CRAN Package Check Results for Package neotoma2

Last updated on 2024-06-12 19:54:29 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.3 21.07 165.67 186.74 OK
r-devel-linux-x86_64-debian-gcc 1.0.3 0.81 1.89 2.70 ERROR
r-devel-linux-x86_64-fedora-clang 1.0.3 234.11 OK
r-devel-linux-x86_64-fedora-gcc 1.0.3 228.01 OK
r-devel-windows-x86_64 1.0.3 17.00 192.00 209.00 OK
r-patched-linux-x86_64 1.0.3 23.22 123.79 147.01 ERROR
r-release-linux-x86_64 1.0.3 12.34 156.76 169.10 OK
r-release-macos-arm64 1.0.3 118.00 OK
r-release-macos-x86_64 1.0.3 173.00 OK
r-release-windows-x86_64 1.0.3 19.00 213.00 232.00 OK
r-oldrel-macos-arm64 1.0.3 119.00 OK
r-oldrel-macos-x86_64 1.0.3 199.00 OK
r-oldrel-windows-x86_64 1.0.3 23.00 224.00 247.00 OK

Additional issues

ATLAS

Check Details

Version: 1.0.3
Check: package dependencies
Result: ERROR Packages required but not available: 'purrr', 'lubridate', 'dplyr', 'stringr', 'progress', 'tidyr' Packages suggested but not available for checking: 'testthat', 'pkgdown', 'Bchron', 'ggplot2' See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.0.3
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 neotoma2::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. Calls: get_datasets ... get_datasets.numeric -> <Anonymous> -> stop_for_status Execution halted Flavor: r-patched-linux-x86_64

Version: 1.0.3
Check: tests
Result: ERROR Running ‘testthat.R’ [7s/550s] 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 49 | PASS 11 ] ══ Skipped tests (49) ══════════════════════════════════════════════════════════ • On CRAN (49): '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:69:3', '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 49 | PASS 11 ] Error: Test failures Execution halted Flavor: r-patched-linux-x86_64

Version: 1.0.3
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘neotoma2-package.Rmd’ using rmarkdown Quitting from lines 77-84 [getSiteBySiteID] (neotoma2-package.Rmd) 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