Running ‘testthat.R’ [38s/77s]
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(metamorphr)
  > 
  > test_check("metamorphr")
  `impute_bpca` output:
  
  
  `impute_bpca` output:
  
  
  `impute_bpca` output:
  
  
  `impute_bpca` output:
  
  
  Cluster size 2308 broken into 1247 1061 
  Done cluster 1247 
  Done cluster 1061 
  Cluster size 2308 broken into 1406 902 
  Done cluster 1406 
  Done cluster 902 
  Cluster size 2308 broken into 1247 1061 
  Done cluster 1247 
  Done cluster 1061 
  Finished iteration 2.
  Finished iteration 3.
  Successfully ran 3 iterations.
  Finished iteration 1.
  Finished iteration 2.
  Finished iteration 3.
  11 Samples: Sample1, Sample2, Sample3, Sample4, Sample5
  
  # 6 more samples
  
  # Use the n_samples_max argument to see more
  
  10 Features: 161.10519 Da 26.98 s, 276.13647 Da 27.28 s, 304.24023 Da 32.86 s, 417.23236 Da 60.08 s, 104.10753 Da 170.31 s
  
  # 5 more features
  
  # Use the n_features_max argument to see more
  
  0 % missing values (NA): 0 out of 110.
  
  11 Samples: Sample1, Sample2, Sample3, Sample4, Sample5
  
  # 6 more samples
  
  # Use the n_samples_max argument to see more
  
  10 Features: 161.10519 Da 26.98 s, 276.13647 Da 27.28 s, 304.24023 Da 32.86 s, 417.23236 Da 60.08 s, 104.10753 Da 170.31 s
  
  # 5 more features
  
  # Use the n_features_max argument to see more
  
  0 % missing values (NA): 0 out of 110.
  
  11 Samples: Sample1, Sample2, Sample3, Sample4, Sample5
  
  # 6 more samples
  
  # Use the n_samples_max argument to see more
  
  10 Features: 161.10519 Da 26.98 s, 276.13647 Da 27.28 s, 304.24023 Da 32.86 s, 417.23236 Da 60.08 s, 104.10753 Da 170.31 s
  
  # 5 more features
  
  # Use the n_features_max argument to see more
  
  0 % missing values (NA): 0 out of 110.
  
  11 Samples: Sample1, Sample2, Sample3, Sample4, Sample5
  
  # 6 more samples
  
  # Use the n_samples_max argument to see more
  
  10 Features: 161.10519 Da 26.98 s, 276.13647 Da 27.28 s, 304.24023 Da 32.86 s, 417.23236 Da 60.08 s, 104.10753 Da 170.31 s
  
  # 5 more features
  
  # Use the n_features_max argument to see more
  
  0 % missing values (NA): 0 out of 110.
  
  11 Samples: Sample1, Sample2, Sample3, Sample4, Sample5
  
  # 6 more samples
  
  # Use the n_samples_max argument to see more
  
  10 Features: 161.10519 Da 26.98 s, 276.13647 Da 27.28 s, 304.24023 Da 32.86 s, 417.23236 Da 60.08 s, 104.10753 Da 170.31 s
  
  # 5 more features
  
  # Use the n_features_max argument to see more
  
  0 % missing values (NA): 0 out of 110.
  
  11 Samples: Sample1, Sample2, Sample3, Sample4, Sample5
  
  # 6 more samples
  
  # Use the n_samples_max argument to see more
  
  10 Features: 161.10519 Da 26.98 s, 276.13647 Da 27.28 s, 304.24023 Da 32.86 s, 417.23236 Da 60.08 s, 104.10753 Da 170.31 s
  
  # 5 more features
  
  # Use the n_features_max argument to see more
  
  0 % missing values (NA): 0 out of 110.
  
  Finished iteration 1.
  Finished iteration 2.
  Finished iteration 3.
  Finished iteration 4.
  Finished iteration 5.
  Finished iteration 6.
  Finished iteration 1.
  nipals calculated PCA
  Importance of component(s):
                   PC1    PC2
  R2            0.4315 0.2422
  Cumulative R2 0.4315 0.6736
  10 	Variables
  11 	Samples
  33 	NAs ( 30 %)
  2 	Calculated component(s)
  Data was mean centered before running PCA 
  Data was NOT scaled before running PCA 
  Scores structure:
  [1] 11  2
  Loadings structure:
  [1] 10  2
  # 6 more samples
  
  # Use the n_samples_max argument to see more
  
  10 Features: 161.10519 Da 26.98 s, 276.13647 Da 27.28 s, 304.24023 Da 32.86 s, 417.23236 Da 60.08 s, 104.10753 Da 170.31 s
  
  # 5 more features
  
  # Use the n_features_max argument to see more
  
  30 % missing values (NA): 33 out of 110.
  
