Running ‘test-all.R’ [7s/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: KT951664.1][1] "SeqRec [ID: KT951664.1]"
  Formal class 'SeqRec' [package "phylotaR"] with 16 slots
    ..@ id     : chr "KT951664.1"
    ..@ nm     : chr ""
    ..@ accssn : chr "KT951664"
    ..@ vrsn   : chr "KT951664.1"
    ..@ url    : chr "https://www.ncbi.nlm.nih.gov/nuccore/KT951664.1"
    ..@ txid   : chr "1767026"
    ..@ orgnsm : chr "Milnesium variefidum"
    ..@ sq     : raw [1:1754] 61 67 61 74 ...
    ..@ dfln   : chr "Milnesium variefidum 18S ribosomal RNA gene, complete sequence"
    ..@ ml_typ : chr "DNA"
    ..@ rec_typ: chr "whole"
    ..@ nncltds: int 1754
    ..@ nambgs : int 2
    ..@ pambgs : num 0.00114
    ..@ gcr    : num 0.524
    ..@ age    : int 915
  SeqRec [ID: KT951664.1]Archive of sequence record(s)
   - [945] sequences
   - [261] unique txids
   - [680] median sequence length
   - [0] median ambiguous nucleotides
  [1] "Archive of sequence record(s)\n - [945] sequences\n - [261] unique txids\n - [680] median sequence length\n - [0] median ambiguous nucleotides\n"
  Formal class 'SeqArc' [package "phylotaR"] with 5 slots
    ..@ ids    : chr [1:945] "KT951664.1" "KT951663.1" "KT951667.1" "KT951666.1" ...
    ..@ nncltds: num [1:945] 1754 673 570 570 1746 ...
    ..@ nambgs : num [1:945] 2 0 0 0 3 0 1 0 4 0 ...
    ..@ txids  : chr [1:945] "1767026" "1767026" "1767026" "1767026" ...
    ..@ sqs    :List of 945
  Archive of sequence record(s)
   - [945] sequences
   - [261] unique txids
   - [680] median sequence length
   - [0] median ambiguous nucleotides
  Cluster Record [id 0]
   - [subtree] type
   - [KP013607.1] seed sequence
   - [441] sequences
   - [151] taxa
  [1] "Cluster Record [id 0]\n - [subtree] type\n - [KP013607.1] seed sequence\n - [441] sequences\n - [151] taxa\n"
  Formal class 'ClstrRec' [package "phylotaR"] with 8 slots
    ..@ id   : int 0
    ..@ sids : chr [1:441] "AY598769.1" "AY598771.1" "AY598772.1" "AY598773.1" ...
    ..@ nsqs : int 441
    ..@ txids: chr [1:441] "1767026" "1767025" "1353345" "1353345" ...
    ..@ ntx  : int 151
    ..@ typ  : chr "subtree"
    ..@ prnt : chr "42242"
    ..@ seed : chr "KP013607.1"
  Cluster Record [id 0]
   - [subtree] type
   - [KP013607.1] seed sequence
   - [441] sequences
   - [151] taxa
  Archive of cluster record(s)
   - [195] clusters
  [1] "Archive of cluster record(s)\n - [195] clusters\n"
  Formal class 'ClstrArc' [package "phylotaR"] with 2 slots
    ..@ ids   : chr [1:195] "0" "1" "2" "3" ...
    ..@ clstrs:List of 195
  Archive of cluster record(s)
   - [195] clusters
  TaxRec [id 1767026 (Milnesium variefidum)]
  [1] "TaxRec [id 1767026 (Milnesium variefidum)]\n"
  Formal class 'TaxRec' [package "phylotaR"] with 6 slots
    ..@ id  : chr "1767026"
    ..@ scnm: chr "Milnesium variefidum"
    ..@ cmnm: chr ""
    ..@ rnk : chr "species"
    ..@ lng :List of 2
    ..@ prnt: chr "46459"
  TaxRec [id 1767026 (Milnesium variefidum)]
  Taxonomic dictionary [386] recs, parent [id 42242]
  [1] "Taxonomic dictionary [386] recs, parent [id 42242]\n"
  Formal class 'TaxDict' [package "phylotaR"] with 4 slots
    ..@ txids: chr [1:386] "2163178" "2163177" "2163176" "2163175" ...
    ..@ recs :<environment: 0x5600aac87ab8> 
    ..@ txtr :Formal class 'TreeMan' [package "treeman"] with 17 slots
    ..@ prnt : chr "42242"
  Taxonomic dictionary [386] recs, parent [id 42242]
  Phylota Table (Eutardigrada)
  - [195] clusters
  - [945] sequences
  - [261] source taxa
  [1] "Phylota Table (Eutardigrada)\n- [195] clusters\n- [945] sequences\n- [261] source taxa\n"
  Formal class 'Phylota' [package "phylotaR"] with 8 slots
    ..@ cids   : chr [1:195] "0" "1" "2" "3" ...
    ..@ txids  : chr [1:261] "1767026" "1767025" "1353345" "467049" ...
    ..@ sids   : chr [1:945] "KT951664.1" "KT951663.1" "KT951667.1" "KT951666.1" ...
    ..@ 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 "42242"
    ..@ prnt_nm: chr "Eutardigrada"
  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