Running ‘testthat.R’ [11s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(promor)
  > 
  > test_check("promor")
  0 empty row(s) removed.
  2 empty column(s) removed.
  1 protein(s) (rows) only identified by site removed.
  4 protein(s) identified by 2 or fewer unique peptides removed.
  Zeros have been replaced with NAs.
  Data have been log-transformed.
  4 proteins with higher than 33% NAs in at least one group removed.
  0 empty row(s) removed.
  4 empty column(s) removed.
  10 protein contaminant(s) (rows) removed.
  0 protein(s) identified by 2 or fewer unique peptides removed.
  Zeros have been replaced with NAs.
  Data have been log-transformed.
  change in estimate:  0.02415548 
  change in estimate:  0.02101209 
  change in estimate:  0.01821531 
  change in estimate:  0.0157772 
  change in estimate:  0.01367284 
  change in estimate:  0.01186459 
  change in estimate:  0.01031291 
  change in estimate:  0.008980791 
  Saving _problems/test-protein_analysis-424.R
  1 siginificantly differentially expressed proteins found.
  
  Testing glm...
  
  
  Testing rf...
  
  
  Testing svmRadial...
  
  
  Done!
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 20 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-protein_analysis.R:419:3'): normalization works for cyclicloess ──
  Expected `normalize_data(df_mp, method = "cyclicloess")` to equal `df_norm_c`.
  Differences:
  actual vs expected
                       [,1]     [,2]      [,3]
  - actual[1, ]   10.086035 20.13598 70.205445
  + expected[1, ]  8.875947 21.90757 81.928810
  - actual[2, ]   34.229368 34.59707 29.475138
  + expected[2, ] 35.918001 38.54878 35.918001
  - actual[3, ]   20.748909 34.27025 17.497403
  + expected[3, ] 24.161291 24.16129 24.161291
  - actual[4, ]   65.531947 57.33665 -6.608449
  + expected[4, ] 43.541565 43.54156 43.541565
  - actual[5, ]   18.860601 11.89760 20.730052
  + expected[5, ] 17.339630 17.33963 17.339630
  - actual[6, ]   42.446533 35.35054 45.603037
  + expected[6, ] 44.825964 44.82596 44.825964
  
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 20 ]
  Error:
  ! Test failures.
  Execution halted