Last updated on 2024-12-22 05:49:25 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.2 | 10.90 | 145.99 | 156.89 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.1.2 | 6.64 | 103.58 | 110.22 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.1.2 | 266.35 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 0.1.2 | 271.45 | OK | |||
| r-devel-windows-x86_64 | 0.1.2 | 14.00 | 165.00 | 179.00 | OK | |
| r-patched-linux-x86_64 | 0.1.2 | 9.44 | 139.69 | 149.13 | ERROR | |
| r-release-linux-x86_64 | 0.1.2 | 10.49 | 140.27 | 150.76 | ERROR | |
| r-release-macos-arm64 | 0.1.2 | 82.00 | OK | |||
| r-release-macos-x86_64 | 0.1.2 | 135.00 | OK | |||
| r-release-windows-x86_64 | 0.1.2 | 16.00 | 165.00 | 181.00 | OK | |
| r-oldrel-macos-arm64 | 0.1.2 | 90.00 | OK | |||
| r-oldrel-macos-x86_64 | 0.1.2 | 149.00 | OK | |||
| r-oldrel-windows-x86_64 | 0.1.2 | 16.00 | 202.00 | 218.00 | OK |
Version: 0.1.2
Check: examples
Result: ERROR
Running examples in ‘PvSTATEM-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: generate_plate_report
> ### Title: Generate a report for a plate.
> ### Aliases: generate_plate_report
>
> ### ** Examples
>
>
> plate_file <- system.file("extdata", "CovidOISExPONTENT_CO_reduced.csv", package = "PvSTATEM")
> # a plate file with reduced number of analytes to speed up the computation
> layout_file <- system.file("extdata", "CovidOISExPONTENT_CO_layout.xlsx", package = "PvSTATEM")
> note <- "This is a test report.\n**Author**: Jane Doe \n**Tester**: John Doe"
>
> plate <- read_luminex_data(plate_file, layout_file, verbose = FALSE)
> example_dir <- tempdir(check = TRUE) # a temporary directory
> generate_plate_report(plate,
+ output_dir = example_dir,
+ counts_lower_threshold = 40,
+ counts_higher_threshold = 50,
+ additional_notes = note
+ )
Generating report...This will take approximately 30 seconds.
Error in file(con, "w") : cannot open the connection
Calls: generate_plate_report ... <Anonymous> -> <Anonymous> -> write_utf8 -> writeLines -> file
In addition: Warning message:
In file(con, "w") :
cannot open file 'plate_report_template.knit.md': Read-only file system
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 0.1.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [47s/63s]
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: '/home/hornik/tmp/scratch/Rtmp4rsV4i/output'
(<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] "Parsing file/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/PvSTATEM/extdata/external/Chul_IgG3_1.csv"
[1] "Parsing successful"
[1] "Parsing file/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/PvSTATEM/extdata/external/Chul_TotalIgG_2.csv"
[1] "Parsing successful"
[1] "Parsing file/home/hornik/tmp/R.check/r-devel-clang/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-clang/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-clang/Work/build/Packages/PvSTATEM/extdata/external/pone.0187901.s001.csv"
[1] "Parsing successful"
Reading Luminex data from: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/PvSTATEM/extdata/CovidOISExPONTENT_CO.csv
using format xPONENT
(<1b>[31mWARNING<1b>[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.
<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-clang/Work/build/Packages/PvSTATEM/extdata/CovidOISExPONTENT_CO.csv
using format xPONENT
(<1b>[31mWARNING<1b>[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.
<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-clang/Work/build/Packages/PvSTATEM/extdata/CovidOISExPONTENT_CO.csv
using format xPONENT
(<1b>[31mWARNING<1b>[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.
<1b>[32m
New plate object has been created with name: CovidOISExPONTENT_CO!
<1b>[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: '/home/hornik/tmp/scratch/Rtmp4rsV4i/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: '/home/hornik/tmp/scratch/Rtmp4rsV4i/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: '/home/hornik/tmp/scratch/Rtmp4rsV4i/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: '/home/hornik/tmp/scratch/Rtmp4rsV4i/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: '/home/hornik/tmp/scratch/Rtmp4rsV4i/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: '/home/hornik/tmp/scratch/Rtmp4rsV4i/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
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.1.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [31s/40s]
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/Rtmpyem96A/output'
(<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] "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
(<1b>[31mWARNING<1b>[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.
