Last updated on 2022-09-11 12:56:40 CEST.
Package | ERROR | WARN | NOTE | OK |
---|---|---|---|---|
arkdb | 1 | 1 | 11 | |
codemeta | 13 | |||
codemetar | 13 | |||
contentid | 13 | |||
EcoNetGen | 13 | |||
EML | 13 | |||
emld | 13 | |||
gbifdb | 1 | 12 | ||
knitcitations | 13 | |||
neonstore | 1 | 12 | ||
piggyback | 13 | |||
pmc | 13 | |||
rdflib | 13 | |||
rfigshare | 13 | |||
rfishbase | 13 | |||
RNeXML | 13 | |||
sarsop | 7 | 6 | ||
taxadb | 8 | 5 | ||
taxalight | 13 | |||
treebase | 13 | |||
virtuoso | 13 |
Current CRAN status: WARN: 1, NOTE: 1, OK: 11
Version: 0.0.15
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘arrow’
Flavor: r-release-linux-x86_64
Version: 0.0.15
Check: for unstated dependencies in ‘tests’
Result: WARN
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Flavor: r-oldrel-windows-ix86+x86_64
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: NOTE: 13
Version: 0.2.3
Check: LazyData
Result: NOTE
'LazyData' is specified without a 'data' directory
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64
Current CRAN status: OK: 13
Current CRAN status: NOTE: 13
Version: 0.5.1
Check: LazyData
Result: NOTE
'LazyData' is specified without a 'data' directory
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64
Current CRAN status: ERROR: 1, OK: 12
Version: 0.1.2
Check: package dependencies
Result: ERROR
Package required but not available: ‘arrow’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-release-linux-x86_64
Current CRAN status: OK: 13
Current CRAN status: NOTE: 1, OK: 12
Version: 0.4.4
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘rhdf5’
Flavor: r-release-macos-arm64
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: NOTE: 7, OK: 6
Version: 0.6.10
Check: installed package size
Result: NOTE
installed size is 6.6Mb
sub-directories of 1Mb or more:
bin 5.8Mb
Flavors: r-devel-windows-x86_64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-x86_64
Version: 0.6.9
Check: installed package size
Result: NOTE
installed size is 5.3Mb
sub-directories of 1Mb or more:
bin 4.4Mb
Flavors: r-release-macos-arm64, r-oldrel-macos-arm64, r-oldrel-windows-ix86+x86_64
Current CRAN status: ERROR: 8, OK: 5
Version: 0.1.5
Check: tests
Result: ERROR
Running 'spelling.R' [0s/0s]
Running 'testthat.R' [11s/17s]
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:
x
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:
x
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:
x
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:
x
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:
x
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:
x
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:
x
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:
x
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:
x
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:
x
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:
x
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-clang
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
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13