Last updated on 2025-12-04 07:51:36 CET.
| Package | ERROR | OK |
|---|---|---|
| neotoma2 | 9 | 4 |
Current CRAN status: ERROR: 9, OK: 4
Version: 1.0.9
Check: tests
Result: ERROR
Running ‘testthat.R’ [27s/190s]
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_filter-30.R
[ FAIL 1 | WARN 5 | SKIP 94 | PASS 48 ]
══ Skipped tests (94) ══════════════════════════════════════════════════════════
• On CRAN (89): '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_datasets.R:84:3', 'test_get_documentation.R:6:3',
'test_get_documentation.R:11:3', 'test_get_downloads.R:7:3',
'test_get_downloads.R:19:13', 'test_get_downloads.R:38:3',
'test_get_downloads.R:59:3', 'test_get_downloads.R:77:3',
'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_samples.R:80:3', '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_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
[ FAIL 1 | WARN 5 | SKIP 94 | PASS 48 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.9
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:126-129 [sitewithwildcardname]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `value[[3L]]()`:
! API call failed: Bad Gateway (HTTP 502). 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(sitename = "Alex%")
2. └─neotoma2:::get_sites.default(sitename = "Alex%")
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: processing vignette 'neotoma2-package.Rmd' failed with diagnostics:
API call failed: Bad Gateway (HTTP 502). 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: 1.0.9
Check: tests
Result: ERROR
Running ‘testthat.R’ [17s/206s]
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_filter-30.R
[ FAIL 1 | WARN 5 | SKIP 94 | PASS 48 ]
══ Skipped tests (94) ══════════════════════════════════════════════════════════
• On CRAN (89): '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_datasets.R:84:3', 'test_get_documentation.R:6:3',
'test_get_documentation.R:11:3', 'test_get_downloads.R:7:3',
'test_get_downloads.R:19:13', 'test_get_downloads.R:38:3',
'test_get_downloads.R:59:3', 'test_get_downloads.R:77:3',
'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_samples.R:80:3', '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_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
[ FAIL 1 | WARN 5 | SKIP 94 | PASS 48 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0.9
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:126-129 [sitewithwildcardname]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `value[[3L]]()`:
! API call failed: 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(sitename = "Alex%")
2. └─neotoma2:::get_sites.default(sitename = "Alex%")
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: processing vignette 'neotoma2-package.Rmd' failed with diagnostics:
API call failed: 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-devel-linux-x86_64-debian-gcc
Version: 1.0.9
Check: tests
Result: ERROR
Running ‘testthat.R’ [46s/333s]
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_filter-30.R
[ FAIL 1 | WARN 5 | SKIP 94 | PASS 48 ]
══ Skipped tests (94) ══════════════════════════════════════════════════════════
• On CRAN (89): '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_datasets.R:84:3', 'test_get_documentation.R:6:3',
'test_get_documentation.R:11:3', 'test_get_downloads.R:7:3',
'test_get_downloads.R:19:13', 'test_get_downloads.R:38:3',
'test_get_downloads.R:59:3', 'test_get_downloads.R:77:3',
'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_samples.R:80:3', '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_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
[ FAIL 1 | WARN 5 | SKIP 94 | PASS 48 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.0.9
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:126-129 [sitewithwildcardname]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `value[[3L]]()`:
! API call failed: 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(sitename = "Alex%")
2. └─neotoma2:::get_sites.default(sitename = "Alex%")
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: processing vignette 'neotoma2-package.Rmd' failed with diagnostics:
API call failed: 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
Flavors: r-devel-linux-x86_64-fedora-clang, r-release-windows-x86_64
Version: 1.0.9
Check: tests
Result: ERROR
Running ‘testthat.R’ [44s/264s]
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_filter-30.R
[ FAIL 1 | WARN 5 | SKIP 94 | PASS 48 ]
══ Skipped tests (94) ══════════════════════════════════════════════════════════
• On CRAN (89): '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_datasets.R:84:3', 'test_get_documentation.R:6:3',
'test_get_documentation.R:11:3', 'test_get_downloads.R:7:3',
'test_get_downloads.R:19:13', 'test_get_downloads.R:38:3',
'test_get_downloads.R:59:3', 'test_get_downloads.R:77:3',
'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_samples.R:80:3', '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_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
[ FAIL 1 | WARN 5 | SKIP 94 | PASS 48 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.0.9
