Running ‘test-all.R’ [47s/84s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  > test_check("RNeXML")
  Loading required package: RNeXML
  Loading required package: ape
  Namespace prefix xhtml on div is not defined
  A nexml object representing:
   	 0 phylogenetic tree blocks, where: 
   	 block 1 contains NULL phylogenetic trees
  	 block 0 contains  phylogenetic trees 
   	 19 meta elements 
   	 0 character matrices 
   	 0 taxonomic units 
   Taxa: 	  ... 
  
   NeXML generated by RNeXML using schema version: 0.9 
   size: 21.8 Kb 
  Done simulation(s).
  
  Retrieving data for taxon 'Trogoniformes'
  
  Not found. Consider checking the spelling or alternate classification
  
  Retrieving data for taxon 'Coraciiformes'
  
  Not found. Consider checking the spelling or alternate classification
  
  Retrieving data for taxon 'Coliiformes'
  
  Not found. Consider checking the spelling or alternate classification
  
  Retrieving data for taxon 'Cuculiformes'
  
  Not found. Consider checking the spelling or alternate classification
  
  Retrieving data for taxon 'Psittaciformes'
  
  Not found. Consider checking the spelling or alternate classification
  
  Retrieving data for taxon 'Apodiformes'
  
  Not found. Consider checking the spelling or alternate classification
  
  Retrieving data for taxon 'Trochiliformes'
  
  Not found. Consider checking the spelling or alternate classification
  
  Retrieving data for taxon 'Musophagiformes'
  
  Not found. Consider checking the spelling or alternate classification
  
  Retrieving data for taxon 'Strigiformes'
  
  Not found. Consider checking the spelling or alternate classification
  
  Retrieving data for taxon 'Columbiformes'
  
  Not found. Consider checking the spelling or alternate classification
  
  Retrieving data for taxon 'Gruiformes'
  
  Not found. Consider checking the spelling or alternate classification
  
  Retrieving data for taxon 'Ciconiiformes'
  
  
  Retrieving data for taxon 'Passeriformes'
  
  
  Retrieving data for taxon 'Myotis_yesoensis'
  
  Not found. Consider checking the spelling or alternate classification
  
  Retrieving data for taxon 'Myotis_atacamensis'
  
  
  Retrieving data for taxon 'Myotis_dominicensis'
  
  
  Retrieving data for taxon 'Myotis_elegans'
  
  
  Retrieving data for taxon 'Myotis_findleyi'
  
  Not found. Consider checking the spelling or alternate classification
  
  Retrieving data for taxon 'Myotis_keaysi'
  
  
  Retrieving data for taxon 'Myotis_martiniquensis'
  
  
  Retrieving data for taxon 'Myotis_nesopolus'
  
  
  Retrieving data for taxon 'Myotis_nigricans'
  
  
  Retrieving data for taxon 'Myotis_sodalis'
  
  
  Retrieving data for taxon 'Myotis_keaysi'
  
  
  Retrieving data for taxon 'Myotis_martiniquensis'
  
  
  Retrieving data for taxon 'Myotis_nesopolus'
  
  
  Retrieving data for taxon 'Myotis_nigricans'
  
  
  Retrieving data for taxon 'Myotis_sodalis'
  
  1. Error: taxize_nexml correctly collects ncbi identifiers (@test_taxonomy.R#22) 
  subscript out of bounds
  1: expect_is(birds@otus@.Data[[1]]@otu[[1]]@meta[[1]], "meta") at testthat/test_taxonomy.R:22
  2: klass(object)
  3: paste(class(x), collapse = "/")
  
  testthat results ================================================================
  OK: 179 SKIPPED: 0 FAILED: 1
  1. Error: taxize_nexml correctly collects ncbi identifiers (@test_taxonomy.R#22) 
  
  Error: testthat unit tests failed
  In addition: There were 13 warnings (use warnings() to see them)
  Execution halted