Running ‘testthat.R’ [10s/116s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ptm)
  > 
  > test_check("ptm")
    ordinary text without R code
  
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   $ echo     : logi FALSE
  
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  MUSCLE v3.8.31 by Robert C. Edgar
  
  http://www.drive5.com/muscle
  This software is donated to the public domain.
  Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97.
  
  file6afa19463e48 2 seqs, max length 418, avg  length 406
  906 MB(1%)00:00:00                Iter   1   33.33%  K-mer dist pass 1
  906 MB(1%)00:00:00                Iter   1  100.00%  K-mer dist pass 1
  906 MB(1%)00:00:00                Iter   1   33.33%  K-mer dist pass 2
  906 MB(1%)00:00:00                Iter   1  100.00%  K-mer dist pass 2
  906 MB(1%)00:00:00                Iter   1  100.00%  Align node       
  906 MB(1%)00:00:00                Iter   1  100.00%  Align node
  906 MB(1%)00:00:00                Iter   1   50.00%  Root alignment
  906 MB(1%)00:00:00                Iter   1  100.00%  Root alignment
  906 MB(1%)00:00:00                Iter   1  100.00%  Root alignment
  file6afac83704 2 seqs, max length 418, avg  length 406
  914 MB(1%)00:00:00                Iter   1   33.33%  K-mer dist pass 1
  914 MB(1%)00:00:00                Iter   1  100.00%  K-mer dist pass 1
  914 MB(1%)00:00:00                Iter   1   33.33%  K-mer dist pass 2
  914 MB(1%)00:00:00                Iter   1  100.00%  K-mer dist pass 2
  914 MB(1%)00:00:00                Iter   1  100.00%  Align node       
  914 MB(1%)00:00:00                Iter   1  100.00%  Align node
  914 MB(1%)00:00:00                Iter   1   50.00%  Root alignment
  914 MB(1%)00:00:00                Iter   1  100.00%  Root alignment
  914 MB(1%)00:00:00                Iter   1  100.00%  Root alignment
  
  *** WARNING *** Assuming Amino (see -seqtype option), invalid letters found: O
  file6afa30912947 2 seqs, max length 394, avg  length 204
  924 MB(1%)00:00:00                Iter   1   33.33%  K-mer dist pass 1
  924 MB(1%)00:00:00                Iter   1  100.00%  K-mer dist pass 1
  924 MB(1%)00:00:00                Iter   1   33.33%  K-mer dist pass 2
  924 MB(1%)00:00:00                Iter   1  100.00%  K-mer dist pass 2
  924 MB(1%)00:00:00                Iter   1  100.00%  Align node       
  924 MB(1%)00:00:00                Iter   1  100.00%  Align node
  924 MB(1%)00:00:00                Iter   1   50.00%  Root alignment
  924 MB(1%)00:00:00                Iter   1  100.00%  Root alignment
  924 MB(1%)00:00:00                Iter   1  100.00%  Root alignment
  
  *** WARNING *** Assuming Amino (see -seqtype option), invalid letters found: 
  file6afa6662e87f 2 seqs, max length 418, avg  length 406
  936 MB(1%)00:00:00                Iter   1   33.33%  K-mer dist pass 1
  936 MB(1%)00:00:00                Iter   1  100.00%  K-mer dist pass 1
  936 MB(1%)00:00:00                Iter   1   33.33%  K-mer dist pass 2
  936 MB(1%)00:00:00                Iter   1  100.00%  K-mer dist pass 2
  936 MB(1%)00:00:00                Iter   1  100.00%  Align node       
  936 MB(1%)00:00:00                Iter   1  100.00%  Align node
  936 MB(1%)00:00:00                Iter   1   50.00%  Root alignment
  936 MB(1%)00:00:00                Iter   1  100.00%  Root alignment
  936 MB(1%)00:00:00                Iter   1  100.00%  Root alignment
  
  *** WARNING *** Assuming Amino (see -seqtype option), invalid letters found: O
  file6afa539dc75a 2 seqs, max length 394, avg  length 204
  944 MB(1%)00:00:00                Iter   1   33.33%  K-mer dist pass 1
  944 MB(1%)00:00:00                Iter   1  100.00%  K-mer dist pass 1
  944 MB(1%)00:00:00                Iter   1   33.33%  K-mer dist pass 2
  944 MB(1%)00:00:00                Iter   1  100.00%  K-mer dist pass 2
  944 MB(1%)00:00:00                Iter   1  100.00%  Align node       
  944 MB(1%)00:00:00                Iter   1  100.00%  Align node
  944 MB(1%)00:00:00                Iter   1   50.00%  Root alignment
  944 MB(1%)00:00:00                Iter   1  100.00%  Root alignment
  944 MB(1%)00:00:00                Iter   1  100.00%  Root alignment
  
  *** WARNING *** Assuming Amino (see -seqtype option), invalid letters found: 
  file6afa13870038 2 seqs, max length 476, avg  length 476
  953 MB(1%)00:00:00                Iter   1   33.33%  K-mer dist pass 1
  953 MB(1%)00:00:00                Iter   1  100.00%  K-mer dist pass 1
  953 MB(1%)00:00:00                Iter   1   33.33%  K-mer dist pass 2
  953 MB(1%)00:00:00                Iter   1  100.00%  K-mer dist pass 2
  953 MB(1%)00:00:00                Iter   1  100.00%  Align node       
  953 MB(1%)00:00:00                Iter   1  100.00%  Align node
  953 MB(1%)00:00:00                Iter   1   50.00%  Root alignment
  953 MB(1%)00:00:00                Iter   1  100.00%  Root alignment
  953 MB(1%)00:00:00                Iter   1  100.00%  Root alignment
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  ● On CRAN (63)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test_aa.R:38:3): aa.at() using uniprot = TRUE ──────────────────────
  nchar(aa.at(100, "P01009")) not equal to 1.
  1/1 mismatches
  [1] 43 - 1 == 42
  ── Error (test_ptmScan.R:112:3): ptm.scan() works properly ─────────────────────
  Error: replacement has 409 rows, data has 1
  Backtrace:
      █
   1. ├─base::suppressWarnings(ptm.scan("O14757")) test_ptmScan.R:112:2
   2. │ └─base::withCallingHandlers(...)
   3. └─ptm::ptm.scan("O14757")
   4.   ├─base::`$<-`(...)
   5.   └─base::`$<-.data.frame`(...)
  
  [ FAIL 2 | WARN 7 | SKIP 63 | PASS 181 ]
  Error: Test failures
  Execution halted