Last updated on 2025-12-07 04:50:09 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.3.1 | 13.69 | 319.34 | 333.03 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.3.1 | 8.40 | 103.12 | 111.52 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.3.1 | 54.00 | 462.11 | 516.11 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.3.1 | 29.00 | 470.95 | 499.95 | OK | |
| r-devel-windows-x86_64 | 1.3.1 | 16.00 | 291.00 | 307.00 | OK | |
| r-patched-linux-x86_64 | 1.3.1 | 14.43 | 298.17 | 312.60 | OK | |
| r-release-linux-x86_64 | 1.3.1 | 11.84 | 301.21 | 313.05 | OK | |
| r-release-macos-arm64 | 1.3.1 | OK | ||||
| r-release-macos-x86_64 | 1.3.1 | 15.00 | 352.00 | 367.00 | OK | |
| r-release-windows-x86_64 | 1.3.1 | 17.00 | 289.00 | 306.00 | OK | |
| r-oldrel-macos-arm64 | 1.3.1 | OK | ||||
| r-oldrel-macos-x86_64 | 1.3.1 | 20.00 | 329.00 | 349.00 | OK | |
| r-oldrel-windows-x86_64 | 1.3.1 | 24.00 | 390.00 | 414.00 | OK |
Version: 1.3.1
Check: package dependencies
Result: WARN
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'
VignetteBuilder package required for checking but not installed: ‘knitr’
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.3.1
Check: examples
Result: ERROR
Running examples in ‘SerolyzeR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: generate_levey_jennings_report
> ### Title: Generate a Levey-Jennings Report for Multiple Plates.
> ### Aliases: generate_levey_jennings_report
>
> ### ** Examples
>
> output_dir <- tempdir(check = TRUE)
>
> dir_with_luminex_files <- system.file("extdata", "multiplate_lite",
+ package = "SerolyzeR", mustWork = TRUE
+ )
> list_of_plates <- process_dir(dir_with_luminex_files,
+ return_plates = TRUE, format = "xPONENT", output_dir = output_dir
+ )
Reading Luminex data from: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/SerolyzeR/extdata/multiplate_lite/CovidOISExPONTENT.csv
using format xPONENT
Failed to extract from BatchMetadata: BatchStartTime not found in BatchMetadata.
Failed to extract from raw header: BatchStartTime not found in raw header.
Fallback datetime successfully extracted from ProgramMetadata.
Could not parse datetime string using default datetime format. Trying other possibilies.
Successfully parsed datetime string using order: mdY IM p
<1b>[32m
New plate object has been created with name: CovidOISExPONTENT!
<1b>[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
Failed to extract from BatchMetadata: BatchStartTime not found in BatchMetadata.
Failed to extract from raw header: BatchStartTime not found in raw header.
Fallback datetime successfully extracted from ProgramMetadata.
Could not parse datetime string using default datetime format. Trying other possibilies.
Successfully parsed datetime string using order: mdY IM p
<1b>[32m
New plate object has been created with name: CovidOISExPONTENT2!
<1b>[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/RtmpXA3JuH/merged_MFI_20251206_132009.csv
Fitting the models and predicting RAU for each analyte
Fitting the models and predicting RAU for each analyte
Merged output saved to: /tmp/RtmpXA3JuH/merged_RAU_20251206_132009.csv
Computing nMFI values for each analyte
Computing nMFI values for each analyte
Merged output saved to: /tmp/RtmpXA3JuH/merged_nMFI_20251206_132009.csv
> note <- "This is a Levey-Jennings report.\n**Author**: Jane Doe \n**Tester**: John Doe"
>
> generate_levey_jennings_report(
+ list_of_plates = list_of_plates,
+ report_title = "QC Report",
+ dilutions = c("1/100", "1/200"),
+ output_dir = tempdir(),
+ additional_notes = note
+ )
Generating report... For large reports with more than 30 plates, this will take a few minutes.
Error in loadNamespace(x) : there is no package called ‘rmarkdown’
Calls: generate_levey_jennings_report ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.3.1
Check: tests
Result: ERROR
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
<1b>[32m
New plate object has been created with name: IGG_CO_1_xponent!
<1b>[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
<1b>[32m
New plate object has been created with name: IGG_CO_2_xponent!
<1b>[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
<1b>[32m
New plate object has been created with name: IGG_CO_3_xponent!
<1b>[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
(<1b>[31mWARNING<1b>[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
<1b>[32m
New plate object has been created with name: CovidOISExPONTENT_CO!
<1b>[39m
Reading Luminex data from: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/SerolyzeR/extdata/CovidOISExPONTENT_CO.csv
using format xPONENT
<1b>[32m
New plate object has been created with name: CovidOISExPONTENT_CO!
<1b>[39m
Reading Luminex data from: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/SerolyzeR/extdata/CovidOISExPONTENT_CO.csv
using format xPONENT
<1b>[32m
New plate object has been created with name: CovidOISExPONTENT_CO!
<1b>[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
<1b>[32m
New plate object has been created with name: IGG_CO_1_xponent!
<1b>[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
<1b>[32m
New plate object has been created with name: IGG_CO_2_xponent!
<1b>[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
<1b>[32m
New plate object has been created with name: IGG_CO_3_xponent!
<1b>[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
<1b>[32m
New plate object has been created with name: CovidOISExPONTENT!
<1b>[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
<1b>[32m
New plate object has been created with name: CovidOISExPONTENT2!
<1b>[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
<1b>[32m
New plate object has been created with name: IGG_CO_1_xponent!
<1b>[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
<1b>[32m
New plate object has been created with name: IGG_CO_2_xponent!
<1b>[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
<1b>[32m
New plate object has been created with name: IGG_CO_3_xponent!
<1b>[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
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.3.1
Check: package vignettes
Result: NOTE
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Flavor: r-devel-linux-x86_64-debian-gcc