Running ‘testthat.R’ [12s/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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   $ 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.
  
  file4b1c3ec3d1e9 2 seqs, max length 418, avg  length 406
  889 MB(1%)00:00:00                Iter   1   33.33%  K-mer dist pass 1
  889 MB(1%)00:00:00                Iter   1  100.00%  K-mer dist pass 1
  889 MB(1%)00:00:00                Iter   1   33.33%  K-mer dist pass 2
  889 MB(1%)00:00:00                Iter   1  100.00%  K-mer dist pass 2
  889 MB(1%)00:00:00                Iter   1  100.00%  Align node       
  889 MB(1%)00:00:00                Iter   1  100.00%  Align node
  889 MB(1%)00:00:00                Iter   1   50.00%  Root alignment
  889 MB(1%)00:00:00                Iter   1  100.00%  Root alignment
  889 MB(1%)00:00:00                Iter   1  100.00%  Root alignment
  file4b1c66050656 2 seqs, max length 418, avg  length 406
  900 MB(1%)00:00:00                Iter   1   33.33%  K-mer dist pass 1
  900 MB(1%)00:00:00                Iter   1  100.00%  K-mer dist pass 1
  900 MB(1%)00:00:00                Iter   1   33.33%  K-mer dist pass 2
  900 MB(1%)00:00:00                Iter   1  100.00%  K-mer dist pass 2
  900 MB(1%)00:00:00                Iter   1  100.00%  Align node       
  900 MB(1%)00:00:00                Iter   1  100.00%  Align node
  900 MB(1%)00:00:00                Iter   1   50.00%  Root alignment
  900 MB(1%)00:00:00                Iter   1  100.00%  Root alignment
  900 MB(1%)00:00:00                Iter   1  100.00%  Root alignment
  file4b1c3c135541 2 seqs, max length 418, avg  length 406
  908 MB(1%)00:00:00                Iter   1   33.33%  K-mer dist pass 1
  908 MB(1%)00:00:00                Iter   1  100.00%  K-mer dist pass 1
  908 MB(1%)00:00:00                Iter   1   33.33%  K-mer dist pass 2
  908 MB(1%)00:00:00                Iter   1  100.00%  K-mer dist pass 2
  908 MB(1%)00:00:00                Iter   1  100.00%  Align node       
  908 MB(1%)00:00:00                Iter   1  100.00%  Align node
  908 MB(1%)00:00:00                Iter   1   50.00%  Root alignment
  908 MB(1%)00:00:00                Iter   1  100.00%  Root alignment
  908 MB(1%)00:00:00                Iter   1  100.00%  Root alignment
  file4b1c3240f7fb 2 seqs, max length 418, avg  length 406
  927 MB(1%)00:00:00                Iter   1   33.33%  K-mer dist pass 1
  927 MB(1%)00:00:00                Iter   1  100.00%  K-mer dist pass 1
  927 MB(1%)00:00:00                Iter   1   33.33%  K-mer dist pass 2
  927 MB(1%)00:00:00                Iter   1  100.00%  K-mer dist pass 2
  927 MB(1%)00:00:00                Iter   1  100.00%  Align node       
  927 MB(1%)00:00:00                Iter   1  100.00%  Align node
  927 MB(1%)00:00:00                Iter   1   50.00%  Root alignment
  927 MB(1%)00:00:00                Iter   1  100.00%  Root alignment
  927 MB(1%)00:00:00                Iter   1  100.00%  Root alignment
  file4b1c5799eb6c 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
  file4b1c65f136ea 2 seqs, max length 476, avg  length 476
  943 MB(1%)00:00:00                Iter   1   33.33%  K-mer dist pass 1
  943 MB(1%)00:00:00                Iter   1  100.00%  K-mer dist pass 1
  943 MB(1%)00:00:00                Iter   1   33.33%  K-mer dist pass 2
  943 MB(1%)00:00:00                Iter   1  100.00%  K-mer dist pass 2
  943 MB(1%)00:00:00                Iter   1  100.00%  Align node       
  943 MB(1%)00:00:01                Iter   1  100.00%  Align node
  943 MB(1%)00:00:01                Iter   1   50.00%  Root alignment
  943 MB(1%)00:00:01                Iter   1  100.00%  Root alignment
  943 MB(1%)00:00:01                Iter   1  100.00%  Root alignment
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  ● On CRAN (63)
  
  ══ Warnings ════════════════════════════════════════════════════════════════════
  ── Warning (test_accdpx.R:99:1): (code run outside of `test_that()`) ───────────
  cannot remove file './pdb/1U8F_getarea.Rda', reason 'No such file or directory'
  Backtrace:
   1. base::file.remove("./pdb/1U8F_getarea.Rda") test_accdpx.R:99:0
  ── Warning (test_accdpx.R:100:1): (code run outside of `test_that()`) ──────────
  cannot remove file './pdb/1U8F_getarea.txt', reason 'No such file or directory'
  Backtrace:
   1. base::file.remove("./pdb/1U8F_getarea.txt") test_accdpx.R:100:0
  ── Warning (test_evolutionary.R:125:1): (code run outside of `test_that()`) ────
  cannot remove file '1u8f_insertions.Rda', reason 'No such file or directory'
  Backtrace:
   1. base::file.remove(...) test_evolutionary.R:125:0
  ── Warning (test_evolutionary.R:125:1): (code run outside of `test_that()`) ────
  cannot remove file '1u8f_aln.Rda', reason 'No such file or directory'
  Backtrace:
   1. base::file.remove(...) test_evolutionary.R:125:0
  ── Warning (test_evolutionary.R:125:1): (code run outside of `test_that()`) ────
  cannot remove file '1u8f_profile.Rda', reason 'No such file or directory'
  Backtrace:
   1. base::file.remove(...) test_evolutionary.R:125:0
  ── Warning (test_evolutionary.R:125:1): (code run outside of `test_that()`) ────
  cannot remove file '1u8f_seq_list.Rda', reason 'No such file or directory'
  Backtrace:
   1. base::file.remove(...) test_evolutionary.R:125:0
  ── Warning (test_pdb_ancillary.R:47:1): (code run outside of `test_that()`) ────
  cannot remove file '2hhb.fa', reason 'No such file or directory'
  Backtrace:
   1. base::file.remove("2hhb.fa") test_pdb_ancillary.R:47:0
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_ptmScan.R:114:3): ptm.scan() works properly ─────────────────────
  Error: replacement has 2 rows, data has 1
  Backtrace:
      █
   1. ├─base::suppressWarnings(ptm.scan("Q15796")) test_ptmScan.R:114:2
   2. │ └─base::withCallingHandlers(...)
   3. └─ptm::ptm.scan("Q15796")
   4.   ├─base::`$<-`(`*tmp*`, "p", value = c(NA, TRUE))
   5.   └─base::`$<-.data.frame`(`*tmp*`, "p", value = c(NA, TRUE))
  
  [ FAIL 1 | WARN 7 | SKIP 63 | PASS 182 ]
  Error: Test failures
  Execution halted