R Under development (unstable) (2024-12-20 r87452 ucrt) -- "Unsuffered Consequences"
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> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(TrIdent)
> 
> test_check("TrIdent")
Reformatting pileup files
Starting pattern-matching...
A quarter of the way done with pattern-matching
Half of the way done with pattern-matching
Almost done with pattern-matching!
Determining sizes (bp) of pattern matches
Identifying highly active/abundant or heterogenously integrated
        Prophage-like elements
Finalizing output
Execution time: 34.32secs
1 contigs were filtered out based on low read coverage
0 contigs were filtered out based on length

HighCovNoPattern        NoPattern    Prophage-like          Sloping 
               1                1                4                3 
3 of the prophage-like classifications are highly active or abundant
1 of the prophage-like classifications are mixed, i.e. heterogenously
        integrated into their bacterial host population
Reformatting pileup files
Starting pattern-matching...
A quarter of the way done with pattern-matching
Half of the way done with pattern-matching
Almost done with pattern-matching!
Determining sizes (bp) of pattern matches
Identifying highly active/abundant or heterogenously integrated
        Prophage-like elements
Finalizing output
Execution time: 32.36secs
1 contigs were filtered out based on low read coverage
0 contigs were filtered out based on length

HighCovNoPattern        NoPattern    Prophage-like          Sloping 
               1                1                4                3 
3 of the prophage-like classifications are highly active or abundant
1 of the prophage-like classifications are mixed, i.e. heterogenously
        integrated into their bacterial host population
Reformatting pileup files
Starting pattern-matching...
A quarter of the way done with pattern-matching
Half of the way done with pattern-matching
Almost done with pattern-matching!
Determining sizes (bp) of pattern matches
Identifying highly active/abundant or heterogenously integrated
        Prophage-like elements
Finalizing output
Execution time: 33.12secs
1 contigs were filtered out based on low read coverage
0 contigs were filtered out based on length

HighCovNoPattern        NoPattern    Prophage-like          Sloping 
               1                1                4                3 
3 of the prophage-like classifications are highly active or abundant
1 of the prophage-like classifications are mixed, i.e. heterogenously
        integrated into their bacterial host population
2 contigs have potential specialized transduction
We recommend that you also view the results of this search with
      logScale=TRUE
1 contigs have potential specialized transduction
We recommend that you also view the results of this search with
      logScale=TRUE
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 5 ]
> 
> proc.time()
   user  system elapsed 
  89.39   13.29  102.62