Running ‘testthat.R’ [36s/44s]
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
  > 
  > require(testthat)
  Loading required package: testthat
  > require(SerolyzeR)
  Loading required package: SerolyzeR
  > 
  > test_check("SerolyzeR")
  Saving _problems/test-generate_report-43.R
  Saving _problems/test-generate_report-44.R
  Saving _problems/test-generate_report-46.R
  Saving _problems/test-generate_report-48.R
  Saving _problems/test-generate_report-53.R
  Saving _problems/test-generate_report-63.R
  Saving _problems/test-generate_report-64.R
  Saving _problems/test-generate_report-65.R
  Creating the output directory: '/tmp/RtmpLZOsSB/output'
  Reading Luminex data from: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/SerolyzeR/extdata/multiplate_reallife_reduced/IGG_CO_1_xponent.csv
  using format xPONENT
  [32m
  New plate object has been created with name: IGG_CO_1_xponent!
  [39m
  Processing plate 'IGG_CO_1_xponent'
  Reading Luminex data from: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/SerolyzeR/extdata/multiplate_reallife_reduced/IGG_CO_2_xponent.csv
  using format xPONENT
  [32m
  New plate object has been created with name: IGG_CO_2_xponent!
  [39m
  Processing plate 'IGG_CO_2_xponent'
  Reading Luminex data from: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/SerolyzeR/extdata/multiplate_reallife_reduced/IGG_CO_3_xponent.csv
  using format xPONENT
  [32m
  New plate object has been created with name: IGG_CO_3_xponent!
  [39m
  Processing plate 'IGG_CO_3_xponent'
  Extracting the raw MFI to the output dataframe
  Extracting the raw MFI to the output dataframe
  Extracting the raw MFI to the output dataframe
  Merged output saved to: /tmp/RtmpLZOsSB/merged_MFI_20251206_132022.csv
  Fitting the models and predicting RAU for each analyte
  Fitting the models and predicting RAU for each analyte
  Fitting the models and predicting RAU for each analyte
  Merged output saved to: /tmp/RtmpLZOsSB/merged_RAU_20251206_132022.csv
  Computing nMFI values for each analyte
  Computing nMFI values for each analyte
  Computing nMFI values for each analyte
  Merged output saved to: /tmp/RtmpLZOsSB/merged_nMFI_20251206_132022.csv
  ([31mWARNING[39m)
  Using less than five samples to fit the logistic model. For now, using the basic nplr method to fit the logistic model - should be modified in the futureInstance of the Model class fitted for analyte ' Spike_6P_IPP ': 
   - fitted with 2 parameters
   - using 2 samples
   - using log residuals (mfi):  TRUE 
   - using log dilution:  TRUE 
   - top asymptote: 100 
   - bottom asymptote: 50 
   - goodness of fit: 1 
   - weighted goodness of fit: 1 
  [1] -0.1  1.1
  [1] "Parsing file/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/SerolyzeR/extdata/external/Chul_IgG3_1.csv"
  [1] "Parsing successful"
  [1] "Parsing file/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/SerolyzeR/extdata/external/Chul_TotalIgG_2.csv"
  [1] "Parsing successful"
  [1] "Parsing file/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/SerolyzeR/extdata/external/New_Batch_14_20140513_082522.csv"
  [1] "Parsing successful"
  [1] "Parsing file/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/SerolyzeR/extdata/external/New_Batch_6_20160309_174224.csv"
  [1] "Parsing successful"
  [1] "Parsing file/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/SerolyzeR/extdata/external/pone.0187901.s001.csv"
  [1] "Parsing successful"
  Reading Luminex data from: non-existent-data.csv
  using format xPONENT
  Reading Luminex data from: non-existent-data.csv
  using format xPONENT
  Reading Luminex data from: non-existent-data.csv
  using format xPONENT
  Reading Luminex data from: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/SerolyzeR/extdata/CovidOISExPONTENT_CO.csv
  using format xPONENT
  [32m
  New plate object has been created with name: CovidOISExPONTENT_CO!
  [39m
  Reading Luminex data from: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/SerolyzeR/extdata/CovidOISExPONTENT_CO.csv
  using format xPONENT
  [32m
  New plate object has been created with name: CovidOISExPONTENT_CO!
