Running ‘test-all.R’ [60s/154s]
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: 23.2 Kb 
  1. Error: we can read nexml from a url (@test_nexml_read.R#14) -----------------
  Timeout was reached: Operation timed out after 10001 milliseconds with 0 out of 0 bytes received
  1: read.nexml(url) at testthat/test_nexml_read.R:14
  2: nexml_read.character(url)
  3: GET(x)
  4: request_perform(req, hu$handle$handle)
  5: request_fetch(req$output, req$url, handle)
  6: request_fetch.write_memory(req$output, req$url, handle)
  7: curl::curl_fetch_memory(url, handle = handle)
  
  2. Error: we can read nexml from a XMLInternalDocument object (@test_nexml_read.R#31) 
  Timeout was reached: Operation timed out after 10001 milliseconds with 0 out of 0 bytes received
  1: xmlParse(content(GET(url))) at testthat/test_nexml_read.R:31
  2: content(GET(url))
  3: stopifnot(is.response(x))
  4: withCallingHandlers(tryCatch(...elt(i), error = function(e) {
         e$call <- cl.i
         stop(e)
     }), warning = function(w) {
         w$call <- cl.i
         w
     })
  5: tryCatch(...elt(i), error = function(e) {
         e$call <- cl.i
         stop(e)
     })
  6: tryCatchList(expr, classes, parentenv, handlers)
  7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  8: value[[3L]](cond)
  
  3. Error: we can read nexml from a XMLInternalNode object (@test_nexml_read.R#41) 
  Timeout was reached: Operation timed out after 10001 milliseconds with 0 out of 0 bytes received
  1: xmlParse(content(GET(url))) at testthat/test_nexml_read.R:41
  2: content(GET(url))
  3: stopifnot(is.response(x))
  4: withCallingHandlers(tryCatch(...elt(i), error = function(e) {
         e$call <- cl.i
         stop(e)
     }), warning = function(w) {
         w$call <- cl.i
         w
     })
  5: tryCatch(...elt(i), error = function(e) {
         e$call <- cl.i
         stop(e)
     })
  6: tryCatchList(expr, classes, parentenv, handlers)
  7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  8: value[[3L]](cond)
  
  Done simulation(s).
  
  Retrieving data for taxon 'Trogoniformes'
  
  
  Retrieving data for taxon 'Coraciiformes'
  
  
  Retrieving data for taxon 'Coliiformes'
  
  
  Retrieving data for taxon 'Cuculiformes'
  
  
  Retrieving data for taxon 'Psittaciformes'
  
  
  Retrieving data for taxon 'Apodiformes'
  
  
  Retrieving data for taxon 'Trochiliformes'
  
  
  Retrieving data for taxon 'Musophagiformes'
  
  
  Retrieving data for taxon 'Strigiformes'
  
  
  Retrieving data for taxon 'Columbiformes'
  
  
  Retrieving data for taxon 'Gruiformes'
  
  
  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'
  
  testthat results ================================================================
  OK: 172 SKIPPED: 0 FAILED: 3
  1. Error: we can read nexml from a url (@test_nexml_read.R#14) 
  2. Error: we can read nexml from a XMLInternalDocument object (@test_nexml_read.R#31) 
  3. Error: we can read nexml from a XMLInternalNode object (@test_nexml_read.R#41) 
  
  Error: testthat unit tests failed
  In addition: Warning messages:
  1: In taxize_nexml(chir, "NCBI") :
    ID for otu Myotis_yesoensis not found. Consider checking the spelling or alternate classification
  2: In taxize_nexml(chir, "NCBI") :
    ID for otu Myotis_findleyi not found. Consider checking the spelling or alternate classification
  Execution halted