• using R Under development (unstable) (2025-11-30 r89082)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 21.1.6 (2)     Debian flang version 21.1.6 (2)
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘neotoma2/DESCRIPTION’ ... OK
• this is package ‘neotoma2’ version ‘1.0.9’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [2s/2s] OK
• 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/3s] OK
• checking whether the package can be unloaded cleanly ... [2s/3s] OK
• checking whether the namespace can be loaded with stated dependencies ... [2s/3s] 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 ... [20s/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 ... [4s/12s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [27s/190s] 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
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [4s/211s] 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
• checking PDF version of manual ... [9s/11s] OK
• checking HTML version of manual ... [6s/10s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 2 ERRORs