Running ‘testthat.R’ [6s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # 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(demulticoder)
  > 
  > test_check("demulticoder")
  cutadapt is not installed, skipping tests.
  cutadapt is not installed, skipping tests.
  cutadapt is not installed, skipping tests.
  cutadapt is not installed, skipping tests.
  Existing files found in the output directory. Overwriting existing files.
  Rows: 2 Columns: 25
  -- Column specification --------------------------------------------------------
  Delimiter: ","
  chr  (3): primer_name, forward, reverse
  dbl (18): minCutadaptlength, maxN, maxEE_forward, maxEE_reverse, truncLen_fo...
  lgl  (4): already_trimmed, count_all_samples, multithread, verbose
  
  i Use `spec()` to retrieve the full column specification for this data.
  i Specify the column types or set `show_col_types = FALSE` to quiet this message.
  Rows: 2 Columns: 25
  -- Column specification --------------------------------------------------------
  Delimiter: ","
  chr  (3): primer_name, forward, reverse
  dbl (18): minCutadaptlength, maxN, maxEE_forward, maxEE_reverse, truncLen_fo...
  lgl  (4): already_trimmed, count_all_samples, multithread, verbose
  
  i Use `spec()` to retrieve the full column specification for this data.
  i Specify the column types or set `show_col_types = FALSE` to quiet this message.
  Rows: 4 Columns: 3
  -- Column specification --------------------------------------------------------
  Delimiter: ","
  chr (3): sample_name, primer_name, organism
  
  i Use `spec()` to retrieve the full column specification for this data.
  i Specify the column types or set `show_col_types = FALSE` to quiet this message.
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_prepare_reads.R:2:3'): prepare_reads works correctly ───────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'dada2'
  Backtrace:
      ▆
   1. ├─demulticoder::prepare_reads(...) at test_prepare_reads.R:2:3
   2. │ └─demulticoder:::read_prefilt_fastq(...)
   3. │   └─demulticoder:::remove_ns(...)
   4. └─base::loadNamespace(x)
   5.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   6.     └─base (local) withOneRestart(expr, restarts[[1L]])
   7.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted