CRAN Package Check Results for Package neotoma2

Last updated on 2025-07-09 10:48:58 CEST.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-clang	1.0.6	17.43	115.36	132.79	ERROR
r-devel-linux-x86_64-debian-gcc	1.0.6	12.40	79.62	92.02	ERROR
r-devel-linux-x86_64-fedora-clang	1.0.6			206.33	ERROR
r-devel-linux-x86_64-fedora-gcc	1.0.6			207.96	ERROR
r-devel-windows-x86_64	1.0.6	21.00	252.00	273.00	OK
r-patched-linux-x86_64	1.0.6	19.36	102.56	121.92	ERROR
r-release-linux-x86_64	1.0.6	16.81	130.74	147.55	OK
r-release-macos-arm64	1.0.5			168.00	OK
r-release-macos-x86_64	1.0.6			247.00	OK
r-release-windows-x86_64	1.0.6	20.00	156.00	176.00	ERROR
r-oldrel-macos-arm64	1.0.5			116.00	OK
r-oldrel-macos-x86_64	1.0.6			250.00	OK
r-oldrel-windows-x86_64	1.0.6	24.00	180.00	204.00	ERROR

Additional issues

M1mac

Check Details

Version: 1.0.6
Check: examples
Result: ERROR Running examples in ‘neotoma2-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: cite_data,sites-method > ### Title: Obtain data citations from multiple records. > ### Aliases: cite_data,sites-method > > ### ** Examples > > { + ds <- get_datasets(1) + cite_data(ds) + } Error in `map()`: ℹ In index: 1. Caused by error in `map()`: ℹ In index: 1. Caused by error in `x$agerange[[1]]`: ! subscript out of bounds Backtrace: ▆ 1. ├─neotoma2::get_datasets(1) 2. ├─neotoma2:::get_datasets.numeric(1) 3. │ └─neotoma2:::parse_dataset(result) 4. │ └─purrr::map(...) 5. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress) 6. │ ├─purrr:::with_indexed_errors(...) 7. │ │ └─base::withCallingHandlers(...) 8. │ ├─purrr:::call_with_cleanup(...) 9. │ └─neotoma2 (local) .f(.x[[i]], ...) 10. │ └─purrr::map(x$site$datasets, build_dataset) 11. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress) 12. │ ├─purrr:::with_indexed_errors(...) 13. │ │ └─base::withCallingHandlers(...) 14. │ ├─purrr:::call_with_cleanup(...) 15. │ └─neotoma2 (local) .f(.x[[i]], ...) 16. │ ├─methods::new(...) 17. │ │ ├─methods::initialize(value, ...) 18. │ │ └─methods::initialize(value, ...) 19. │ ├─neotoma2:::use_na(testNull(x$agerange[[1]]$ageold, NA), "int") 20. │ └─neotoma2:::testNull(x$agerange[[1]]$ageold, NA) 21. └─purrr (local) `<fn>`(`<sbscOOBE>`) 22. └─cli::cli_abort(...) 23. └─rlang::abort(...) Execution halted Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 1.0.6
Check: examples
Result: ERROR Running examples in ‘neotoma2-Ex.R’ failed The error most likely occurred in: > ### Name: cite_data,sites-method > ### Title: Obtain data citations from multiple records. > ### Aliases: cite_data,sites-method > > ### ** Examples > > { + ds <- get_datasets(1) + cite_data(ds) + } Error in `map()`: ℹ In index: 1. Caused by error in `map()`: ℹ In index: 1. Caused by error in `x$agerange[[1]]`: ! subscript out of bounds Backtrace: ▆ 1. ├─neotoma2::get_datasets(1) 2. ├─neotoma2:::get_datasets.numeric(1) 3. │ └─neotoma2:::parse_dataset(result) 4. │ └─purrr::map(...) 5. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress) 6. │ ├─purrr:::with_indexed_errors(...) 7. │ │ └─base::withCallingHandlers(...) 8. │ ├─purrr:::call_with_cleanup(...) 9. │ └─neotoma2 (local) .f(.x[[i]], ...) 10. │ └─purrr::map(x$site$datasets, build_dataset) 11. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress) 12. │ ├─purrr:::with_indexed_errors(...) 13. │ │ └─base::withCallingHandlers(...) 14. │ ├─purrr:::call_with_cleanup(...) 15. │ └─neotoma2 (local) .f(.x[[i]], ...) 16. │ ├─methods::new(...) 17. │ │ ├─methods::initialize(value, ...) 18. │ │ └─methods::initialize(value, ...) 19. │ ├─neotoma2:::use_na(testNull(x$agerange[[1]]$ageold, NA), "int") 20. │ └─neotoma2:::testNull(x$agerange[[1]]$ageold, NA) 21. └─purrr (local) `<fn>`(`<sbscOOBE>`) 22. └─cli::cli_abort(...) 23. └─rlang::abort(...) Execution halted Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-release-windows-x86_64, r-oldrel-windows-x86_64

