Running ‘test-all.R’ [32s/35s]
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: MG670582.1/72..978][1] "SeqRec [ID: MG670582.1/72..978]"
  Formal class 'SeqRec' [package "phylotaR"] with 16 slots
    ..@ id     : chr "MG670582.1/72..978"
    ..@ nm     : chr "D-loop"
    ..@ accssn : chr "MG670582"
    ..@ vrsn   : chr "MG670582.1"
    ..@ url    : chr "https://www.ncbi.nlm.nih.gov/nuccore/MG670582.1/72..978"
    ..@ txid   : chr "328639"
    ..@ orgnsm : chr "Acipenser ruthenus x Huso huso"
    ..@ sq     : raw [1:907] 67 74 74 61 ...
    ..@ dfln   : chr "Acipenser ruthenus x Huso huso isolate 6A2F455 tRNA-Pro gene and D-loop, complete sequence; and tRNA-Phe gene, "| __truncated__
    ..@ ml_typ : chr "DNA"
    ..@ rec_typ: chr "feature"
    ..@ nncltds: int 907
    ..@ nambgs : int 0
    ..@ pambgs : num 0
    ..@ gcr    : num 0.637
    ..@ age    : int 130
  SeqRec [ID: MG670582.1/72..978]Archive of sequence record(s)
   - [2417] sequences
   - [51] unique txids
   - [639] median sequence length
   - [0] median ambiguous nucleotides
  [1] "Archive of sequence record(s)\n - [2417] sequences\n - [51] unique txids\n - [639] median sequence length\n - [0] median ambiguous nucleotides\n"
  Formal class 'SeqArc' [package "phylotaR"] with 5 slots
    ..@ ids    : chr [1:2417] "MG670582.1/72..978" "MG670581.1/63..1129" "MG670580.1/64..1130" "MG670579.1/71..1137" ...
    ..@ nncltds: num [1:2417] 907 1067 1067 1067 1067 ...
    ..@ nambgs : num [1:2417] 0 0 0 0 0 0 0 0 0 0 ...
    ..@ txids  : chr [1:2417] "328639" "328639" "328639" "328639" ...
    ..@ sqs    :List of 2417
  Archive of sequence record(s)
   - [2417] sequences
   - [51] unique txids
   - [639] median sequence length
   - [0] median ambiguous nucleotides
  Cluster Record [id 0]
   - [subtree] type
   - [MG670577.1/64..1130] seed sequence
   - [448] sequences
   - [18] taxa
  [1] "Cluster Record [id 0]\n - [subtree] type\n - [MG670577.1/64..1130] seed sequence\n - [448] sequences\n - [18] taxa\n"
  Formal class 'ClstrRec' [package "phylotaR"] with 8 slots
    ..@ id   : int 0
    ..@ sids : chr [1:448] "AF176341.1/47..808" "AF184106.1" "AF184108.1" "AF224873.1/47..808" ...
    ..@ nsqs : int 448
    ..@ txids: chr [1:448] "328639" "328639" "328639" "328639" ...
    ..@ ntx  : int 18
    ..@ typ  : chr "subtree"
    ..@ prnt : chr "7900"
    ..@ seed : chr "MG670577.1/64..1130"
  Cluster Record [id 0]
   - [subtree] type
   - [MG670577.1/64..1130] seed sequence
   - [448] sequences
   - [18] taxa
  Archive of cluster record(s)
   - [332] clusters
  [1] "Archive of cluster record(s)\n - [332] clusters\n"
  Formal class 'ClstrArc' [package "phylotaR"] with 2 slots
    ..@ ids   : chr [1:332] "0" "1" "2" "3" ...
    ..@ clstrs:List of 332
  Archive of cluster record(s)
   - [332] clusters
  TaxRec [id 328639 (Acipenser ruthenus x Huso huso)]
  [1] "TaxRec [id 328639 (Acipenser ruthenus x Huso huso)]\n"
  Formal class 'TaxRec' [package "phylotaR"] with 6 slots
    ..@ id  : chr "328639"
    ..@ scnm: chr "Acipenser ruthenus x Huso huso"
    ..@ cmnm: chr ""
    ..@ rnk : chr "species"
    ..@ lng :List of 2
    ..@ prnt: chr "1358437"
  TaxRec [id 328639 (Acipenser ruthenus x Huso huso)]
  Taxonomic dictionary [81] recs, parent [id 7900]
  [1] "Taxonomic dictionary [81] recs, parent [id 7900]\n"
  Formal class 'TaxDict' [package "phylotaR"] with 4 slots
    ..@ txids: chr [1:81] "2054245" "2045007" "1940317" "1851548" ...
    ..@ recs :<environment: 0x5636fd5585f0> 
    ..@ txtr :Formal class 'TreeMan' [package "treeman"] with 17 slots
    ..@ prnt : chr "7900"
  Taxonomic dictionary [81] recs, parent [id 7900]
  Phylota Table (Acipenseridae)
  - [332] clusters
  - [2417] sequences
  - [51] source taxa
  [1] "Phylota Table (Acipenseridae)\n- [332] clusters\n- [2417] sequences\n- [51] source taxa\n"
  Formal class 'Phylota' [package "phylotaR"] with 8 slots
    ..@ cids   : chr [1:332] "0" "1" "2" "3" ...
    ..@ txids  : chr [1:51] "328639" "1358436" "228914" "1358431" ...
    ..@ sids   : chr [1:2417] "MG670582.1/72..978" "MG670581.1/63..1129" "MG670580.1/64..1130" "MG670579.1/71..1137" ...
    ..@ 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 "7900"
    ..@ prnt_nm: chr "Acipenseridae"
  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