Running ‘testthat.R’ [13s/73s]
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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   $ fig.align: chr "left"
   $ echo     : logi FALSE
  
    ordinary text without R code
  
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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.
  
  file53d097c3c1a 2 seqs, max length 418, avg  length 406
  904 MB(1%)00:00:00                Iter   1   33.33%  K-mer dist pass 1
  904 MB(1%)00:00:00                Iter   1  100.00%  K-mer dist pass 1
  904 MB(1%)00:00:00                Iter   1   33.33%  K-mer dist pass 2
  904 MB(1%)00:00:00                Iter   1  100.00%  K-mer dist pass 2
  904 MB(1%)00:00:00                Iter   1  100.00%  Align node       
  904 MB(1%)00:00:00                Iter   1  100.00%  Align node
  904 MB(1%)00:00:00                Iter   1   50.00%  Root alignment
  904 MB(1%)00:00:00                Iter   1  100.00%  Root alignment
  904 MB(1%)00:00:00                Iter   1  100.00%  Root alignment
  file53d012a2fb36 2 seqs, max length 418, avg  length 406
  913 MB(1%)00:00:00                Iter   1   33.33%  K-mer dist pass 1
  913 MB(1%)00:00:00                Iter   1  100.00%  K-mer dist pass 1
  913 MB(1%)00:00:00                Iter   1   33.33%  K-mer dist pass 2
  913 MB(1%)00:00:00                Iter   1  100.00%  K-mer dist pass 2
  913 MB(1%)00:00:00                Iter   1  100.00%  Align node       
  913 MB(1%)00:00:00                Iter   1  100.00%  Align node
  913 MB(1%)00:00:00                Iter   1   50.00%  Root alignment
  913 MB(1%)00:00:00                Iter   1  100.00%  Root alignment
  913 MB(1%)00:00:00                Iter   1  100.00%  Root alignment
  file53d0a81484a 2 seqs, max length 418, avg  length 406
  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
  file53d01cbf49a0 2 seqs, max length 418, avg  length 406
  935 MB(1%)00:00:00                Iter   1   33.33%  K-mer dist pass 1
  935 MB(1%)00:00:00                Iter   1  100.00%  K-mer dist pass 1
  935 MB(1%)00:00:00                Iter   1   33.33%  K-mer dist pass 2
  935 MB(1%)00:00:00                Iter   1  100.00%  K-mer dist pass 2
  935 MB(1%)00:00:00                Iter   1  100.00%  Align node       
  935 MB(1%)00:00:00                Iter   1  100.00%  Align node
  935 MB(1%)00:00:00                Iter   1   50.00%  Root alignment
  935 MB(1%)00:00:00                Iter   1  100.00%  Root alignment
  935 MB(1%)00:00:00                Iter   1  100.00%  Root alignment
  file53d051a399a 2 seqs, max length 418, avg  length 406
  945 MB(1%)00:00:00                Iter   1   33.33%  K-mer dist pass 1
  945 MB(1%)00:00:00                Iter   1  100.00%  K-mer dist pass 1
  945 MB(1%)00:00:00                Iter   1   33.33%  K-mer dist pass 2
  945 MB(1%)00:00:00                Iter   1  100.00%  K-mer dist pass 2
  946 MB(1%)00:00:00                Iter   1  100.00%  Align node       
  946 MB(1%)00:00:00                Iter   1  100.00%  Align node
  946 MB(1%)00:00:00                Iter   1   50.00%  Root alignment
  946 MB(1%)00:00:00                Iter   1  100.00%  Root alignment
  946 MB(1%)00:00:00                Iter   1  100.00%  Root alignment
  
  *** WARNING *** Assuming Amino (see -seqtype option), invalid letters found: O
  file53d06e38ef16 2 seqs, max length 476, avg  length 245
  957 MB(1%)00:00:00                Iter   1   33.33%  K-mer dist pass 1
  957 MB(1%)00:00:00                Iter   1  100.00%  K-mer dist pass 1
  957 MB(1%)00:00:00                Iter   1   33.33%  K-mer dist pass 2
  957 MB(1%)00:00:00                Iter   1  100.00%  K-mer dist pass 2
  957 MB(1%)00:00:00                Iter   1  100.00%  Align node       
  957 MB(1%)00:00:00                Iter   1  100.00%  Align node
  957 MB(1%)00:00:00                Iter   1   50.00%  Root alignment
  957 MB(1%)00:00:00                Iter   1  100.00%  Root alignment
  957 MB(1%)00:00:00                Iter   1  100.00%  Root alignment
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (63)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test_ptmScan.R:122:3): ptm.scan() works properly ───────────────────
  nrow(b) not equal to 54.
  1/1 mismatches
  [1] 53 - 54 == -1
  
  [ FAIL 1 | WARN 7 | SKIP 63 | PASS 192 ]
  Error: Test failures
  Execution halted