* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/occCite.Rcheck’
* using R Under development (unstable) (2026-02-07 r89380)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
    GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
* running under: Fedora Linux 42 (Workstation Edition)
* using session charset: UTF-8
* current time: 2026-02-08 08:03:55 UTC
* using option ‘--no-stop-on-test-error’
* checking for file ‘occCite/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘occCite’ version ‘0.6.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Packages suggested but not available for checking: 'taxize', 'waffle'
* 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 ‘occCite’ can be installed ... [19s/28s] 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 ... OK
* checking whether the package can be loaded with stated dependencies ... 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 ... 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 ... [27s/48s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [13s/32s]
 [14s/33s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(occCite)
  > 
  > test_check("occCite")
  	
   OccCite query occurred on: 20 June, 2024
  	
   User query type: User-supplied list of taxa.
  	
   Sources for taxonomic rectification: GBIF Backbone Taxonomy
   	
  	
   Taxonomic cleaning results: 	
  
           Input Name                Best Match Taxonomic Databases w/ Matches
  1 Protea cynaroides Protea cynaroides (L.) L.         GBIF Backbone Taxonomy
  	
   Sources for occurrence data: gbif, bien
   	
                      Species Occurrences Sources
  1 Protea cynaroides (L.) L.        2334      17
  	
   GBIF dataset DOIs: 	
  
                      Species GBIF Access Date           GBIF DOI
  1 Protea cynaroides (L.) L.       2022-03-02 10.15468/dl.ztbx8c
  	
   OccCite query occurred on: 20 June, 2024
  	
   User query type: User-supplied list of taxa.
  	
   Sources for taxonomic rectification: GBIF Backbone Taxonomy
   	
  	
   Taxonomic cleaning results: 	
  
           Input Name                Best Match Taxonomic Databases w/ Matches
  1 Protea cynaroides Protea cynaroides (L.) L.         GBIF Backbone Taxonomy
  	
   Sources for occurrence data: gbif
   	
                      Species Occurrences Sources
  1 Protea cynaroides (L.) L.        2189      13
  	
   GBIF dataset DOIs: 	
  
                      Species GBIF Access Date           GBIF DOI
  1 Protea cynaroides (L.) L.       2022-03-02 10.15468/dl.ztbx8c
  	
   OccCite query occurred on: 20 June, 2024
  	
   User query type: User-supplied list of taxa.
  	
   Sources for taxonomic rectification: GBIF Backbone Taxonomy
   	
  	
   Taxonomic cleaning results: 	
  
           Input Name                Best Match Taxonomic Databases w/ Matches
  1 Protea cynaroides Protea cynaroides (L.) L.         GBIF Backbone Taxonomy
  	
   Sources for occurrence data: bien
   	
                      Species Occurrences Sources
  1 Protea cynaroides (L.) L.         145       4
  [1] "Checking ggplot version...4.0.2"
  Failed with error:  'there is no package called 'waffle''
  Failed with error:  'there is no package called 'waffle''
  Failed with error:  'there is no package called 'waffle''
  Failed with error:  'there is no package called 'waffle''
  Failed with error:  'there is no package called 'waffle''
  Failed with error:  'there is no package called 'waffle''
  Failed with error:  'there is no package called 'waffle''
  Saving _problems/test-taxonRectification-49.R
  Saving _problems/test-taxonRectification-50.R
  [ FAIL 2 | WARN 4 | SKIP 19 | PASS 158 ]
  
  ══ Skipped tests (19) ══════════════════════════════════════════════════════════
  • !requireNamespace("taxize", quietly = TRUE) is TRUE (1):
    'test-taxonRectification.R:13:3'
  • !requireNamespace("waffle") is TRUE (2): 'test-sumFig.R:43:3',
    'test-sumFig.R:52:3'
  • GBIF login available (1): 'test-GBIFLoginManager.R:16:3'
  • On CRAN (14): 'test-GBIFLoginManager.R:24:3', 'test-GBIFtableCleanup.R:6:3',
    'test-gbifRetriever.R:6:3', 'test-gbifRetriever.R:29:3',
    'test-getBIENpoints.R:6:3', 'test-getBIENpoints.R:28:3',
    'test-getGBIFpoints.R:6:3', 'test-getGBIFpoints.R:24:3',
    'test-occCitation.R:26:3', 'test-prevGBIFdownload.R:6:3',
    'test-prevGBIFdownload.R:34:3', 'test-tabGBIF.R:9:3', 'test-tabGBIF.R:24:3',
    'test-tabGBIF.R:48:3'
  • internet connection established (1): 'test-occCitation.R:115:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-taxonRectification.R:49:3'): taxonRectification performs as expected ──
  Expected `testResult$`Best Match`[1] == "Buteo buteo"` to be TRUE.
  Differences:
  `actual`:   FALSE
  `expected`: TRUE 
  
  ── Failure ('test-taxonRectification.R:50:3'): taxonRectification performs as expected ──
  Expected `testResult$`Searched Taxonomic Databases w/ Matches` == "NCBI"` to be TRUE.
  Differences:
  `actual`:   FALSE
  `expected`: TRUE 
  
  
  [ FAIL 2 | WARN 4 | SKIP 19 | PASS 158 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [18s/49s] OK
* checking PDF version of manual ... [7s/18s] OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR
See
  ‘/data/gannet/ripley/R/packages/tests-Suggests/occCite.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 5:44.18, 180.92 + 17.32