Running 'testthat.R' [72s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(ptm)
  > 
  > test_check("ptm")
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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.
  
  filec16c6173780a 2 seqs, max length 418, avg  length 406
  72 MB(0%)00:00:00                Iter   1   33.33%  K-mer dist pass 1
  4278 MB(26%)00:00:00                Iter   1  100.00%  K-mer dist pass 1
  4278 MB(26%)00:00:00                Iter   1   33.33%  K-mer dist pass 2
  4278 MB(26%)00:00:00                Iter   1  100.00%  K-mer dist pass 2
  4278 MB(26%)00:00:00                Iter   1  100.00%  Align node       
  4278 MB(26%)00:00:00                Iter   1  100.00%  Align node
  4278 MB(26%)00:00:00                Iter   1   50.00%  Root alignment
  4278 MB(26%)00:00:00                Iter   1  100.00%  Root alignment
  4278 MB(26%)00:00:00                Iter   1  100.00%  Root alignment
  filec16cf4966c3 2 seqs, max length 418, avg  length 406
  4278 MB(26%)00:00:00                Iter   1   33.33%  K-mer dist pass 1
  4278 MB(26%)00:00:00                Iter   1  100.00%  K-mer dist pass 1
  4278 MB(26%)00:00:00                Iter   1   33.33%  K-mer dist pass 2
  4278 MB(26%)00:00:00                Iter   1  100.00%  K-mer dist pass 2
  4278 MB(26%)00:00:00                Iter   1  100.00%  Align node       
  4278 MB(26%)00:00:00                Iter   1  100.00%  Align node
  4278 MB(26%)00:00:00                Iter   1   50.00%  Root alignment
  4278 MB(26%)00:00:00                Iter   1  100.00%  Root alignment
  4278 MB(26%)00:00:00                Iter   1  100.00%  Root alignment
  filec16c4ab31f 2 seqs, max length 418, avg  length 406
  4278 MB(26%)00:00:00                Iter   1   33.33%  K-mer dist pass 1
  4278 MB(26%)00:00:00                Iter   1  100.00%  K-mer dist pass 1
  4278 MB(26%)00:00:00                Iter   1   33.33%  K-mer dist pass 2
  4278 MB(26%)00:00:00                Iter   1  100.00%  K-mer dist pass 2
  4278 MB(26%)00:00:00                Iter   1  100.00%  Align node       
  4278 MB(26%)00:00:00                Iter   1  100.00%  Align node
  4278 MB(26%)00:00:00                Iter   1   50.00%  Root alignment
  4278 MB(26%)00:00:00                Iter   1  100.00%  Root alignment
  4278 MB(26%)00:00:00                Iter   1  100.00%  Root alignment
  filec16cbed5e65 2 seqs, max length 418, avg  length 406
  4278 MB(26%)00:00:00                Iter   1   33.33%  K-mer dist pass 1
  4278 MB(26%)00:00:00                Iter   1  100.00%  K-mer dist pass 1
  4278 MB(26%)00:00:00                Iter   1   33.33%  K-mer dist pass 2
  4278 MB(26%)00:00:00                Iter   1  100.00%  K-mer dist pass 2
  4278 MB(26%)00:00:00                Iter   1  100.00%  Align node       
  4278 MB(26%)00:00:00                Iter   1  100.00%  Align node
  4278 MB(26%)00:00:00                Iter   1   50.00%  Root alignment
  4278 MB(26%)00:00:00                Iter   1  100.00%  Root alignment
  4278 MB(26%)00:00:00                Iter   1  100.00%  Root alignment
  filec16c4e585724 2 seqs, max length 418, avg  length 406
  4278 MB(26%)00:00:00                Iter   1   33.33%  K-mer dist pass 1
  4278 MB(26%)00:00:00                Iter   1  100.00%  K-mer dist pass 1
  4278 MB(26%)00:00:00                Iter   1   33.33%  K-mer dist pass 2
  4278 MB(26%)00:00:00                Iter   1  100.00%  K-mer dist pass 2
  4278 MB(26%)00:00:00                Iter   1  100.00%  Align node       
  4278 MB(26%)00:00:00                Iter   1  100.00%  Align node
  4278 MB(26%)00:00:00                Iter   1   50.00%  Root alignment
  4278 MB(26%)00:00:00                Iter   1  100.00%  Root alignment
  4278 MB(26%)00:00:00                Iter   1  100.00%  Root alignment
  filec16c1fcb261a 2 seqs, max length 476, avg  length 476
  4278 MB(26%)00:00:00                Iter   1   33.33%  K-mer dist pass 1
  4278 MB(26%)00:00:00                Iter   1  100.00%  K-mer dist pass 1
  4278 MB(26%)00:00:00                Iter   1   33.33%  K-mer dist pass 2
  4278 MB(26%)00:00:00                Iter   1  100.00%  K-mer dist pass 2
  4278 MB(26%)00:00:00                Iter   1  100.00%  Align node       
  4278 MB(26%)00:00:00                Iter   1  100.00%  Align node
  4278 MB(26%)00:00:00                Iter   1   50.00%  Root alignment
  4278 MB(26%)00:00:00                Iter   1  100.00%  Root alignment
  4278 MB(26%)00:00:00                Iter   1  100.00%  Root alignment
  == Skipped tests ===============================================================
  * On CRAN (63)
  
  == Failed tests ================================================================
  -- Failure (test_aa.R:13:3): aa.at() using named arguments with order ----------
  `t` not equal to "Q".
  1/1 mismatches
  x[1]: "28 isn't a valid position for this protein"
  y[1]: "Q"
  -- Failure (test_aa.R:15:3): aa.at() using named arguments with order ----------
  nchar(t) not equal to 1.
  1/1 mismatches
  [1] 42 - 1 == 41
  
  [ FAIL 2 | WARN 7 | SKIP 63 | PASS 191 ]
  Error: Test failures
  Execution halted