  [39m
  Reading Luminex data from: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/SerolyzeR/extdata/CovidOISExPONTENT_CO.csv
  using format xPONENT
  [32m
  New plate object has been created with name: CovidOISExPONTENT_CO!
  [39m
  Reading Luminex data from: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/SerolyzeR/extdata/multiplate_reallife_reduced/IGG_CO_1_xponent.csv
  using format xPONENT
  [32m
  New plate object has been created with name: IGG_CO_1_xponent!
  [39m
  Processing plate 'IGG_CO_1_xponent'
  Reading Luminex data from: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/SerolyzeR/extdata/multiplate_reallife_reduced/IGG_CO_2_xponent.csv
  using format xPONENT
  [32m
  New plate object has been created with name: IGG_CO_2_xponent!
  [39m
  Processing plate 'IGG_CO_2_xponent'
  Reading Luminex data from: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/SerolyzeR/extdata/multiplate_reallife_reduced/IGG_CO_3_xponent.csv
  using format xPONENT
  [32m
  New plate object has been created with name: IGG_CO_3_xponent!
  [39m
  Processing plate 'IGG_CO_3_xponent'
  Extracting the raw MFI to the output dataframe
  Extracting the raw MFI to the output dataframe
  Extracting the raw MFI to the output dataframe
  Merged output saved to: /tmp/RtmpLZOsSB/merged_MFI_20251206_132041.csv
  Fitting the models and predicting RAU for each analyte
  Fitting the models and predicting RAU for each analyte
  Fitting the models and predicting RAU for each analyte
  Merged output saved to: /tmp/RtmpLZOsSB/merged_RAU_20251206_132041.csv
  Computing nMFI values for each analyte
  Computing nMFI values for each analyte
  Computing nMFI values for each analyte
  Merged output saved to: /tmp/RtmpLZOsSB/merged_nMFI_20251206_132041.csv
  Reading Luminex data from: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/SerolyzeR/extdata/multiplate_lite/CovidOISExPONTENT.csv
  using format xPONENT
  [32m
  New plate object has been created with name: CovidOISExPONTENT!
  [39m
  Processing plate 'CovidOISExPONTENT'
  Reading Luminex data from: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/SerolyzeR/extdata/multiplate_lite/CovidOISExPONTENT2.csv
  using format xPONENT
  [32m
  New plate object has been created with name: CovidOISExPONTENT2!
  [39m
  Processing plate 'CovidOISExPONTENT2'
  Extracting the raw MFI to the output dataframe
  Extracting the raw MFI to the output dataframe
  Merged output saved to: /tmp/RtmpLZOsSB/merged_MFI_20251206_132045.csv
  Fitting the models and predicting RAU for each analyte
  Fitting the models and predicting RAU for each analyte
  Merged output saved to: /tmp/RtmpLZOsSB/merged_RAU_20251206_132045.csv
  Computing nMFI values for each analyte
  Computing nMFI values for each analyte
  Merged output saved to: /tmp/RtmpLZOsSB/merged_nMFI_20251206_132045.csv
  Saving _problems/test-process-dir-134.R
  Reading Luminex data from: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/SerolyzeR/extdata/multiplate_reallife_reduced/IGG_CO_1_xponent.csv
  using format xPONENT
  [32m
  New plate object has been created with name: IGG_CO_1_xponent!
  [39m
  Processing plate 'IGG_CO_1_xponent'
  Reading Luminex data from: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/SerolyzeR/extdata/multiplate_reallife_reduced/IGG_CO_2_xponent.csv
  using format xPONENT
  [32m
  New plate object has been created with name: IGG_CO_2_xponent!
  [39m
  Processing plate 'IGG_CO_2_xponent'
  Reading Luminex data from: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/SerolyzeR/extdata/multiplate_reallife_reduced/IGG_CO_3_xponent.csv
  using format xPONENT
  [32m
  New plate object has been created with name: IGG_CO_3_xponent!
