Running ‘testthat.R’ [64s/170s]
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(normfluodbf)
  
  == Welcome to normfluodbf - Developed by Tingwei Adeck and Tesla Adeck (Jesus Followers) ===========================================================================
  If you find this package useful, please leave a star:
     https://github.com/AlphaPrime7/normfluodbf
  
  If you want to support me in my learning and development journey:
   https://www.buymeacoffee.com/tingweiadeck
  
  If you encounter a bug or want to request an enhancement please file an issue at:
     https://github.com/AlphaPrime7/normfluodbf/issues
  
  
  Thank you for using normfluodbf!
  
  
  Attaching package: 'normfluodbf'
  
  The following object is masked from 'package:stats':
  
      step
  
  The following object is masked from 'package:utils':
  
      demo
  
  The following object is masked from 'package:base':
  
      subset
  
  > 
  > test_check("normfluodbf")
  Crikee, some values in your original data violate thresholds 🐷 🐫
  [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
  [[1]]
  [1] "C9"
  
  Crikee, some values in your original data violate thresholds 🐷 🐫
  [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
  [[1]]
  [1] "C9"
  
  Crikee, some values in your original data violate thresholds 🐷 🐫
  [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
  [[1]]
  [1] "C9"
  
  Crikee, some values in your original data violate thresholds 🐷 🐫
  [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
  [[1]]
  [1] "C9"
  
  Crikee, some values in your original data violate thresholds 🐷 🐫
  [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
  [[1]]
  [1] "27"
  
  Crikee, some values in your original data violate thresholds 🐷 🐫
  Crikee, some values in your original data violate thresholds 🐷 🐫
  [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
  [[1]]
  [1] "A01"
  
  [[2]]
  [1] "A02"
  
  [[3]]
  [1] "A03"
  
  [[4]]
  [1] "B01"
  
  [[5]]
  [1] "B02"
  
  [[6]]
  [1] "B03"
  
  [[7]]
  [1] "C01"
  
  [[8]]
  [1] "C02"
  
  [[9]]
  [1] "C03"
  
  Crikee, some values in your original data violate thresholds 🐷 🐫
  [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
  [[1]]
  [1] "A01"
  
  [[2]]
  [1] "A02"
  
  [[3]]
  [1] "A03"
  
  [[4]]
  [1] "B01"
  
  [[5]]
  [1] "B02"
  
  [[6]]
  [1] "B03"
  
  [[7]]
  [1] "C01"
  
  [[8]]
  [1] "C02"
  
  [[9]]
  [1] "C03"
  
  The upload_data step needs to be completed
  Initializing Data ...
  [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
  [[1]]
  [1] "C9"
  
  Data Initialized step DONE...
  DONE (2 seconds)
  The upload_data step needs to be completed
  Initializing Data ...
  [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
  [[1]]
  [1] "A01"
  
  [[2]]
  [1] "A02"
  
  [[3]]
  [1] "A03"
  
  [[4]]
  [1] "B01"
  
  [[5]]
  [1] "B02"
  
  [[6]]
  [1] "B03"
  
  [[7]]
  [1] "C01"
  
  [[8]]
  [1] "C02"
  
  [[9]]
  [1] "C03"
  
  Data Initialized step DONE...
  DONE (0 seconds)
  The upload_data step needs to be completed
  Initializing Data ...
  [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
  [[1]]
  [1] "C9"
  
  Data Initialized step DONE...
  DONE (2 seconds)
  [1] "Steps left:4"
  [1] "Next step function: format_plate_data"
  Formating Plate Data ...
  Data Formatted step DONE...
  DONE (0 seconds)
  [1] "Next step function: normalize_by_well"
  Normalizing Data ...
  Data Normalized step DONE...
  DONE (0 seconds)
  [1] "Next step function: modify_plate_data"
  [1] "Next step function: analyze_ready"
  Process complete
  The upload_data step needs to be completed
  Initializing Data ...
  [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
  [[1]]
  [1] "C9"
  
