Running ‘testthat.R’ [31s/37s]
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(PvSTATEM)
  Loading required package: PvSTATEM
  > 
  > test_check("PvSTATEM")
  Creating the output directory: '/tmp/Rtmp39VFms/output'
  ([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] "Parsing file/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/PvSTATEM/extdata/external/Chul_IgG3_1.csv"
  [1] "Parsing successful"
  [1] "Parsing file/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/PvSTATEM/extdata/external/Chul_TotalIgG_2.csv"
  [1] "Parsing successful"
  [1] "Parsing file/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/PvSTATEM/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/PvSTATEM/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/PvSTATEM/extdata/external/pone.0187901.s001.csv"
  [1] "Parsing successful"
  Reading Luminex data from: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/PvSTATEM/extdata/CovidOISExPONTENT_CO.csv
  using format xPONENT
  ([31mWARNING[39m)
  Number of layout fields is higher than the number of samples. Please check the layout file. Using only first 49 dilutions from the layout file. 
  [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/PvSTATEM/extdata/CovidOISExPONTENT_CO.csv
  using format xPONENT
  ([31mWARNING[39m)
  Number of layout fields is higher than the number of samples. Please check the layout file. Using only first 49 dilutions from the layout file. 
  [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/PvSTATEM/extdata/CovidOISExPONTENT_CO.csv
  using format xPONENT
  ([31mWARNING[39m)
  Number of layout fields is higher than the number of samples. Please check the layout file. Using only first 49 dilutions from the layout file. 
  [32m
  New plate object has been created with name: CovidOISExPONTENT_CO!
  [39m
  Fitting the models and predicting RAU for each analyte
  Adding the raw MFI values to the output dataframe
  Saving the computed RAU values to a CSV file located in: '/tmp/Rtmp39VFms/output.csv'
  Fitting the models and predicting RAU for each analyte
  Adding the raw MFI values to the output dataframe
  Saving the computed RAU values to a CSV file located in: '/tmp/Rtmp39VFms/output.csv'
  Fitting the models and predicting RAU for each analyte
  Computing nMFI values for each analyte
  Adding the raw MFI values to the output dataframe
  Saving the computed nMFI values to a CSV file located in: '/tmp/Rtmp39VFms/output.csv'
  Computing nMFI values for each analyte
  Adding the raw MFI values to the output dataframe
  Saving the computed nMFI values to a CSV file located in: '/tmp/Rtmp39VFms/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/Rtmp39VFms/output.csv'
  Computing nMFI values for each analyte
  Adding the raw MFI values to the output dataframe
  Saving the computed nMFI values to a CSV file located in: '/tmp/Rtmp39VFms/output.csv'
  [ FAIL 7 | WARN 12 | SKIP 9 | PASS 172 ]
  
  ══ Skipped tests (9) ═══════════════════════════════════════════════════════════
  • empty test (9): 'test-get-nmfi.R:3:1', 'test-integration.R:55:1',
    'test-plots_mfi.R:27:1', 'test-plots_plate.R:38:1',
    'test-plots_plate.R:57:1', 'test-process-plate.R:70:1',
    'test-standard_curve.R:27:1', 'test-standard_curve.R:32:1',
    'test-standard_curve.R:37:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-generate_report.R:33:3'): Test generate_plate_report function ──
  Expected `generate_plate_report(plate, output_dir = tmp_dir)` to run without any errors.
  ℹ Actually got a <simpleError> with text:
    cannot open the connection
  ── Failure ('test-generate_report.R:34:3'): Test generate_plate_report function ──
  Expected `generate_plate_report(plate, output_dir = tmp_dir, filename = "test_report.html")` to run without any errors.
  ℹ Actually got a <simpleError> with text:
    cannot open the connection
  ── Failure ('test-generate_report.R:36:3'): Test generate_plate_report function ──
  Expected `generate_plate_report(...)` to run without any errors.
  ℹ Actually got a <simpleError> with text:
    cannot open the connection
  ── Failure ('test-generate_report.R:38:3'): Test generate_plate_report function ──
  Expected `generate_plate_report(...)` to run without any errors.
  ℹ Actually got a <simpleError> with text:
    cannot open the connection
  ── Failure ('test-generate_report.R:43:3'): Test generate_plate_report function ──
  Expected `generate_plate_report(...)` to run without any errors.
  ℹ Actually got a <simpleError> with text:
    cannot open the connection
  ── Failure ('test-generate_report.R:53:3'): Test generate_levey_jennings_report function ──
  Expected `generate_levey_jennings_report(list(plate), output_dir = tmp_dir)` to run without any errors.
  ℹ Actually got a <simpleError> with text:
    cannot open the connection
  ── Failure ('test-generate_report.R:54:3'): Test generate_levey_jennings_report function ──
  Expected `generate_levey_jennings_report(...)` to run without any errors.
  ℹ Actually got a <simpleError> with text:
    cannot open the connection
  
  [ FAIL 7 | WARN 12 | SKIP 9 | PASS 172 ]
  Error: Test failures
  Execution halted