Running 'testthat.R' [17s/67s]
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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  List of 3
   $ out.width: chr "50px"
   $ fig.align: chr "left"
   $ echo     : logi FALSE
  
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    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.
  
  file7ac32bfe8f6b 2 seqs, max length 418, avg  length 406
  890 MB(3%)00:00:00                Iter   1   33.33%  K-mer dist pass 1
  890 MB(3%)00:00:00                Iter   1  100.00%  K-mer dist pass 1
  890 MB(3%)00:00:00                Iter   1   33.33%  K-mer dist pass 2
  890 MB(3%)00:00:00                Iter   1  100.00%  K-mer dist pass 2
  890 MB(3%)00:00:00                Iter   1  100.00%  Align node       
  890 MB(3%)00:00:00                Iter   1  100.00%  Align node
  890 MB(3%)00:00:00                Iter   1   50.00%  Root alignment
  890 MB(3%)00:00:00                Iter   1  100.00%  Root alignment
  890 MB(3%)00:00:00                Iter   1  100.00%  Root alignment
  file7ac33a89d1ce 2 seqs, max length 418, avg  length 406
  899 MB(3%)00:00:00                Iter   1   33.33%  K-mer dist pass 1
  899 MB(3%)00:00:00                Iter   1  100.00%  K-mer dist pass 1
  899 MB(3%)00:00:00                Iter   1   33.33%  K-mer dist pass 2
  899 MB(3%)00:00:00                Iter   1  100.00%  K-mer dist pass 2
  899 MB(3%)00:00:00                Iter   1  100.00%  Align node       
  899 MB(3%)00:00:00                Iter   1  100.00%  Align node
  899 MB(3%)00:00:00                Iter   1   50.00%  Root alignment
  899 MB(3%)00:00:00                Iter   1  100.00%  Root alignment
  899 MB(3%)00:00:00                Iter   1  100.00%  Root alignment
  file7ac33bc292d8 2 seqs, max length 418, avg  length 406
  908 MB(3%)00:00:00                Iter   1   33.33%  K-mer dist pass 1
  908 MB(3%)00:00:00                Iter   1  100.00%  K-mer dist pass 1
  908 MB(3%)00:00:00                Iter   1   33.33%  K-mer dist pass 2
  908 MB(3%)00:00:00                Iter   1  100.00%  K-mer dist pass 2
  908 MB(3%)00:00:00                Iter   1  100.00%  Align node       
  908 MB(3%)00:00:00                Iter   1  100.00%  Align node
  908 MB(3%)00:00:00                Iter   1   50.00%  Root alignment
  908 MB(3%)00:00:00                Iter   1  100.00%  Root alignment
  908 MB(3%)00:00:00                Iter   1  100.00%  Root alignment
  file7ac351e2fefb 2 seqs, max length 418, avg  length 406
  929 MB(3%)00:00:00                Iter   1   33.33%  K-mer dist pass 1
  929 MB(3%)00:00:00                Iter   1  100.00%  K-mer dist pass 1
  929 MB(3%)00:00:00                Iter   1   33.33%  K-mer dist pass 2
  929 MB(3%)00:00:00                Iter   1  100.00%  K-mer dist pass 2
  929 MB(3%)00:00:00                Iter   1  100.00%  Align node       
  929 MB(3%)00:00:00                Iter   1  100.00%  Align node
  929 MB(3%)00:00:00                Iter   1   50.00%  Root alignment
  929 MB(3%)00:00:00                Iter   1  100.00%  Root alignment
  929 MB(3%)00:00:00                Iter   1  100.00%  Root alignment
  file7ac35ebfab42 2 seqs, max length 418, avg  length 406
  938 MB(3%)00:00:00                Iter   1   33.33%  K-mer dist pass 1
  938 MB(3%)00:00:00                Iter   1  100.00%  K-mer dist pass 1
  938 MB(3%)00:00:00                Iter   1   33.33%  K-mer dist pass 2
  938 MB(3%)00:00:00                Iter   1  100.00%  K-mer dist pass 2
  938 MB(3%)00:00:00                Iter   1  100.00%  Align node       
  938 MB(3%)00:00:00                Iter   1  100.00%  Align node
  938 MB(3%)00:00:00                Iter   1   50.00%  Root alignment
  938 MB(3%)00:00:00                Iter   1  100.00%  Root alignment
  938 MB(3%)00:00:00                Iter   1  100.00%  Root alignment
  file7ac3631afb51 2 seqs, max length 476, avg  length 476
  946 MB(3%)00:00:00                Iter   1   33.33%  K-mer dist pass 1
  946 MB(3%)00:00:00                Iter   1  100.00%  K-mer dist pass 1
  946 MB(3%)00:00:00                Iter   1   33.33%  K-mer dist pass 2
  946 MB(3%)00:00:00                Iter   1  100.00%  K-mer dist pass 2
  946 MB(3%)00:00:00                Iter   1  100.00%  Align node       
  946 MB(3%)00:00:00                Iter   1  100.00%  Align node
  946 MB(3%)00:00:00                Iter   1   50.00%  Root alignment
  946 MB(3%)00:00:00                Iter   1  100.00%  Root alignment
  946 MB(3%)00:00:00                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
  -- Warning (test_ptmScan.R:55:3): ub.scan() works properly ---------------------
  cannot open URL 'https://github.com/jcaledo/ub_db/raw/master/ub_db_B0I1T2.Rda': HTTP status was '502 Bad Gateway'
  Backtrace:
   1. ptm::ub.scan("B0I1T2") test_ptmScan.R:55:2
   7. base::load(url(call))
  
  == Failed tests ================================================================
  -- Failure (test_ptmScan.R:57:3): ub.scan() works properly ---------------------
  `a` inherits from `character` not `data.frame`.
  -- Failure (test_ptmScan.R:58:3): ub.scan() works properly ---------------------
  nrow(a) not equal to 36.
  target is NULL, current is numeric
  -- Failure (test_ptmScan.R:59:3): ub.scan() works properly ---------------------
  ncol(a) not equal to 4.
  target is NULL, current is numeric
  -- Error (test_ptmScan.R:60:3): ub.scan() works properly -----------------------
  Error: $ operator is invalid for atomic vectors
  Backtrace:
      x
   1. \-testthat::expect_equal(a$modification[1], "K87-ub") test_ptmScan.R:60:2
   2.   \-testthat::quasi_label(enquo(object), label, arg = "object")
   3.     \-rlang::eval_bare(expr, quo_get_env(quo))
  
  [ FAIL 4 | WARN 8 | SKIP 63 | PASS 188 ]
  Error: Test failures
  Execution halted