Version: 1.0.6
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building ‘neotoma2-package.Rmd’ using rmarkdown Quitting from neotoma2-package.Rmd:228-232 [getdatasetsbyid] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NULL ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'neotoma2-package.Rmd' failed with diagnostics: ℹ In index: 1. Caused by error in `map()`: ℹ In index: 1. Caused by error in `x$agerange[[1]]`: ! subscript out of bounds --- failed re-building ‘neotoma2-package.Rmd’ SUMMARY: processing the following file failed: ‘neotoma2-package.Rmd’ Error: Vignette re-building failed. Execution halted Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-release-windows-x86_64, r-oldrel-windows-x86_64

Version: 1.0.6
Check: tests
Result: ERROR Running ‘testthat.R’ [6s/348s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(neotoma2) Attaching package: 'neotoma2' The following object is masked from 'package:stats': filter > > test_check("neotoma2") [ FAIL 7 | WARN 0 | SKIP 48 | PASS 11 ] ══ Skipped tests (48) ══════════════════════════════════════════════════════════ • On CRAN (48): 'test-toJSON.R:2:3', 'test_c.R:10:3', 'test_check_contacts.R:10:3', 'test_chroncontrols.R:5:3', 'test_chroncontrols.R:22:3', 'test_chroncontrols.R:36:3', 'test_clean.R:5:3', 'test_datasets.R:3:3', 'test_datasets.R:19:3', 'test_datasets.R:39:3', 'test_datasets.R:86:3', 'test_datasets.R:109:3', 'test_download.R:3:3', 'test_download.R:32:3', 'test_examples.R:3:3', 'test_filter.R:4:3', 'test_filter.R:27:3', 'test_filter.R:50:3', 'test_filter.R:74:3', 'test_filter.R:111:3', 'test_filter.R:138:3', 'test_filter.R:166:3', 'test_filter.R:192:3', 'test_filter.R:208:3', 'test_filter.R:223:3', 'test_generaltests.R:6:3', 'test_generaltests.R:17:3', 'test_generaltests.R:22:3', 'test_generaltests.R:40:3', 'test_generaltests.R:70:3', 'test_generaltests.R:78:5', 'test_generaltests.R:99:3', 'test_methods.R:3:3', 'test_plotLeaflet.r:6:3', 'test_plotLeaflet.r:18:3', 'test_samples.R:11:3', 'test_setsample.R:8:3', 'test_setsite.r:8:3', 'test_sites.R:9:3', 'test_sites.R:21:3', 'test_sites.R:37:3', 'test_sites.R:49:3', 'test_sites.R:62:3', 'test_sites.R:90:3', 'test_specimens.R:3:3', 'test_specimens.R:11:3', 'test_specimens.R:18:3', 'test_toWide.R:10:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-get_contacts.R:2:3'): Non integer x returns nothing: ─────────── <http_504/http_500/http_error/error/condition> Error in `parseURL(baseURL, ...)`: Gateway Timeout (HTTP 504). Failed to Could not connect to the Neotoma API. Check that the path is valid, and check the current status of the Neotoma API services at http://data.neotomadb.org. Backtrace: ▆ 1. ├─neotoma2::get_contacts(x = "Goring") at test-get_contacts.R:2:3 2. ├─neotoma2:::get_contacts.default(x = "Goring") 3. │ ├─parseURL(baseURL, ...) %>% cleanNULL() 4. │ └─neotoma2::parseURL(baseURL, ...) 5. │ └─httr::stop_for_status(response, task = "Could not connect to the Neotoma API.\n Check that the path is valid, and check the current\n status of the Neotoma API services at\n http://data.neotomadb.org") 6. └─neotoma2:::cleanNULL(.) 