CRAN Package Check Results for Package neotoma2

Last updated on 2025-07-22 20:51:09 CEST.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-clang	1.0.7	14.58	112.92	127.50	ERROR
r-devel-linux-x86_64-debian-gcc	1.0.7	9.97	102.76	112.73	OK
r-devel-linux-x86_64-fedora-clang	1.0.7			259.12	OK
r-devel-linux-x86_64-fedora-gcc	1.0.7			263.95	OK
r-devel-windows-x86_64	1.0.7	17.00	243.00	260.00	ERROR
r-patched-linux-x86_64	1.0.7	15.28	138.01	153.29	OK
r-release-linux-x86_64	1.0.7	13.91	139.09	153.00	OK
r-release-macos-arm64	1.0.7			104.00	OK
r-release-macos-x86_64	1.0.7			183.00	OK
r-release-windows-x86_64	1.0.7	19.00	219.00	238.00	OK
r-oldrel-macos-arm64	1.0.7			104.00	OK
r-oldrel-macos-x86_64	1.0.7			158.00	OK
r-oldrel-windows-x86_64	1.0.7	26.00	286.00	312.00	OK

Check Details

Version: 1.0.7
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: get_publications.numeric > ### Title: Get publications using their unique identifier. > ### Aliases: get_publications.numeric > > ### ** Examples > > { + # We want the paper identified in Neotoma as 666: + get_publications(666) + } Error in get_response(baseurl, x, query) : 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_publications ... cleanNULL -> parseURL -> get_response -> <Anonymous> Execution halted Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.0.7
Check: tests
Result: ERROR Running ‘testthat.R’ [6s/210s] 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 47 | PASS 10 ] ══ Skipped tests (47) ══════════════════════════════════════════════════════════ • Not ready yet (1): 'test_specimens.R:25:3' • On CRAN (46): 'test-toJSON.R:2:3', 'test_c.R:10:3', 'test_check_contacts.R:10:3', 'test_chroncontrols.R:4:3', 'test_chroncontrols.R:21:3', 'test_chroncontrols.R:35:3', '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:30:3', '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:96:3', '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:90:3', 'test_specimens.R:3:3', 'test_specimens.R:10:3', '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_500/http_error/error/condition> Error in `get_response(baseurl, x, query)`: 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_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. │ └─neotoma2 (local) get_response(baseurl, x, query) 6. │ └─httr::stop_for_status(response, task = "Could not connect to the Neotoma API.\n Check that the path is valid, and \n check the current status of the\n Neotoma API services at \n http://data.neotomadb.org") 7. └─neotoma2:::cleanNULL(.) ── Error ('test-get_table.R:11:3'): We can apply the limits for get_table() ──── <http_500/http_error/error/condition> Error in `get_response(baseurl, x, query)`: 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. ├─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. └─neotoma2 (local) get_response(baseurl, x, query) 8. └─httr::stop_for_status(response, task = "Could not connect to the Neotoma API.\n Check that the path is valid, and \n check the current status of the\n 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_500/http_error/error/condition> Error in `get_response(baseurl, x, query)`: 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. ├─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, offset = 1)) 5. └─neotoma2::get_table("agetypes", limit = 1, offset = 1) 6. └─neotoma2:::parseURL(...) 7. └─neotoma2 (local) get_response(baseurl, x, query) 8. └─httr::stop_for_status(response, task = "Could not connect to the Neotoma API.\n Check that the path is valid, and \n check the current status of the\n Neotoma API services at \n http://data.neotomadb.org") ── Error ('test_generaltests.R:112:3'): Testing the publications calls. ──────── <http_500/http_error/error/condition> Error in `get_response(baseurl, x, query)`: 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() at test_generaltests.R:112:3 2. └─neotoma2:::get_publications.default() 3. └─neotoma2:::parseURL(baseURL, ...) 4. └─neotoma2 (local) get_response(baseurl, x, query) 5. └─httr::stop_for_status(response, task = "Could not connect to the Neotoma API.\n Check that the path is valid, and \n check the current status of the\n Neotoma API services at \n http://data.neotomadb.org") [ FAIL 4 | WARN 0 | SKIP 47 | PASS 10 ] Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.0.7
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 `get_response()`: ! 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_sites(c(24, 47)) 2. └─neotoma2:::get_sites.numeric(c(24, 47)) 3. └─neotoma2:::parseURL(base_url, ...) 4. └─neotoma2 (local) get_response(baseurl, x, query) 5. └─httr::stop_for_status(response, task = "Could not connect to the Neotoma API.\n Check that the path is valid, and \n check the current status of the\n Neotoma API services at \n http://data.neotomadb.org") ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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-devel-linux-x86_64-debian-clang

