Running ‘test-all.R’ [26s/27s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("phylotaR")
  Loading required package: phylotaR
  
  Attaching package: 'phylotaR'
  
  The following object is masked from 'package:testthat':
  
      setup
  
  SeqRec [ID: EU737940.1][1] "SeqRec [ID: EU737940.1]"
  Formal class 'SeqRec' [package "phylotaR"] with 16 slots
    ..@ id     : chr "EU737940.1"
    ..@ nm     : chr ""
    ..@ accssn : chr "EU737940"
    ..@ vrsn   : chr "EU737940.1"
    ..@ url    : chr "https://www.ncbi.nlm.nih.gov/nuccore/EU737940.1"
    ..@ txid   : chr "8805"
    ..@ orgnsm : chr "Eudromia elegans"
    ..@ sq     : raw [1:688] 67 74 74 61 ...
    ..@ dfln   : chr "Eudromia elegans brain-derived neurotrophic factor (BDNF) gene, exon 1 and partial cds"
    ..@ ml_typ : chr "DNA"
    ..@ rec_typ: chr "whole"
    ..@ nncltds: int 688
    ..@ nambgs : int 0
    ..@ pambgs : num 0
    ..@ gcr    : num 0.381
    ..@ age    : int 3624
  SeqRec [ID: EU737940.1]Archive of sequence record(s)
   - [250] sequences
   - [25] unique txids
   - [679.5] median sequence length
   - [0] median ambiguous nucleotides
  [1] "Archive of sequence record(s)\n - [250] sequences\n - [25] unique txids\n - [679.5] median sequence length\n - [0] median ambiguous nucleotides\n"
  Formal class 'SeqArc' [package "phylotaR"] with 5 slots
    ..@ ids    : chr [1:250] "EU737940.1" "EU737938.1" "EU737484.1/1..469" "EU737481.1/1..475" ...
    ..@ nncltds: num [1:250] 688 688 469 475 458 467 560 577 561 558 ...
    ..@ nambgs : num [1:250] 0 1 0 2 0 0 3 0 2 11 ...
    ..@ txids  : chr [1:250] "8805" "458187" "94827" "30464" ...
    ..@ sqs    :List of 250
  Archive of sequence record(s)
   - [250] sequences
   - [25] unique txids
   - [679.5] median sequence length
   - [0] median ambiguous nucleotides
  Cluster Record [id 0]
   - [subtree] type
   - [JQ174588.1] seed sequence
   - [57] sequences
   - [21] taxa
  [1] "Cluster Record [id 0]\n - [subtree] type\n - [JQ174588.1] seed sequence\n - [57] sequences\n - [21] taxa\n"
  Formal class 'ClstrRec' [package "phylotaR"] with 8 slots
    ..@ id   : int 0
    ..@ sids : chr [1:57] "FJ027462.1" "FJ027565.1" "FJ027566.1" "FJ027567.1" ...
    ..@ nsqs : int 57
    ..@ txids: chr [1:57] "1109099" "555361" "555278" "555278" ...
    ..@ ntx  : int 21
    ..@ typ  : chr "subtree"
    ..@ prnt : chr "8802"
    ..@ seed : chr "JQ174588.1"
  Cluster Record [id 0]
   - [subtree] type
   - [JQ174588.1] seed sequence
   - [57] sequences
   - [21] taxa
  Archive of cluster record(s)
   - [98] clusters
  [1] "Archive of cluster record(s)\n - [98] clusters\n"
  Formal class 'ClstrArc' [package "phylotaR"] with 2 slots
    ..@ ids   : chr [1:98] "0" "1" "2" "3" ...
    ..@ clstrs:List of 98
  Archive of cluster record(s)
   - [98] clusters
  TaxRec [id 8805 (Eudromia elegans)]
  [1] "TaxRec [id 8805 (Eudromia elegans)]\n"
  Formal class 'TaxRec' [package "phylotaR"] with 6 slots
    ..@ id  : chr "8805"
    ..@ scnm: chr "Eudromia elegans"
    ..@ cmnm: chr "elegant crested-tinamou"
    ..@ rnk : chr "species"
    ..@ lng :List of 2
    ..@ prnt: chr "8804"
  TaxRec [id 8805 (Eudromia elegans)]
  Taxonomic dictionary [40] recs, parent [id 8802]
  [1] "Taxonomic dictionary [40] recs, parent [id 8802]\n"
  Formal class 'TaxDict' [package "phylotaR"] with 4 slots
    ..@ txids: chr [1:40] "1977171" "1977170" "1503223" "1118538" ...
    ..@ recs :<environment: 0x556b35d74f60> 
    ..@ txtr :Formal class 'TreeMan' [package "treeman"] with 17 slots
    ..@ prnt : chr "8802"
  Taxonomic dictionary [40] recs, parent [id 8802]
  Phylota Table (Tinamiformes)
  - [98] clusters
  - [250] sequences
  - [25] source taxa
  [1] "Phylota Table (Tinamiformes)\n- [98] clusters\n- [250] sequences\n- [25] source taxa\n"
  Formal class 'Phylota' [package "phylotaR"] with 8 slots
    ..@ cids   : chr [1:98] "0" "1" "2" "3" ...
    ..@ txids  : chr [1:25] "8805" "458187" "94827" "30464" ...
    ..@ sids   : chr [1:250] "EU737940.1" "EU737938.1" "EU737484.1/1..469" "EU737481.1/1..475" ...
    ..@ txdct  :Formal class 'TaxDict' [package "phylotaR"] with 4 slots
    ..@ sqs    :Formal class 'SeqArc' [package "phylotaR"] with 5 slots
    ..@ clstrs :Formal class 'ClstrArc' [package "phylotaR"] with 2 slots
    ..@ prnt_id: chr "8802"
    ..@ prnt_nm: chr "Tinamiformes"
  BLASTing [10 sqs] ....
  Identified [1] clusters
  [1] "x"
  [1] "x"
  [1] "x"
  [1] "x"
  [1] "x"
  [1] "x"
  Read 5 items
  Read 2 items
  Read 3 items
  ... Taxise
  ... Download
  ... Cluster
  ... Cluster2
  ... Taxise
  ... Download
  ... Cluster
  ... Cluster2
  ── 1. Failure: drop_by_rank() works (@test-user-drop.R#36)  ────────────────────
  length(small_phylota@sids) > length(res@sids) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 175 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: drop_by_rank() works (@test-user-drop.R#36) 
  
  Error: testthat unit tests failed
  Execution halted