  Data Initialized step DONE...
  DONE (2 seconds)
  [1] "Steps left:4"
  [1] "Next step function: format_plate_data"
  Formating Plate Data ...
  Data Formatted step DONE...
  DONE (0 seconds)
  [1] "Next step function: normalize_by_well"
  Normalizing Data ...
  Data Normalized step DONE...
  DONE (0 seconds)
  [1] "Next step function: modify_plate_data"
  [1] "Next step function: analyze_ready"
  Process complete
  List of 9
   $ plate_meta  : tibble [96 x 5] (S3: tbl_df/tbl/data.frame)
    ..$ well    : chr [1:96] "A1" "A2" "A3" "A4" ...
    ..$ sample  : logi [1:96] NA NA NA NA NA NA ...
    ..$ well_row: Factor w/ 8 levels "A","B","C","D",..: 1 1 1 1 1 1 1 1 1 1 ...
    ..$ well_col: Factor w/ 12 levels "1","2","3","4",..: 1 2 3 4 5 6 7 8 9 10 ...
    ..$ used    : logi [1:96] FALSE FALSE FALSE FALSE FALSE FALSE ...
   $ plate_data  : md_nrmf_ [1,500 x 8] (S3: mod_normfluodbf_data/tbl_df/tbl/data.frame)
    ..$ well         : chr [1:1500] "A1" "A1" "A1" "A1" ...
    ..$ well_row     : chr [1:1500] "A" "A" "A" "A" ...
    ..$ well_col     : Factor w/ 12 levels "1","10","11",..: 1 1 1 1 1 1 1 1 1 1 ...
    ..$ used         : logi [1:1500] TRUE TRUE TRUE TRUE TRUE TRUE ...
    ..$ Cycle_Number : num [1:1500] 1 2 3 4 5 6 7 8 9 10 ...
    ..$ fluor_values : num [1:1500] 1 0.872 0.788 0.715 0.731 ...
    ..$ outlier      : logi [1:1500] FALSE FALSE FALSE FALSE FALSE FALSE ...
    ..$ outlier_color: chr [1:1500] "#EE3B3B" "#EE3B3B" "#EE3B3B" "#EE3B3B" ...
   $ steps       : num 0
   $ status      : num 5
   $ dirty       : logi TRUE
   $ version     : chr "2.0.0"
   $ params      :List of 3
    ..$ GENERAL   :List of 5
    .. ..$ X_VAR_ONE      : chr "Time"
    .. ..$ X_VAR_TWO      : chr "Cycle_Number"
    .. ..$ Y_VAR          : chr "FLUORESCENCE"
    .. ..$ X_VAR_ONE_LABEL: chr "TIME"
    .. ..$ X_VAR_TWO_LABEL: chr "CYCLE NUMBER"
    ..$ THRESHOLDS:List of 4
    .. ..$ MAX_FLUOR         : num 65536
    .. ..$ MIN_FLUOR         : num 128
    .. ..$ CUTOFF_UPPER_LIMIT: num 32768
    .. ..$ CUTOFF_LOWER_LIMIT: num 4096
    ..$ COLORS    :List of 4
    .. ..$ POS    : chr "#7FFFD4"
    .. ..$ TEST   : chr "#0000CD"
    .. ..$ NEG    : chr "#EE3B3B"
    .. ..$ NEUTRAL: chr "#BF3EFF"
   $ dataset_name: chr "dat_1"
   $ data_summary: chr "36 Wells Used"
   - attr(*, "class")= chr [1:3] "96well_plate" "normfluodbf_plate" "list"
  The upload_data step needs to be completed
  Initializing Data ...
  [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
  [[1]]
  [1] "C9"
  
  Data Initialized step DONE...
  DONE (2 seconds)
  [1] "Steps left:4"
  [1] "Next step function: format_plate_data"
  Formating Plate Data ...
  Data Formatted step DONE...
  DONE (0 seconds)
  [1] "Next step function: normalize_by_well"
  Normalizing Data ...
  Data Normalized step DONE...
  DONE (0 seconds)
  [1] "Next step function: modify_plate_data"
  [1] "Next step function: analyze_ready"
  Process complete
  The upload_data step needs to be completed
  Initializing Data ...
  [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
  [[1]]
  [1] "C9"
  
  Data Initialized step DONE...
  DONE (2 seconds)
  [1] "Steps left:4"
  [1] "Next step function: format_plate_data"
  Formating Plate Data ...
  Data Formatted step DONE...
  DONE (0 seconds)
  [1] "Next step function: normalize_by_well"
  Normalizing Data ...
  Data Normalized step DONE...
  DONE (0 seconds)
  [1] "Next step function: modify_plate_data"
  [1] "Next step function: analyze_ready"
  Process complete
  Crikee, some values in your original data violate thresholds 🐷 🐫
  [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
  [[1]]
  [1] "C9"
  
  The upload_data step needs to be completed
  Initializing Data ...
  [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
  [[1]]
  [1] "C9"
  
  Data Initialized step DONE...
  DONE (2 seconds)
  [1] "Steps left:5"
  [1] "Next step function: format_plate_data"
  Formating Plate Data ...
  Data Formatted step DONE...
  DONE (0 seconds)
  [1] "Next step function: remove_outliers"
  [1] "Next step function: normalize_by_well"
  Normalizing Data ...
  Data Normalized step DONE...
  DONE (0 seconds)
  [1] "Next step function: modify_plate_data"
  [1] "Next step function: analyze_ready"
  Process complete
  [ FAIL 1 | WARN 617 | SKIP 0 | PASS 23 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_plot.R:21:3'): test normfluodbf plot ─────────────────────────
  "gg" (`actual`) not equal to class(plt.obj)[1] (`expected`).
  
  `actual`:   "gg"             
  `expected`: "ggplot2::ggplot"
  
  [ FAIL 1 | WARN 617 | SKIP 0 | PASS 23 ]
  Error: Test failures
  Execution halted