7. └─base::rapply(...) ── Error ('test-get_contacts.R:7:3'): Integer x returns sets of contacts: ────── <http_504/http_500/http_error/error/condition> Error in `parseURL(baseURL)`: Gateway Timeout (HTTP 504). Failed to Could not connect to the Neotoma API. Check that the path is valid, and check the current status of the Neotoma API services at http://data.neotomadb.org. Backtrace: ▆ 1. ├─neotoma2::get_contacts(x = 1) at test-get_contacts.R:7:3 2. ├─neotoma2:::get_contacts.numeric(x = 1) 3. │ ├─parseURL(baseURL) %>% cleanNULL() 4. │ └─neotoma2::parseURL(baseURL) 5. │ └─httr::stop_for_status(response, task = "Could not connect to the Neotoma API.\n Check that the path is valid, and check the current\n status of the Neotoma API services at\n http://data.neotomadb.org") 6. └─neotoma2:::cleanNULL(.) 7. └─base::rapply(...) ── Error ('test-get_table.R:6:3'): Call a single database table: ─────────────── <http_504/http_500/http_error/error/condition> Error in `parseURL(paste0("dbtables/table?table=", x, "&limit=", limit, "&offset=", offset))`: Gateway Timeout (HTTP 504). Failed to Could not connect to the Neotoma API. Check that the path is valid, and check the current status of the Neotoma API services at http://data.neotomadb.org. Backtrace: ▆ 1. ├─testthat::expect_is(get_table("agetypes"), "data.frame") at test-get_table.R:6:3 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─neotoma2::get_table("agetypes") 5. └─neotoma2::parseURL(...) 6. └─httr::stop_for_status(response, task = "Could not connect to the Neotoma API.\n Check that the path is valid, and check the current\n status of the Neotoma API services at\n http://data.neotomadb.org") ── Error ('test-get_table.R:11:3'): We can apply the limits for get_table() ──── <http_504/http_500/http_error/error/condition> Error in `parseURL(paste0("dbtables/table?table=", x, "&limit=", limit, "&offset=", offset))`: Gateway Timeout (HTTP 504). Failed to Could not connect to the Neotoma API. Check that the path is valid, and check the current status of the Neotoma API services at http://data.neotomadb.org. Backtrace: ▆ 1. ├─testthat::expect_equal(...) at test-get_table.R:11:3 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─base::nrow(get_table("agetypes", limit = 1)) 5. └─neotoma2::get_table("agetypes", limit = 1) 6. └─neotoma2::parseURL(...) 7. └─httr::stop_for_status(response, task = "Could not connect to the Neotoma API.\n Check that the path is valid, and check the current\n status of the Neotoma API services at\n http://data.neotomadb.org") ── Error ('test-get_table.R:16:3'): Limit and offsets work for the get_table() call ── <http_504/http_500/http_error/error/condition> Error in `parseURL(paste0("dbtables/table?table=", x, "&limit=", limit, "&offset=", offset))`: Gateway Timeout (HTTP 504). Failed to Could not connect to the Neotoma API. Check that the path is valid, and check the current status of the Neotoma API services at http://data.neotomadb.org. Backtrace: ▆ 1. ├─testthat::expect_false(...) at test-get_table.R:16:3 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─rlang::hash(get_table("agetypes", limit = 1)) 5. └─neotoma2::get_table("agetypes", limit = 1) 6. └─neotoma2::parseURL(...) 7. └─httr::stop_for_status(response, task = "Could not connect to the Neotoma API.