Running ‘testthat.R’ [5s/13s]
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")
  Saving _problems/test_c-14.R
  Saving _problems/test_doi-6.R
  Saving _problems/test_filter-30.R
  Saving _problems/test_filter-61.R
  Saving _problems/test_get_contacts-6.R
  Saving _problems/test_get_contacts-20.R
  Saving _problems/test_get_downloads-54.R
  Saving _problems/test_get_publications-6.R
  Saving _problems/test_get_publications-16.R
  Saving _problems/test_get_publications-22.R
  Saving _problems/test_get_table-7.R
  Saving _problems/test_get_table-12.R
  Saving _problems/test_get_table-14.R
  Saving _problems/test_get_table-22.R
  Saving _problems/test_get_table-29.R
  Saving _problems/test_get_taxa-6.R
  Saving _problems/test_get_taxon-5.R
  [ FAIL 17 | WARN 2 | SKIP 90 | PASS 7 ]
  
  ══ Skipped tests (90) ══════════════════════════════════════════════════════════
  • On CRAN (85): 'test_add_chronology.R:6:3', 'test_c.R:6:3',
    'test_chroncontrols.R:7:3', 'test_chronologies.R:6:3',
    'test_cite_data.R:8:3', 'test_cite_data.R:15:3', 'test_clean.R:9:3',
    'test_collunits.R:5:3', 'test_coordinates.R:6:3', 'test_datasets.R:5:3',
    'test_filter.R:7:3', 'test_filter.R:35:3', 'test_filter.R:51:13',
    'test_filter.R:72:3', 'test_filter.R:84:3', 'test_filter.R:95:14',
    'test_filter.R:105:3', 'test_get_datasets.R:7:3', 'test_get_datasets.R:16:3',
    'test_get_datasets.R:29:3', 'test_get_datasets.R:57:3',
    'test_get_documentation.R:6:3', 'test_get_documentation.R:11:3',
    'test_get_downloads.R:7:3', 'test_get_downloads.R:19:3',
    'test_get_downloads.R:38:3', 'test_get_manual.R:6:3',
    'test_get_manual.R:11:3', 'test_get_sites.R:6:3', 'test_get_sites.R:15:3',
    'test_get_sites.R:28:3', 'test_get_sites.R:51:3', 'test_get_sites.R:76:13',
    'test_get_stats.R:6:3', 'test_get_stats.R:14:3', 'test_get_stats.R:23:3',
    'test_getids.R:7:3', 'test_getids.R:14:3', 'test_getids.R:21:3',
    'test_length.R:7:3', 'test_length.R:14:3', 'test_length.R:27:3',
    'test_plot.R:6:3', 'test_plot.R:12:3', 'test_plotLeaflet.r:7:3',
    'test_plotLeaflet.r:14:3', 'test_samples.R:6:3', 'test_samples.R:21:3',
    'test_samples.R:28:3', 'test_samples.R:52:22', 'test_samples.R:52:22',
    'test_samples.R:52:22', 'test_samples.R:52:22', 'test_samples.R:52:22',
    'test_samples.R:52:22', 'test_samples.R:52:22', 'test_samples.R:52:22',
    'test_samples.R:52:22', 'test_samples.R:52:22', 'test_samples.R:52:22',
    'test_samples.R:52:22', 'test_samples.R:52:22', 'test_set_chronology.R:6:3',
    'test_set_collunit.R:6:3', 'test_set_collunit.R:24:3',
    'test_set_contact.R:6:3', 'test_set_dataset.R:6:3',
    'test_set_dataset.R:22:3', 'test_set_default.R:5:3',
    'test_set_publication.R:6:3', 'test_set_publication.R:17:3',
    'test_set_sample.R:6:3', 'test_set_sample.R:19:3', 'test_set_site.R:6:3',
    'test_set_site.R:21:3', 'test_sites.R:8:3', 'test_sites.R:19:3',
    'test_sites.R:34:3', 'test_sites.R:45:3', 'test_sites.R:86:3',
    'test_summary.R:5:3', 'test_taxa.R:6:3', 'test_toWide.R:7:3',
    'test_toWide.R:24:3', 'test_toWide.R:40:3'
  • Skipping all tests in this file (5): 'test_examples.R:1:1',
    'test_get_speleothems.R:1:1', 'test_set_speleothem.R:1:1',
    'test_specimens.R:1:1', 'test_speleothems.R:1:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_c.R:14:3'): c() removes duplicates properly. ───────────────────
  Error in `value[[3L]](cond)`: API call failed: Not Found (HTTP 404). 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) at test_c.R:14:3
   2. └─neotoma2:::get_sites.numeric(24)
   3.   └─base::tryCatch(...)
   4.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   5.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   6.         └─value[[3L]](cond)
  ── Error ('test_doi.R:6:3'):  ──────────────────────────────────────────────────
  Error in `value[[3L]](cond)`: API call failed: Not Found (HTTP 404). 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_datasets(c(24, 100, 101)) at test_doi.R:6:3
   2. └─neotoma2:::get_datasets.numeric(c(24, 100, 101))
   3.   └─base::tryCatch(...)
   4.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   5.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   6.         └─value[[3L]](cond)
  ── Error ('test_filter.R:30:3'): filter datasettype + loc ──────────────────────
  Error in `brazil_summary$dataset_types`: $ operator is invalid for atomic vectors
  Backtrace:
      ▆
   1. └─base::unique(brazil_summary$dataset_types) at test_filter.R:30:3
  ── Error ('test_filter.R:61:3'): filter by 2 datasettypes ──────────────────────
  Error in `value[[3L]](cond)`: API call failed: Not Found (HTTP 404). 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() at test_filter.R:61:3
   2. └─neotoma2:::get_sites.default()
   3.   └─base::tryCatch(...)
   4.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   5.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   6.         └─value[[3L]](cond)
  ── Error ('test_get_contacts.R:6:3'): `get_contacts()` numeric ─────────────────
  Error in `value[[3L]](cond)`: API call failed: Not Found (HTTP 404). 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:6:3
   2. └─neotoma2:::get_contacts.numeric(x = 1)
   3.   └─base::tryCatch(...)
   4.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   5.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   6.         └─value[[3L]](cond)
  ── Error ('test_get_contacts.R:20:3'): `get_contacts()` query ──────────────────
  Error in `value[[3L]](cond)`: API call failed: Not Found (HTTP 404). 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(familyname = "Goring") at test_get_contacts.R:20:3
   2. └─neotoma2:::get_contacts.default(familyname = "Goring")
   3.   └─base::tryCatch(...)
   4.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   5.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   6.         └─value[[3L]](cond)
  ── Error ('test_get_downloads.R:54:3'): Faunmap dataset ────────────────────────
  Error in `value[[3L]](cond)`: API call failed: Not Found (HTTP 404). 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_get_downloads.R:54:3
   2. └─neotoma2:::get_downloads.numeric(7032)
   3.   └─base::tryCatch(...)
   4.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   5.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   6.         └─value[[3L]](cond)
  ── Error ('test_get_publications.R:6:3'): `get_publications` numeric ───────────
  Error in `value[[3L]](cond)`: API call failed: Not Found (HTTP 404). 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_get_publications.R:6:3
   2. └─neotoma2:::get_publications.default()
   3.   └─base::tryCatch(...)
   4.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   5.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   6.         └─value[[3L]](cond)
  ── Error ('test_get_publications.R:16:3'): `get_publications` default ──────────
  Error in `value[[3L]](cond)`: API call failed: Not Found (HTTP 404). 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_get_publications.R:16:3
   2. └─neotoma2:::get_publications.default(search = "pollen")
   3.   └─base::tryCatch(...)
   4.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   5.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   6.         └─value[[3L]](cond)
  ── Error ('test_get_publications.R:22:3'): `get_publications` publications ─────
  Error in `value[[3L]](cond)`: API call failed: Not Found (HTTP 404). 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(c(1, 2, 3, 4)) at test_get_publications.R:22:3
   2. └─neotoma2:::get_publications.numeric(c(1, 2, 3, 4))
   3.   └─base::tryCatch(...)
   4.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   5.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   6.         └─value[[3L]](cond)
  ── Failure ('test_get_table.R:7:3'): Call a single database table: ─────────────
  Expected `tb` to inherit from "character".
  Actual inheritance: "NULL"
  ── Failure ('test_get_table.R:12:3'): Apply limits for get_table() ─────────────
  Expected `nrow(tb)` to equal 1.
  Differences:
  target is NULL, current is numeric
  ── Failure ('test_get_table.R:14:3'): Apply limits for get_table() ─────────────
  Expected `nrow(tb)` to equal 3.
  Differences:
  target is NULL, current is numeric
  ── Failure ('test_get_table.R:21:13'): Limit and offsets work as expected.
            Offsetting by one returns a different result. ──
  Expected `rlang::hash(tb1) == rlang::hash(tb2)` to be FALSE.
  Differences:
  `actual`:   TRUE 
  `expected`: FALSE
  
