CRAN Package Check Results for Package PvSTATEM

Last updated on 2024-12-26 07:51:13 CET.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-clang	0.1.2	9.78	146.21	155.99	ERROR
r-devel-linux-x86_64-debian-gcc	0.1.2	6.93	100.23	107.16	ERROR
r-devel-linux-x86_64-fedora-clang	0.1.2			266.35	OK
r-devel-windows-x86_64	0.1.2	13.00	166.00	179.00	OK
r-patched-linux-x86_64	0.1.2	10.89	140.40	151.29	ERROR
r-release-linux-x86_64	0.1.2	10.85	138.86	149.71	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	13.00	160.00	173.00	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	199.00	215.00	OK

Additional issues

rlibro

Check Details

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’ [48s/64s] 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/RtmpEv4Vmz/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/RtmpEv4Vmz/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/RtmpEv4Vmz/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/RtmpEv4Vmz/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/RtmpEv4Vmz/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/RtmpEv4Vmz/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/RtmpEv4Vmz/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’ [30s/41s] 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/RtmpJVfZjK/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/RtmpJVfZjK/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/RtmpJVfZjK/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/RtmpJVfZjK/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/RtmpJVfZjK/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/RtmpJVfZjK/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/RtmpJVfZjK/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/59s] 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/Rtmpn9XKJc/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/Rtmpn9XKJc/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/Rtmpn9XKJc/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/Rtmpn9XKJc/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/Rtmpn9XKJc/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/Rtmpn9XKJc/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/Rtmpn9XKJc/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’ [46s/57s] 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/RtmpbQ3Jlh/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/RtmpbQ3Jlh/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/RtmpbQ3Jlh/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/RtmpbQ3Jlh/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/RtmpbQ3Jlh/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/RtmpbQ3Jlh/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/RtmpbQ3Jlh/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