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:119-122 [getsitename]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `value[[3L]]()`:
! API call failed: 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(sitename = "Alexander Lake")
2. └─neotoma2:::get_sites.default(sitename = "Alexander Lake")
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: processing vignette 'neotoma2-package.Rmd' failed with diagnostics:
API call failed: 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
Flavors: r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-oldrel-windows-x86_64
Version: 1.0.9
Check: tests
Result: ERROR
Running 'testthat.R' [180s]
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_filter-30.R
[ FAIL 1 | WARN 5 | SKIP 94 | PASS 48 ]
══ Skipped tests (94) ══════════════════════════════════════════════════════════
• On CRAN (89): '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_datasets.R:84:3', 'test_get_documentation.R:6:3',
'test_get_documentation.R:11:3', 'test_get_downloads.R:7:3',
'test_get_downloads.R:19:13', 'test_get_downloads.R:38:3',
'test_get_downloads.R:59:3', 'test_get_downloads.R:77:3',
'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_samples.R:80:3', '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_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
[ FAIL 1 | WARN 5 | SKIP 94 | PASS 48 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-windows-x86_64
Version: 1.0.9
Check: tests
Result: ERROR
Running ‘testthat.R’ [26s/226s]
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_filter-30.R
[ FAIL 1 | WARN 5 | SKIP 94 | PASS 48 ]
══ Skipped tests (94) ══════════════════════════════════════════════════════════
• On CRAN (89): '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_datasets.R:84:3', 'test_get_documentation.R:6:3',
'test_get_documentation.R:11:3', 'test_get_downloads.R:7:3',
'test_get_downloads.R:19:13', 'test_get_downloads.R:38:3',
'test_get_downloads.R:59:3', 'test_get_downloads.R:77:3',
'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_samples.R:80:3', '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_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
[ FAIL 1 | WARN 5 | SKIP 94 | PASS 48 ]
Error:
! Test failures.
Execution halted
Flavor: r-patched-linux-x86_64
Version: 1.0.9
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:119-122 [getsitename]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `value[[3L]]()`:
! API call failed: Bad Gateway (HTTP 502). 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(sitename = "Alexander Lake")
2. └─neotoma2:::get_sites.default(sitename = "Alexander Lake")
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: processing vignette 'neotoma2-package.Rmd' failed with diagnostics:
API call failed: Bad Gateway (HTTP 502). 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-patched-linux-x86_64
Version: 1.0.9
Check: tests
Result: ERROR
Running ‘testthat.R’ [26s/182s]
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_filter-30.R
[ FAIL 1 | WARN 5 | SKIP 94 | PASS 48 ]
══ Skipped tests (94) ══════════════════════════════════════════════════════════
• On CRAN (89): '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_datasets.R:84:3', 'test_get_documentation.R:6:3',
'test_get_documentation.R:11:3', 'test_get_downloads.R:7:3',
'test_get_downloads.R:19:13', 'test_get_downloads.R:38:3',
'test_get_downloads.R:59:3', 'test_get_downloads.R:77:3',
'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_samples.R:80:3', '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_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
[ FAIL 1 | WARN 5 | SKIP 94 | PASS 48 ]
Error:
! Test failures.
Execution halted
Flavor: r-release-linux-x86_64
Version: 1.0.9
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:119-122 [getsitename]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `value[[3L]]()`:
! API call failed: 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(sitename = "Alexander Lake")
2. └─neotoma2:::get_sites.default(sitename = "Alexander Lake")
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: processing vignette 'neotoma2-package.Rmd' failed with diagnostics:
API call failed: 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: 1.0.9
Check: tests
Result: ERROR
Running 'testthat.R' [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")
Saving _problems/test_filter-30.R
[ FAIL 1 | WARN 5 | SKIP 94 | PASS 48 ]
══ Skipped tests (94) ══════════════════════════════════════════════════════════
• On CRAN (89): '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_datasets.R:84:3', 'test_get_documentation.R:6:3',
'test_get_documentation.R:11:3', 'test_get_downloads.R:7:3',
'test_get_downloads.R:19:13', 'test_get_downloads.R:38:3',
'test_get_downloads.R:59:3', 'test_get_downloads.R:77:3',
'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_samples.R:80:3', '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_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
[ FAIL 1 | WARN 5 | SKIP 94 | PASS 48 ]
Error:
! Test failures.
Execution halted
Flavor: r-release-windows-x86_64
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