Running 'test-all.R' [13s]
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: GU250484.1][1] "SeqRec [ID: GU250484.1]"
  Formal class 'SeqRec' [package "phylotaR"] with 16 slots
    ..@ id     : chr "GU250484.1"
    ..@ nm     : chr ""
    ..@ accssn : chr "GU250484"
    ..@ vrsn   : chr "GU250484.1"
    ..@ url    : chr "https://www.ncbi.nlm.nih.gov/nuccore/GU250484.1"
    ..@ txid   : chr "933395"
    ..@ orgnsm : chr "Cycas condaoensis"
    ..@ sq     : raw [1:983] 74 61 61 74 ...
    ..@ dfln   : chr "Cycas condaoensis psbM-trnD intergenic spacer, partial sequence; chloroplast"
    ..@ ml_typ : chr "DNA"
    ..@ rec_typ: chr "whole"
    ..@ nncltds: int 983
    ..@ nambgs : int 0
    ..@ pambgs : num 0
    ..@ gcr    : num 0.622
    ..@ age    : int 2727
  SeqRec [ID: GU250484.1]Archive of sequence record(s)
   - [8331] sequences
   - [353] unique txids
   - [700] median sequence length
   - [0] median ambiguous nucleotides
  [1] "Archive of sequence record(s)\n - [8331] sequences\n - [353] unique txids\n - [700] median sequence length\n - [0] median ambiguous nucleotides\n"
  Formal class 'SeqArc' [package "phylotaR"] with 5 slots
    ..@ ids    : chr [1:8331] "GU250484.1" "GU250483.1" "GU250482.1" "GU250481.1" ...
    ..@ nncltds: num [1:8331] 983 983 983 983 982 983 912 905 915 914 ...
    ..@ nambgs : num [1:8331] 0 0 0 0 0 0 0 0 0 0 ...
    ..@ txids  : chr [1:8331] "933395" "747353" "933394" "171016" ...
    ..@ sqs    :List of 8331
  Archive of sequence record(s)
   - [8331] sequences
   - [353] unique txids
   - [700] median sequence length
   - [0] median ambiguous nucleotides
  Cluster Record [id 0]
   - [subtree] type
   - [AF407324.1/1..511] seed sequence
   - [561] sequences
   - [113] taxa
  [1] "Cluster Record [id 0]\n - [subtree] type\n - [AF407324.1/1..511] seed sequence\n - [561] sequences\n - [113] taxa\n"
  Formal class 'ClstrRec' [package "phylotaR"] with 8 slots
    ..@ id   : int 0
    ..@ sids : chr [1:561] "AF407312.1/1..510" "AF407314.1/1..511" "AF407318.1/1..501" "AF407318.1/502..988" ...
    ..@ nsqs : int 561
    ..@ txids: chr [1:561] "58031" "3397" "242200" "242200" ...
    ..@ ntx  : int 113
    ..@ typ  : chr "subtree"
    ..@ prnt : chr "1445963"
    ..@ seed : chr "AF407324.1/1..511"
  Cluster Record [id 0]
   - [subtree] type
   - [AF407324.1/1..511] seed sequence
   - [561] sequences
   - [113] taxa
  Archive of cluster record(s)
   - [540] clusters
  [1] "Archive of cluster record(s)\n - [540] clusters\n"
  Formal class 'ClstrArc' [package "phylotaR"] with 2 slots
    ..@ ids   : chr [1:540] "0" "1" "2" "3" ...
    ..@ clstrs:List of 540
  Archive of cluster record(s)
   - [540] clusters
  TaxRec [id 933395 (Cycas condaoensis)]
  [1] "TaxRec [id 933395 (Cycas condaoensis)]\n"
  Formal class 'TaxRec' [package "phylotaR"] with 6 slots
    ..@ id  : chr "933395"
    ..@ scnm: chr "Cycas condaoensis"
    ..@ cmnm: chr ""
    ..@ rnk : chr "species"
    ..@ lng :List of 2
    ..@ prnt: chr "3395"
  TaxRec [id 933395 (Cycas condaoensis)]
  Taxonomic dictionary [384] recs, parent [id 1445963]
  [1] "Taxonomic dictionary [384] recs, parent [id 1445963]\n"
  Formal class 'TaxDict' [package "phylotaR"] with 4 slots
    ..@ txids: chr [1:384] "2044290" "2043222" "2005476" "2004589" ...
    ..@ recs :<environment: 0x0000000008035720> 
    ..@ txtr :Formal class 'TreeMan' [package "treeman"] with 17 slots
    ..@ prnt : chr "1445963"
  Taxonomic dictionary [384] recs, parent [id 1445963]
  Phylota Table (Cycadidae)
  - [540] clusters
  - [8331] sequences
  - [353] source taxa
  [1] "Phylota Table (Cycadidae)\n- [540] clusters\n- [8331] sequences\n- [353] source taxa\n"
  Formal class 'Phylota' [package "phylotaR"] with 8 slots
    ..@ cids   : chr [1:540] "0" "1" "2" "3" ...
    ..@ txids  : chr [1:353] "933395" "747353" "933394" "171016" ...
    ..@ sids   : chr [1:8331] "GU250484.1" "GU250483.1" "GU250482.1" "GU250481.1" ...
    ..@ 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 "1445963"
    ..@ prnt_nm: chr "Cycadidae"
  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