Check results for 'neotoma2'

using R version 4.4.2 (2024-10-31)
using platform: x86_64-pc-linux-gnu
R was compiled by gcc-14 (Debian 14.2.0-16) 14.2.0 GNU Fortran (Debian 14.2.0-16) 14.2.0
running under: Debian GNU/Linux trixie/sid
using session charset: UTF-8
checking for file ‘neotoma2/DESCRIPTION’ ... OK
this is package ‘neotoma2’ version ‘1.0.5’
package encoding: UTF-8
checking package namespace information ... OK
checking package dependencies ... OK
checking if this is a source package ... OK
checking if there is a namespace ... OK
checking for executable files ... OK
checking for hidden files and directories ... OK
checking for portable file names ... OK
checking for sufficient/correct file permissions ... OK
checking serialization versions ... OK
checking whether package ‘neotoma2’ can be installed ... OK See the install log for details.
checking package directory ... OK
checking for future file timestamps ... OK
checking ‘build’ directory ... OK
checking DESCRIPTION meta-information ... OK
checking top-level files ... OK
checking for left-over files ... OK
checking index information ... OK
checking package subdirectories ... OK
checking code files for non-ASCII characters ... OK
checking R files for syntax errors ... OK
checking whether the package can be loaded ... [2s/3s] OK
checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
checking whether the package can be unloaded cleanly ... [2s/2s] OK
checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
checking whether the namespace can be unloaded cleanly ... [2s/3s] OK
checking loading without being on the library search path ... [2s/3s] OK
checking use of S3 registration ... OK
checking dependencies in R code ... OK
checking S3 generic/method consistency ... OK
checking replacement functions ... OK
checking foreign function calls ... OK
checking R code for possible problems ... [19s/26s] OK
checking Rd files ... [1s/1s] OK
checking Rd metadata ... OK
checking Rd line widths ... OK
checking Rd cross-references ... OK
checking for missing documentation entries ... OK
checking for code/documentation mismatches ... OK
checking Rd \usage sections ... OK
checking Rd contents ... OK
checking for unstated dependencies in examples ... OK
checking installed files from ‘inst/doc’ ... OK
checking files in ‘vignettes’ ... OK
checking examples ... [3s/64s] 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
checking for unstated dependencies in ‘tests’ ... OK
checking tests ... [5s/549s] ERROR Running ‘testthat.R’ [5s/548s] 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
checking for unstated dependencies in vignettes ... OK
checking package vignettes ... OK
checking re-building of vignette outputs ... [3s/65s] 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
checking PDF version of manual ... [9s/13s] OK
checking HTML version of manual ... [5s/9s] OK
checking for non-standard things in the check directory ... OK
DONE

Status: 3 ERRORs