  ── Failure ('test_get_table.R:29:13'): Correct table ───────────────────────────
  Expected `colnames(tb1)` to be identical to `cols`.
  Differences:
  target is NULL, current is character
  ── Error ('test_get_taxa.R:6:3'): get_taxa() sites object ──────────────────────
  Error in `value[[3L]](cond)`: API call failed: Not Found (HTTP 404). 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_taxa(1) at test_get_taxa.R:6:3
   2. └─neotoma2:::get_taxa.numeric(1)
   3.   ├─neotoma2::get_taxon(x, ...)
   4.   └─neotoma2:::get_taxon.numeric(x, ...)
   5.     └─base::tryCatch(...)
   6.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   7.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   8.           └─value[[3L]](cond)
  ── Error ('test_get_taxon.R:5:3'): `get_taxon` yields specific taxon information ──
  Error in `value[[3L]](cond)`: API call failed: Not Found (HTTP 404). 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_taxon(1) at test_get_taxon.R:5:3
   2. └─neotoma2:::get_taxon.numeric(1)
   3.   └─base::tryCatch(...)
   4.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   5.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   6.         └─value[[3L]](cond)
  
  [ FAIL 17 | WARN 2 | SKIP 90 | PASS 7 ]
  Error:
  ! Test failures.
  Execution halted