• using R Under development (unstable) (2024-12-18 r87448)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 19.1.5 (1)     Debian flang-new version 19.1.5 (1)
• running under: Debian GNU/Linux trixie/sid
• using session charset: UTF-8
• checking for file ‘PvSTATEM/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘PvSTATEM’ version ‘0.1.2’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking serialization versions ... OK
• checking whether package ‘PvSTATEM’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... [2s/2s] OK
• checking whether the package can be loaded with stated dependencies ... [2s/3s] OK
• checking whether the package can be unloaded cleanly ... [2s/2s] OK
• checking whether the namespace can be loaded with stated dependencies ... [1s/2s] OK
• checking whether the namespace can be unloaded cleanly ... [2s/3s] OK
• checking loading without being on the library search path ... [2s/3s] OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [14s/17s] OK
• checking Rd files ... [1s/1s] OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [11s/16s] 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
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [48s/63s] 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'   ( [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-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   ( [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-clang/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-clang/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: '/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
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [25s/32s] OK
• checking PDF version of manual ... [6s/8s] OK
• checking HTML version of manual ... [2s/4s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 2 ERRORs