Running ‘test-all.R’ [9s/10s]
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: FJ623078.1][1] "SeqRec [ID: FJ623078.1]"
  Formal class 'SeqRec' [package "phylotaR"] with 16 slots
    ..@ id     : chr "FJ623078.1"
    ..@ nm     : chr ""
    ..@ accssn : chr "FJ623078"
    ..@ vrsn   : chr "FJ623078.1"
    ..@ url    : chr "https://www.ncbi.nlm.nih.gov/nuccore/FJ623078.1"
    ..@ txid   : chr "37293"
    ..@ orgnsm : chr "Aotus nancymaae"
    ..@ sq     : raw [1:1374] 61 74 67 67 ...
    ..@ dfln   : chr "Aotus nancymaae CD4 antigen (CD4) mRNA, complete cds"
    ..@ ml_typ : chr "mRNA"
    ..@ rec_typ: chr "whole"
    ..@ nncltds: int 1374
    ..@ nambgs : int 0
    ..@ pambgs : num 0
    ..@ gcr    : num 0.447
    ..@ age    : int 3412
  SeqRec [ID: FJ623078.1]Archive of sequence record(s)
   - [1499] sequences
   - [13] unique txids
   - [548] median sequence length
   - [0] median ambiguous nucleotides
  [1] "Archive of sequence record(s)\n - [1499] sequences\n - [13] unique txids\n - [548] median sequence length\n - [0] median ambiguous nucleotides\n"
  Formal class 'SeqArc' [package "phylotaR"] with 5 slots
    ..@ ids    : chr [1:1499] "FJ623078.1" "U38998.1" "U88361.1" "AY684995.1" ...
    ..@ nncltds: num [1:1499] 1374 525 465 954 1425 ...
    ..@ nambgs : num [1:1499] 0 0 0 0 0 0 0 0 0 0 ...
    ..@ txids  : chr [1:1499] "37293" "9505" "37293" "9505" ...
    ..@ sqs    :List of 1499
  Archive of sequence record(s)
   - [1499] sequences
   - [13] unique txids
   - [548] median sequence length
   - [0] median ambiguous nucleotides
  Cluster Record [id 0]
   - [subtree] type
   - [AF129794.1] seed sequence
   - [204] sequences
   - [5] taxa
  [1] "Cluster Record [id 0]\n - [subtree] type\n - [AF129794.1] seed sequence\n - [204] sequences\n - [5] taxa\n"
  Formal class 'ClstrRec' [package "phylotaR"] with 8 slots
    ..@ id   : int 0
    ..@ sids : chr [1:204] "AF129792.1" "AF129793.1" "AF129794.1" "AF129795.1" ...
    ..@ nsqs : int 204
    ..@ txids: chr [1:204] "231953" "231953" "231953" "231953" ...
    ..@ ntx  : int 5
    ..@ typ  : chr "subtree"
    ..@ prnt : chr "9504"
    ..@ seed : chr "AF129794.1"
  Cluster Record [id 0]
   - [subtree] type
   - [AF129794.1] seed sequence
   - [204] sequences
   - [5] taxa
  Archive of cluster record(s)
   - [193] clusters
  [1] "Archive of cluster record(s)\n - [193] clusters\n"
  Formal class 'ClstrArc' [package "phylotaR"] with 2 slots
    ..@ ids   : chr [1:193] "0" "1" "2" "3" ...
    ..@ clstrs:List of 193
  Archive of cluster record(s)
   - [193] clusters
  TaxRec [id 37293 (Aotus nancymaae)]
  [1] "TaxRec [id 37293 (Aotus nancymaae)]\n"
  Formal class 'TaxRec' [package "phylotaR"] with 6 slots
    ..@ id  : chr "37293"
    ..@ scnm: chr "Aotus nancymaae"
    ..@ cmnm: chr "Ma's night monkey"
    ..@ rnk : chr "species"
    ..@ lng :List of 2
    ..@ prnt: chr "9504"
  TaxRec [id 37293 (Aotus nancymaae)]
  Taxonomic dictionary [21] recs, parent [id 9504]
  [1] "Taxonomic dictionary [21] recs, parent [id 9504]\n"
  Formal class 'TaxDict' [package "phylotaR"] with 4 slots
    ..@ txids: chr [1:21] "1263727" "1230482" "1090913" "1002694" ...
    ..@ recs :<environment: 0x56181addb6e8> 
    ..@ txtr :Formal class 'TreeMan' [package "treeman"] with 17 slots
    ..@ prnt : chr "9504"
  Taxonomic dictionary [21] recs, parent [id 9504]
  Phylota Table (Aotus)
  - [193] clusters
  - [1499] sequences
  - [13] source taxa
  [1] "Phylota Table (Aotus)\n- [193] clusters\n- [1499] sequences\n- [13] source taxa\n"
  Formal class 'Phylota' [package "phylotaR"] with 8 slots
    ..@ cids   : chr [1:193] "0" "1" "2" "3" ...
    ..@ txids  : chr [1:13] "37293" "9505" "57176" "57175" ...
    ..@ sids   : chr [1:1499] "FJ623078.1" "U38998.1" "U88361.1" "AY684995.1" ...
    ..@ 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 "9504"
    ..@ prnt_nm: chr "Aotus"
  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