  11 Samples: Sample1, Sample2, Sample3, Sample4, Sample5
  
  # 6 more samples
  
  # Use the n_samples_max argument to see more
  
  # 5 more features
  
  # Use the n_features_max argument to see more
  
  30 % missing values (NA): 33 out of 110.
  
  11 Samples: Sample1, Sample2, Sample3, Sample4, Sample5
  
  # 6 more samples
  
  # Use the n_samples_max argument to see more
  
  10 Features: 161.10519 Da 26.98 s, 276.13647 Da 27.28 s, 304.24023 Da 32.86 s, 417.23236 Da 60.08 s, 104.10753 Da 170.31 s
  
  # 5 more features
  
  # Use the n_features_max argument to see more
  
  30 % missing values (NA): 33 out of 110.
  
  11 Samples: Sample1, Sample2, Sample3, Sample4, Sample5
  
  # 6 more samples
  
  # Use the n_samples_max argument to see more
  
  10 Features: 161.10519 Da 26.98 s, 276.13647 Da 27.28 s, 304.24023 Da 32.86 s, 417.23236 Da 60.08 s, 104.10753 Da 170.31 s
  
  # 5 more features
  
  # Use the n_features_max argument to see more
  
  11 Samples: Sample1, Sample2, Sample3, Sample4, Sample5
  
  # 6 more samples
  
  # Use the n_samples_max argument to see more
  
  10 Features: 161.10519 Da 26.98 s, 276.13647 Da 27.28 s, 304.24023 Da 32.86 s, 417.23236 Da 60.08 s, 104.10753 Da 170.31 s
  
  # 5 more features
  
  # Use the n_features_max argument to see more
  
  11 Samples: Sample1, Sample2, Sample3, Sample4, Sample5
  
  # 6 more samples
  
  # Use the n_samples_max argument to see more
  
  10 Features: 161.10519 Da 26.98 s, 276.13647 Da 27.28 s, 304.24023 Da 32.86 s, 417.23236 Da 60.08 s, 104.10753 Da 170.31 s
  
  # 5 more features
  
  # Use the n_features_max argument to see more
  
  11 Samples: Sample1, Sample2, Sample3, Sample4, Sample5
  
  # 6 more samples
  
  # Use the n_samples_max argument to see more
  
  10 Features: 161.10519 Da 26.98 s, 276.13647 Da 27.28 s, 304.24023 Da 32.86 s, 417.23236 Da 60.08 s, 104.10753 Da 170.31 s
  
  # 5 more features
  
  # Use the n_features_max argument to see more
  
  Replicates detected: 1...3
  
  1 Batches: 1
  
  30 % missing values (NA): 33 out of 110.
  
  11 Samples: Sample1, Sample2, Sample3, Sample4, Sample5
  
  # 6 more samples
  
  # Use the n_samples_max argument to see more
  
  10 Features: 161.10519 Da 26.98 s, 276.13647 Da 27.28 s, 304.24023 Da 32.86 s, 417.23236 Da 60.08 s, 104.10753 Da 170.31 s
  
  # 5 more features
  
  # Use the n_features_max argument to see more
  
  4 Groups: control, treatment, QC, blank
  
  1 Batches: 1
  
  30 % missing values (NA): 33 out of 110.
  
  11 Samples: Sample1, Sample2, Sample3, Sample4, Sample5
  
  # 6 more samples
  
  # Use the n_samples_max argument to see more
  
  10 Features: 161.10519 Da 26.98 s, 276.13647 Da 27.28 s, 304.24023 Da 32.86 s, 417.23236 Da 60.08 s, 104.10753 Da 170.31 s
  
  # 5 more features
  
  # Use the n_features_max argument to see more
  
  4 Groups: control, treatment, QC, blank
  
  Replicates detected: 1...3
  
  30 % missing values (NA): 33 out of 110.
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 362 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-impute_knn.R:206:3'): test check_installed_wrapper function ──
  `check_installed_wrapper("abc")` did not throw the expected error.
  ── Error ('test-normalize_quantile_smooth.R:91:3'): normalize_quantile_smooth returns the same values as qsmooth::qsmooth() ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'qsmooth'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-normalize_quantile_smooth.R:91:3
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 362 ]
  Error: Test failures
  Execution halted