<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/PvSTATEM/extdata/CovidOISExPONTENT_CO.csv
using format xPONENT
(<1b>[31mWARNING<1b>[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.
<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/PvSTATEM/extdata/CovidOISExPONTENT_CO.csv
using format xPONENT
(<1b>[31mWARNING<1b>[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.
<1b>[32m
New plate object has been created with name: CovidOISExPONTENT_CO!
<1b>[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/Rtmpyem96A/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/Rtmpyem96A/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/Rtmpyem96A/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/Rtmpyem96A/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/Rtmpyem96A/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/Rtmpyem96A/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
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.1.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [47s/55s]
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: '/home/hornik/tmp/scratch/RtmpcXOTCh/output'
(<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] "Parsing file/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PvSTATEM/extdata/external/Chul_IgG3_1.csv"
[1] "Parsing successful"
[1] "Parsing file/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PvSTATEM/extdata/external/Chul_TotalIgG_2.csv"
[1] "Parsing successful"
[1] "Parsing file/home/hornik/tmp/R.check/r-patched-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-patched-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-patched-gcc/Work/build/Packages/PvSTATEM/extdata/external/pone.0187901.s001.csv"
[1] "Parsing successful"
Reading Luminex data from: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PvSTATEM/extdata/CovidOISExPONTENT_CO.csv
using format xPONENT
(<1b>[31mWARNING<1b>[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.
<1b>[32m
New plate object has been created with name: CovidOISExPONTENT_CO!
<1b>[39m
Reading Luminex data from: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PvSTATEM/extdata/CovidOISExPONTENT_CO.csv
using format xPONENT
(<1b>[31mWARNING<1b>[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.
<1b>[32m
New plate object has been created with name: CovidOISExPONTENT_CO!
<1b>[39m
Reading Luminex data from: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PvSTATEM/extdata/CovidOISExPONTENT_CO.csv
using format xPONENT
(<1b>[31mWARNING<1b>[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.
<1b>[32m
New plate object has been created with name: CovidOISExPONTENT_CO!
<1b>[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: '/home/hornik/tmp/scratch/RtmpcXOTCh/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: '/home/hornik/tmp/scratch/RtmpcXOTCh/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: '/home/hornik/tmp/scratch/RtmpcXOTCh/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: '/home/hornik/tmp/scratch/RtmpcXOTCh/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: '/home/hornik/tmp/scratch/RtmpcXOTCh/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: '/home/hornik/tmp/scratch/RtmpcXOTCh/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
Flavor: r-patched-linux-x86_64
Version: 0.1.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [47s/55s]
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: '/home/hornik/tmp/scratch/RtmpHGL7ld/output'
(<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] "Parsing file/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/PvSTATEM/extdata/external/Chul_IgG3_1.csv"
[1] "Parsing successful"
[1] "Parsing file/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/PvSTATEM/extdata/external/Chul_TotalIgG_2.csv"
[1] "Parsing successful"
[1] "Parsing file/home/hornik/tmp/R.check/r-release-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-release-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-release-gcc/Work/build/Packages/PvSTATEM/extdata/external/pone.0187901.s001.csv"
[1] "Parsing successful"
Reading Luminex data from: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/PvSTATEM/extdata/CovidOISExPONTENT_CO.csv
using format xPONENT
(<1b>[31mWARNING<1b>[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.
<1b>[32m
New plate object has been created with name: CovidOISExPONTENT_CO!
<1b>[39m
Reading Luminex data from: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/PvSTATEM/extdata/CovidOISExPONTENT_CO.csv
using format xPONENT
(<1b>[31mWARNING<1b>[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.
<1b>[32m
New plate object has been created with name: CovidOISExPONTENT_CO!
<1b>[39m
Reading Luminex data from: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/PvSTATEM/extdata/CovidOISExPONTENT_CO.csv
using format xPONENT
(<1b>[31mWARNING<1b>[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.
<1b>[32m
New plate object has been created with name: CovidOISExPONTENT_CO!
<1b>[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: '/home/hornik/tmp/scratch/RtmpHGL7ld/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: '/home/hornik/tmp/scratch/RtmpHGL7ld/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: '/home/hornik/tmp/scratch/RtmpHGL7ld/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: '/home/hornik/tmp/scratch/RtmpHGL7ld/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: '/home/hornik/tmp/scratch/RtmpHGL7ld/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: '/home/hornik/tmp/scratch/RtmpHGL7ld/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
Flavor: r-release-linux-x86_64