Version: 1.0.7
Check: examples
Result: ERROR Running examples in 'neotoma2-Ex.R' failed The error most likely occurred in: > ### Name: get_publications.numeric > ### Title: Get publications using their unique identifier. > ### Aliases: get_publications.numeric > > ### ** Examples > > { + # We want the paper identified in Neotoma as 666: + get_publications(666) + } Error in get_response(baseurl, x, query) : 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_publications ... cleanNULL -> parseURL -> get_response -> <Anonymous> Execution halted Flavor: r-devel-windows-x86_64

Version: 1.0.7
Check: tests
Result: ERROR Running 'testthat.R' [208s] 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 47 | PASS 10 ] ══ Skipped tests (47) ══════════════════════════════════════════════════════════ • Not ready yet (1): 'test_specimens.R:25:3' • On CRAN (46): 'test-toJSON.R:2:3', 'test_c.R:10:3', 'test_check_contacts.R:10:3', 'test_chroncontrols.R:4:3', 'test_chroncontrols.R:21:3', 'test_chroncontrols.R:35:3', '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:30:3', '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:96:3', '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:90:3', 'test_specimens.R:3:3', 'test_specimens.R:10:3', '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_500/http_error/error/condition> Error in `get_response(baseurl, x, query)`: 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_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. │ └─neotoma2 (local) get_response(baseurl, x, query) 6. │ └─httr::stop_for_status(response, task = "Could not connect to the Neotoma API.\n Check that the path is valid, and \n check the current status of the\n Neotoma API services at \n http://data.neotomadb.org") 7. └─neotoma2:::cleanNULL(.) ── Error ('test-get_table.R:11:3'): We can apply the limits for get_table() ──── <http_500/http_error/error/condition> Error in `get_response(baseurl, x, query)`: 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. ├─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. └─neotoma2 (local) get_response(baseurl, x, query) 8. └─httr::stop_for_status(response, task = "Could not connect to the Neotoma API.\n Check that the path is valid, and \n check the current status of the\n 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_500/http_error/error/condition> Error in `get_response(baseurl, x, query)`: 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. ├─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, offset = 1)) 5. └─neotoma2::get_table("agetypes", limit = 1, offset = 1) 6. └─neotoma2:::parseURL(...) 7. └─neotoma2 (local) get_response(baseurl, x, query) 8. └─httr::stop_for_status(response, task = "Could not connect to the Neotoma API.\n Check that the path is valid, and \n check the current status of the\n Neotoma API services at \n http://data.neotomadb.org") ── Error ('test_generaltests.R:112:3'): Testing the publications calls. ──────── <http_500/http_error/error/condition> Error in `get_response(baseurl, x, query)`: 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() at test_generaltests.R:112:3 2. └─neotoma2:::get_publications.default() 3. └─neotoma2:::parseURL(baseURL, ...) 4. └─neotoma2 (local) get_response(baseurl, x, query) 5. └─httr::stop_for_status(response, task = "Could not connect to the Neotoma API.\n Check that the path is valid, and \n check the current status of the\n Neotoma API services at \n http://data.neotomadb.org") [ FAIL 4 | WARN 0 | SKIP 47 | PASS 10 ] Error: Test failures Execution halted Flavor: r-devel-windows-x86_64

Version: 1.0.7
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 `get_response()`: ! 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_sites(c(24, 47)) 2. └─neotoma2:::get_sites.numeric(c(24, 47)) 3. └─neotoma2:::parseURL(base_url, ...) 4. └─neotoma2 (local) get_response(baseurl, x, query) 5. └─httr::stop_for_status(response, task = "Could not connect to the Neotoma API.\n Check that the path is valid, and \n check the current status of the\n Neotoma API services at \n http://data.neotomadb.org") ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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-devel-windows-x86_64