* using log directory ‘/data/gannet/ripley/R/packages/tests-noLD/neotoma2.Rcheck’
* using R Under development (unstable) (2025-05-15 r88204)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-15 (GCC) 15.1.0
    GNU Fortran (GCC) 15.1.0
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* 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 ... INFO
Package suggested but not available for checking: ‘Bchron’
* 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 whether package ‘neotoma2’ can be installed ... [28s/85s] OK
* checking package directory ... 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 ... [4s/12s] OK
* checking whether the package can be loaded with stated dependencies ... [4s/13s] OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... [4s/16s] 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 ... [31s/117s] OK
* checking Rd files ... 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 ... [5s/75s] 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 (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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [9s/329s]
 [9s/330s] ERROR
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 3 | WARN 0 | SKIP 48 | PASS 15 ]
  
  ══ 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_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, offset = 1))
   5. └─neotoma2::get_table("agetypes", limit = 1, offset = 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:116:3'): 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(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 3 | WARN 0 | SKIP 48 | PASS 15 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [19s/110s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘neotoma2-package.Rmd’ using rmarkdown

Quitting from neotoma2-package.Rmd:76-84 [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

* checking PDF version of manual ... [16s/45s] OK
* checking HTML version of manual ... [10s/29s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 3 ERRORs
See
  ‘/data/gannet/ripley/R/packages/tests-noLD/neotoma2.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 18:09.83, 194.77 + 18.94