00	OK
r-release-macos-x86_64	0.1.5			61.00	OK
r-release-windows-x86_64	0.1.5	27.00	125.00	152.00	ERROR
r-oldrel-macos-arm64	0.1.5			43.00	OK
r-oldrel-macos-x86_64	0.1.5			58.00	OK
r-oldrel-windows-ix86+x86_64	0.1.5	20.00	117.00	137.00	OK

Additional issues

M1mac

Check Details

Version: 0.1.5
Check: tests
Result: ERROR
     Running ‘spelling.R’ [0s/1s]
     Running ‘testthat.R’ [8s/16s]
    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
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.1.5
Check: tests
Result: ERROR
     Running ‘spelling.R’
     Running ‘testthat.R’ [11s/18s]
    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
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.1.5
Check: tests
Result: ERROR
     Running ‘spelling.R’
     Running ‘testthat.R’ [12s/36s]
    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
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 0.1.5
Check: tests
Result: ERROR
     Running 'spelling.R' [0s]
     Running 'testthat.R' [19s]
    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
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64

Version: 0.1.5
Check: tests
Result: ERROR
     Running ‘spelling.R’ [0s/0s]
     Running ‘testthat.R’ [10s/16s]
    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
Flavor: r-patched-linux-x86_64

Version: 0.1.5
Check: tests
Result: ERROR
     Running ‘spelling.R’ [0s/1s]
     Running ‘testthat.R’ [10s/15s]
    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
Flavor: r-release-linux-x86_64