\n Check that the path is valid, and check the current\n status of the Neotoma API services at\n http://data.neotomadb.org") ── Error ('test_generaltests.R:65:3'): A faunmap dataset with some contacts actually works ── <http_504/http_500/http_error/error/condition> Error in `parseURL(base_url, ...)`: Gateway Timeout (HTTP 504). Failed to Could not connect to the Neotoma API. Check that the path is valid, and check the current status of the Neotoma API services at http://data.neotomadb.org. Backtrace: ▆ 1. ├─neotoma2::get_downloads(7032) at test_generaltests.R:65:3 2. └─neotoma2:::get_downloads.numeric(7032) 3. └─neotoma2::parseURL(base_url, ...) 4. └─httr::stop_for_status(response, task = "Could not connect to the Neotoma API.\n Check that the path is valid, and check the current\n status of the Neotoma API services at\n http://data.neotomadb.org") ── Error ('test_generaltests.R:115:3'): Testing the publications calls. ──────── <http_504/http_500/http_error/error/condition> Error in `parseURL(baseURL, ...)`: Gateway Timeout (HTTP 504). Failed to Could not connect to the Neotoma API. Check that the path is valid, and check the current status of the Neotoma API services at http://data.neotomadb.org. Backtrace: ▆ 1. ├─neotoma2::get_publications() at test_generaltests.R:115:3 2. ├─neotoma2:::get_publications.default() 3. │ ├─... %>% pluck("result") 4. │ └─neotoma2::parseURL(baseURL, ...) 5. │ └─httr::stop_for_status(response, task = "Could not connect to the Neotoma API.\n Check that the path is valid, and check the current\n status of the Neotoma API services at\n http://data.neotomadb.org") 6. ├─purrr::pluck(., "result") 7. │ └─purrr:::pluck_raw(.x, list2(...), .default = .default) 8. ├─purrr::pluck(., "data") 9. │ └─purrr:::pluck_raw(.x, list2(...), .default = .default) 10. └─neotoma2:::cleanNULL(.) 11. └─base::rapply(...) [ FAIL 7 | WARN 0 | SKIP 48 | PASS 11 ] Error: Test failures Execution halted Flavor: r-patched-linux-x86_64

Version: 1.0.6
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘neotoma2-package.Rmd’ using rmarkdown Quitting from neotoma2-package.Rmd:101-109 [getSiteBySiteID] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `neotoma2::parseURL()`: ! Gateway Timeout (HTTP 504). Failed to Could not connect to the Neotoma API. Check that the path is valid, and check the current status of the Neotoma API services at http://data.neotomadb.org. --- Backtrace: ▆ 1. ├─neotoma2::get_sites(24) 2. └─neotoma2:::get_sites.numeric(24) 3. └─neotoma2::parseURL(base_url, ...) 4. └─httr::stop_for_status(response, task = "Could not connect to the Neotoma API.\n Check that the path is valid, and check the current\n status of the Neotoma API services at\n http://data.neotomadb.org") ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'neotoma2-package.Rmd' failed with diagnostics: Gateway Timeout (HTTP 504). Failed to Could not connect to the Neotoma API. Check that the path is valid, and check the current status of the Neotoma API services at http://data.neotomadb.org. --- failed re-building ‘neotoma2-package.Rmd’ SUMMARY: processing the following file failed: ‘neotoma2-package.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-patched-linux-x86_64