Running ‘test-all.R’ [33s/46s]
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: AF162230.2/1..1536][1] "SeqRec [ID: AF162230.2/1..1536]"
  Formal class 'SeqRec' [package "phylotaR"] with 16 slots
    ..@ id     : chr "AF162230.2/1..1536"
    ..@ nm     : chr "matK"
    ..@ accssn : chr "AF162230"
    ..@ vrsn   : chr "AF162230.2"
    ..@ url    : chr "https://www.ncbi.nlm.nih.gov/nuccore/AF162230.2/1..1536"
    ..@ txid   : chr "100681"
    ..@ orgnsm : chr "Cottendorfia florida"
    ..@ sq     : raw [1:1536] 61 74 67 67 ...
    ..@ dfln   : chr "Cottendorfia florida maturase K (matK) gene, complete cds; chloroplast"
    ..@ ml_typ : chr "DNA"
    ..@ rec_typ: chr "feature"
    ..@ nncltds: int 1536
    ..@ nambgs : int 0
    ..@ pambgs : num 0
    ..@ gcr    : num 0.674
    ..@ age    : int 6844
  SeqRec [ID: AF162230.2/1..1536]Archive of sequence record(s)
   - [9840] sequences
   - [1172] unique txids
   - [718] median sequence length
   - [0] median ambiguous nucleotides
  [1] "Archive of sequence record(s)\n - [9840] sequences\n - [1172] unique txids\n - [718] median sequence length\n - [0] median ambiguous nucleotides\n"
  Formal class 'SeqArc' [package "phylotaR"] with 5 slots
    ..@ ids    : chr [1:9840] "AF162230.2/1..1536" "AY438602.1" "HQ913671.1/54..670" "HQ882722.1/1..573" ...
    ..@ nncltds: num [1:9840] 1536 1556 617 573 523 ...
    ..@ nambgs : num [1:9840] 0 0 0 0 0 0 0 0 0 80 ...
    ..@ txids  : chr [1:9840] "100681" "100681" "100681" "100681" ...
    ..@ sqs    :List of 9840
  Archive of sequence record(s)
   - [9840] sequences
   - [1172] unique txids
   - [718] median sequence length
   - [0] median ambiguous nucleotides
  Cluster Record [id 0]
   - [subtree] type
   - [KX754195.1/60..1595] seed sequence
   - [1841] sequences
   - [917] taxa
  [1] "Cluster Record [id 0]\n - [subtree] type\n - [KX754195.1/60..1595] seed sequence\n - [1841] sequences\n - [917] taxa\n"
  Formal class 'ClstrRec' [package "phylotaR"] with 8 slots
    ..@ id   : int 0
    ..@ sids : chr [1:1841] "AF162226.1" "AF162227.2/1..1536" "AF162228.2/1..1536" "AF162229.1" ...
    ..@ nsqs : int 1841
    ..@ txids: chr [1:1841] "100681" "326798" "1506221" "1506220" ...
    ..@ ntx  : int 917
    ..@ typ  : chr "subtree"
    ..@ prnt : chr "4613"
    ..@ seed : chr "KX754195.1/60..1595"
  Cluster Record [id 0]
   - [subtree] type
   - [KX754195.1/60..1595] seed sequence
   - [1841] sequences
   - [917] taxa
  Archive of cluster record(s)
   - [721] clusters
  [1] "Archive of cluster record(s)\n - [721] clusters\n"
  Formal class 'ClstrArc' [package "phylotaR"] with 2 slots
    ..@ ids   : chr [1:721] "0" "1" "2" "3" ...
    ..@ clstrs:List of 721
  Archive of cluster record(s)
   - [721] clusters
  TaxRec [id 100681 (Cottendorfia florida)]
  [1] "TaxRec [id 100681 (Cottendorfia florida)]\n"
  Formal class 'TaxRec' [package "phylotaR"] with 6 slots
    ..@ id  : chr "100681"
    ..@ scnm: chr "Cottendorfia florida"
    ..@ cmnm: chr ""
    ..@ rnk : chr "species"
    ..@ lng :List of 2
    ..@ prnt: chr "100680"
  TaxRec [id 100681 (Cottendorfia florida)]
  Taxonomic dictionary [1358] recs, parent [id 4613]
  [1] "Taxonomic dictionary [1358] recs, parent [id 4613]\n"
  Formal class 'TaxDict' [package "phylotaR"] with 4 slots
    ..@ txids: chr [1:1358] "2184933" "2184932" "2184931" "2093805" ...
    ..@ recs :<environment: 0x561416cfda90> 
    ..@ txtr :Formal class 'TreeMan' [package "treeman"] with 17 slots
    ..@ prnt : chr "4613"
  Taxonomic dictionary [1358] recs, parent [id 4613]
  Phylota Table (Bromeliaceae)
  - [721] clusters
  - [9840] sequences
  - [1172] source taxa
  [1] "Phylota Table (Bromeliaceae)\n- [721] clusters\n- [9840] sequences\n- [1172] source taxa\n"
  Formal class 'Phylota' [package "phylotaR"] with 8 slots
    ..@ cids   : chr [1:721] "0" "1" "2" "3" ...
    ..@ txids  : chr [1:1172] "100681" "1349380" "1485041" "1485031" ...
    ..@ sids   : chr [1:9840] "AF162230.2/1..1536" "AY438602.1" "HQ913671.1/54..670" "HQ882722.1/1..573" ...
    ..@ 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 "4613"
    ..@ prnt_nm: chr "Bromeliaceae"
  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