CRAN Package Check Results for Package neotoma2

Last updated on 2024-05-18 18:57:24 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.3 21.09 167.36 188.45 OK
r-devel-linux-x86_64-debian-gcc 1.0.3 15.50 120.10 135.60 OK
r-devel-linux-x86_64-fedora-clang 1.0.3 229.67 OK
r-devel-linux-x86_64-fedora-gcc 1.0.3 290.94 OK
r-devel-windows-x86_64 1.0.3 18.00 211.00 229.00 OK
r-patched-linux-x86_64 1.0.3 14.61 156.31 170.92 OK
r-release-linux-x86_64 1.0.3 12.07 122.80 134.87 ERROR
r-release-macos-arm64 1.0.3 118.00 OK
r-release-macos-x86_64 1.0.3 256.00 OK
r-release-windows-x86_64 1.0.3 21.00 216.00 237.00 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 24.00 245.00 269.00 ERROR

Check Details

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 (function (cond) : error in evaluating the argument 'object' in selecting a method for function 'datasets': 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: cite_data ... get_datasets.numeric -> <Anonymous> -> stop_for_status Execution halted Flavor: r-release-linux-x86_64

Version: 1.0.3
Check: tests
Result: ERROR Running ‘testthat.R’ [7s/372s] 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 4 | WARN 0 | SKIP 49 | PASS 14 ] ══ 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: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: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: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 4 | WARN 0 | SKIP 49 | PASS 14 ] Error: Test failures Execution halted Flavor: r-release-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 at 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-release-linux-x86_64

Version: 1.0.3
Check: examples
Result: ERROR Running examples in 'neotoma2-Ex.R' failed The error most likely occurred in: > ### Name: get_datasets.default > ### Title: Get Dataset Default > ### Aliases: get_datasets.default > > ### ** Examples > > { + # To find all datasets with a min altitude of 12 and a max altitude of 25: + sites_12to25 <- get_datasets(altmin=12, altmax=25, limit=2) + # To find all datasets in Brazil + brazil <- '{"type": "Polygon", + "coordinates": [[ + [-73.125, -9.102096738726443], + [-56.953125,-33.137551192346145], + [-36.5625,-7.710991655433217], + [-68.203125,13.923403897723347], + [-73.125,-9.102096738726443]]]}' + brazil_datasets <- get_datasets(loc = brazil[1], limit=2) + } Error in parseURL(base_url) : Internal Server Error (HTTP 500). 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 ... %>% -> cleanNULL -> rapply -> parseURL -> stop_for_status Execution halted Flavor: r-oldrel-windows-x86_64

Version: 1.0.3
Check: tests
Result: ERROR Running 'testthat.R' [42s] 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 1 | WARN 0 | SKIP 49 | PASS 17 ] ══ 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_generaltests.R:116:3'): Testing the publications calls. ──────── <http_500/http_error/error/condition> Error in `parseURL(baseURL, ...)`: Internal Server Error (HTTP 500). 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(search = "pollen") at test_generaltests.R:116:3 2. ├─neotoma2:::get_publications.default(search = "pollen") 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 1 | WARN 0 | SKIP 49 | PASS 17 ] Error: Test failures Execution halted Flavor: r-oldrel-windows-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 at lines 212-215 [getdatasetsbytype] (neotoma2-package.Rmd) Error: processing vignette 'neotoma2-package.Rmd' failed with diagnostics: Internal Server Error (HTTP 500). 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-oldrel-windows-x86_64