Running ‘test-all.R’ [5s/8s]
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: JN615256.1][1] "SeqRec [ID: JN615256.1]"
  Formal class 'SeqRec' [package "phylotaR"] with 16 slots
    ..@ id     : chr "JN615256.1"
    ..@ nm     : chr ""
    ..@ accssn : chr "JN615256"
    ..@ vrsn   : chr "JN615256.1"
    ..@ url    : chr "https://www.ncbi.nlm.nih.gov/nuccore/JN615256.1"
    ..@ txid   : chr "1080975"
    ..@ orgnsm : chr "Anisoptera sp. MD-2011"
    ..@ sq     : raw [1:439] 67 74 63 74 ...
    ..@ dfln   : chr "Anisoptera sp. MD-2011 voucher ZMUC:JD-1506 16S ribosomal RNA gene, partial sequence; mitochondrial"
    ..@ ml_typ : chr "DNA"
    ..@ rec_typ: chr "whole"
    ..@ nncltds: int 439
    ..@ nambgs : int 0
    ..@ pambgs : num 0
    ..@ gcr    : num 0.699
    ..@ age    : int 2329
  SeqRec [ID: JN615256.1]Archive of sequence record(s)
   - [10619] sequences
   - [1143] unique txids
   - [506] median sequence length
   - [0] median ambiguous nucleotides
  [1] "Archive of sequence record(s)\n - [10619] sequences\n - [1143] unique txids\n - [506] median sequence length\n - [0] median ambiguous nucleotides\n"
  Formal class 'SeqArc' [package "phylotaR"] with 5 slots
    ..@ ids    : chr [1:10619] "JN615256.1" "EU055352.1" "EU055329.1" "EU055461.1" ...
    ..@ nncltds: num [1:10619] 439 644 644 326 326 326 522 522 522 522 ...
    ..@ nambgs : num [1:10619] 0 0 0 0 0 0 0 0 0 0 ...
    ..@ txids  : chr [1:10619] "1080975" "476805" "126213" "476689" ...
    ..@ sqs    :List of 10619
  Archive of sequence record(s)
   - [10619] sequences
   - [1143] unique txids
   - [506] median sequence length
   - [0] median ambiguous nucleotides
  Cluster Record [id 0]
   - [subtree] type
   - [KU496893.1] seed sequence
   - [5180] sequences
   - [912] taxa
  [1] "Cluster Record [id 0]\n - [subtree] type\n - [KU496893.1] seed sequence\n - [5180] sequences\n - [912] taxa\n"
  Formal class 'ClstrRec' [package "phylotaR"] with 8 slots
    ..@ id   : int 0
    ..@ sids : chr [1:5180] "AB708563.1" "AB708564.1" "AB708565.1" "AB708566.1" ...
    ..@ nsqs : int 5180
    ..@ txids: chr [1:5180] "229376" "126201" "318824" "318824" ...
    ..@ ntx  : int 912
    ..@ typ  : chr "subtree"
    ..@ prnt : chr "6962"
    ..@ seed : chr "KU496893.1"
  Cluster Record [id 0]
   - [subtree] type
   - [KU496893.1] seed sequence
   - [5180] sequences
   - [912] taxa
  Archive of cluster record(s)
   - [784] clusters
  [1] "Archive of cluster record(s)\n - [784] clusters\n"
  Formal class 'ClstrArc' [package "phylotaR"] with 2 slots
    ..@ ids   : chr [1:784] "0" "1" "2" "3" ...
    ..@ clstrs:List of 784
  Archive of cluster record(s)
   - [784] clusters
  TaxRec [id 1080975 (Anisoptera sp. MD-2011)]
  [1] "TaxRec [id 1080975 (Anisoptera sp. MD-2011)]\n"
  Formal class 'TaxRec' [package "phylotaR"] with 6 slots
    ..@ id  : chr "1080975"
    ..@ scnm: chr "Anisoptera sp. MD-2011"
    ..@ cmnm: chr ""
    ..@ rnk : chr "species"
    ..@ lng :List of 2
    ..@ prnt: chr "1080974"
  TaxRec [id 1080975 (Anisoptera sp. MD-2011)]
  Taxonomic dictionary [1499] recs, parent [id 6962]
  [1] "Taxonomic dictionary [1499] recs, parent [id 6962]\n"
  Formal class 'TaxDict' [package "phylotaR"] with 4 slots
    ..@ txids: chr [1:1499] "2172396" "2100527" "2100526" "2100525" ...
    ..@ recs :<environment: 0x55d22f2a8788> 
    ..@ txtr :Formal class 'TreeMan' [package "treeman"] with 17 slots
    ..@ prnt : chr "6962"
  Taxonomic dictionary [1499] recs, parent [id 6962]
  Phylota Table (Anisoptera)
  - [784] clusters
  - [10619] sequences
  - [1143] source taxa
  [1] "Phylota Table (Anisoptera)\n- [784] clusters\n- [10619] sequences\n- [1143] source taxa\n"
  Formal class 'Phylota' [package "phylotaR"] with 8 slots
    ..@ cids   : chr [1:784] "0" "1" "2" "3" ...
    ..@ txids  : chr [1:1143] "1080975" "476805" "126213" "476689" ...
    ..@ sids   : chr [1:10619] "JN615256.1" "EU055352.1" "EU055329.1" "EU055461.1" ...
    ..@ 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 "6962"
    ..@ prnt_nm: chr "Anisoptera"
  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 FAILED: 1
  1. Failure: drop_by_rank() works (@test-user-drop.R#36) 
  
  Error: testthat unit tests failed
  Execution halted