  [39m
  Processing plate 'IGG_CO_3_xponent'
  Extracting the raw MFI to the output dataframe
  Extracting the raw MFI to the output dataframe
  Extracting the raw MFI to the output dataframe
  Merged output saved to: /tmp/RtmpLZOsSB/merged_MFI_20251206_132047.csv
  Fitting the models and predicting RAU for each analyte
  Fitting the models and predicting RAU for each analyte
  Fitting the models and predicting RAU for each analyte
  Merged output saved to: /tmp/RtmpLZOsSB/merged_RAU_20251206_132047.csv
  Computing nMFI values for each analyte
  Computing nMFI values for each analyte
  Computing nMFI values for each analyte
  Merged output saved to: /tmp/RtmpLZOsSB/merged_nMFI_20251206_132047.csv
  Fitting the models and predicting RAU for each analyte
  Saving the computed RAU values to a CSV file located in: '/tmp/RtmpLZOsSB/output.csv'
  Fitting the models and predicting RAU for each analyte
  Saving the computed RAU values to a CSV file located in: '/tmp/RtmpLZOsSB/output.csv'
  Extracting the raw MFI to the output dataframe
  Saving the computed MFI values to a CSV file located in: '/tmp/RtmpLZOsSB/output.csv'
  Fitting the models and predicting RAU for each analyte
  Computing nMFI values for each analyte
  Saving the computed nMFI values to a CSV file located in: '/tmp/RtmpLZOsSB/output.csv'
  Computing nMFI values for each analyte
  Saving the computed nMFI values to a CSV file located in: '/tmp/RtmpLZOsSB/output.csv'
  Computing nMFI values for each analyte
  Computing nMFI values for each analyte
  Computing nMFI values for each analyte
  Computing nMFI values for each analyte
  Saving the computed nMFI values to a CSV file located in: '/tmp/RtmpLZOsSB/output.csv'
  Computing nMFI values for each analyte
  Saving the computed nMFI values to a CSV file located in: '/tmp/RtmpLZOsSB/output.csv'
  [ FAIL 9 | WARN 57 | SKIP 0 | PASS 422 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-generate_report.R:43:3'): Test generate_plate_report function ──
  Expected `generate_plate_report(plate, output_dir = tmp_dir)` not to throw any errors.
  Actually got a <packageNotFoundError> with message:
    there is no package called 'rmarkdown'
  ── Failure ('test-generate_report.R:44:3'): Test generate_plate_report function ──
  Expected `generate_plate_report(plate, output_dir = tmp_dir, filename = "test_report.html")` not to throw any errors.
  Actually got a <packageNotFoundError> with message:
    there is no package called 'rmarkdown'
  ── Failure ('test-generate_report.R:46:3'): Test generate_plate_report function ──
  Expected `generate_plate_report(...)` not to throw any errors.
  Actually got a <packageNotFoundError> with message:
    there is no package called 'rmarkdown'
  ── Failure ('test-generate_report.R:48:3'): Test generate_plate_report function ──
  Expected `generate_plate_report(...)` not to throw any errors.
  Actually got a <packageNotFoundError> with message:
    there is no package called 'rmarkdown'
  ── Failure ('test-generate_report.R:53:3'): Test generate_plate_report function ──
  Expected `generate_plate_report(...)` not to throw any errors.
  Actually got a <packageNotFoundError> with message:
    there is no package called 'rmarkdown'
  ── Failure ('test-generate_report.R:63:3'): Test generate_levey_jennings_report function ──
  Expected `generate_levey_jennings_report(...)` not to throw any errors.
  Actually got a <packageNotFoundError> with message:
    there is no package called 'rmarkdown'
  ── Failure ('test-generate_report.R:64:3'): Test generate_levey_jennings_report function ──
  Expected `generate_levey_jennings_report(...)` not to throw any errors.
  Actually got a <packageNotFoundError> with message:
    there is no package called 'rmarkdown'
  ── Failure ('test-generate_report.R:65:3'): Test generate_levey_jennings_report function ──
  Expected `generate_levey_jennings_report(...)` not to throw any errors.
  Actually got a <packageNotFoundError> with message:
    there is no package called 'rmarkdown'
  ── Failure ('test-process-dir.R:129:3'): Test processing a directory with a single plate ──
  Expected `capture.output(...)` not to throw any errors.
  Actually got a <packageNotFoundError> with message:
    there is no package called 'rmarkdown'
  
  [ FAIL 9 | WARN 57 | SKIP 0 | PASS 422 ]
  Error:
  ! Test failures.
  Execution halted