* using log directory 'd:/Rcompile/CRANpkg/local/4.4/normfluodbf.Rcheck' * using R version 4.4.3 (2025-02-28 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'normfluodbf/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'normfluodbf' version '2.0.0' * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'normfluodbf' can be installed ... OK * checking installed package size ... OK * checking package directory ... 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 ... [3s] OK * checking whether the package can be loaded with stated dependencies ... [3s] OK * checking whether the package can be unloaded cleanly ... [3s] OK * checking whether the namespace can be loaded with stated dependencies ... [3s] OK * checking whether the namespace can be unloaded cleanly ... [4s] OK * checking loading without being on the library search path ... [3s] OK * checking whether startup messages can be suppressed ... [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 ... [29s] OK * checking Rd files ... [2s] OK * checking Rd metadata ... 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 contents of 'data' directory ... OK * checking data for non-ASCII characters ... [1s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... [14s] OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... [41s] ERROR Running 'testthat.R' [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 > > library(testthat) > library(normfluodbf) == Welcome to normfluodbf - Developed by Tingwei Adeck and Tesla Adeck (Jesus Followers) =========================================================================== If you find this package useful, please leave a star: https://github.com/AlphaPrime7/normfluodbf If you want to support me in my learning and development journey: https://www.buymeacoffee.com/tingweiadeck If you encounter a bug or want to request an enhancement please file an issue at: https://github.com/AlphaPrime7/normfluodbf/issues Thank you for using normfluodbf! Attaching package: 'normfluodbf' The following object is masked from 'package:stats': step The following object is masked from 'package:utils': demo The following object is masked from 'package:base': subset > > test_check("normfluodbf") Crikee, some values in your original data violate thresholds 🐷 🐫 [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)" [[1]] [1] "C9" Crikee, some values in your original data violate thresholds 🐷 🐫 [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)" [[1]] [1] "C9" Crikee, some values in your original data violate thresholds 🐷 🐫 [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)" [[1]] [1] "C9" Crikee, some values in your original data violate thresholds 🐷 🐫 [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)" [[1]] [1] "C9" Crikee, some values in your original data violate thresholds 🐷 🐫 [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)" [[1]] [1] "27" Crikee, some values in your original data violate thresholds 🐷 🐫 Crikee, some values in your original data violate thresholds 🐷 🐫 [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)" [[1]] [1] "A01" [[2]] [1] "A02" [[3]] [1] "A03" [[4]] [1] "B01" [[5]] [1] "B02" [[6]] [1] "B03" [[7]] [1] "C01" [[8]] [1] "C02" [[9]] [1] "C03" Crikee, some values in your original data violate thresholds 🐷 🐫 [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)" [[1]] [1] "A01" [[2]] [1] "A02" [[3]] [1] "A03" [[4]] [1] "B01" [[5]] [1] "B02" [[6]] [1] "B03" [[7]] [1] "C01" [[8]] [1] "C02" [[9]] [1] "C03" The upload_data step needs to be completed Initializing Data ... [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)" [[1]] [1] "C9" Data Initialized step DONE... DONE (1 seconds) The upload_data step needs to be completed Initializing Data ... [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)" [[1]] [1] "A01" [[2]] [1] "A02" [[3]] [1] "A03" [[4]] [1] "B01" [[5]] [1] "B02" [[6]] [1] "B03" [[7]] [1] "C01" [[8]] [1] "C02" [[9]] [1] "C03" Data Initialized step DONE... DONE (0 seconds) The upload_data step needs to be completed Initializing Data ... [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)" [[1]] [1] "C9" Data Initialized step DONE... DONE (1 seconds) [1] "Steps left:4" [1] "Next step function: format_plate_data" Formating Plate Data ... Data Formatted step DONE... DONE (0 seconds) [1] "Next step function: normalize_by_well" Normalizing Data ... Data Normalized step DONE... DONE (0 seconds) [1] "Next step function: modify_plate_data" [1] "Next step function: analyze_ready" Process complete The upload_data step needs to be completed Initializing Data ... [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)" [[1]] [1] "C9" Data Initialized step DONE... DONE (1 seconds) [1] "Steps left:4" [1] "Next step function: format_plate_data" Formating Plate Data ... Data Formatted step DONE... DONE (0 seconds) [1] "Next step function: normalize_by_well" Normalizing Data ... Data Normalized step DONE... DONE (0 seconds) [1] "Next step function: modify_plate_data" [1] "Next step function: analyze_ready" Process complete List of 9 $ plate_meta : tibble [96 x 5] (S3: tbl_df/tbl/data.frame) ..$ well : chr [1:96] "A1" "A2" "A3" "A4" ... ..$ sample : logi [1:96] NA NA NA NA NA NA ... ..$ well_row: Factor w/ 8 levels "A","B","C","D",..: 1 1 1 1 1 1 1 1 1 1 ... ..$ well_col: Factor w/ 12 levels "1","2","3","4",..: 1 2 3 4 5 6 7 8 9 10 ... ..$ used : logi [1:96] FALSE FALSE FALSE FALSE FALSE FALSE ... $ plate_data : md_nrmf_ [1,500 x 8] (S3: mod_normfluodbf_data/tbl_df/tbl/data.frame) ..$ well : chr [1:1500] "A1" "A1" "A1" "A1" ... ..$ well_row : chr [1:1500] "A" "A" "A" "A" ... ..$ well_col : Factor w/ 12 levels "1","10","11",..: 1 1 1 1 1 1 1 1 1 1 ... ..$ used : logi [1:1500] TRUE TRUE TRUE TRUE TRUE TRUE ... ..$ Cycle_Number : num [1:1500] 1 2 3 4 5 6 7 8 9 10 ... ..$ fluor_values : num [1:1500] 1 0.872 0.788 0.715 0.731 ... ..$ outlier : logi [1:1500] FALSE FALSE FALSE FALSE FALSE FALSE ... ..$ outlier_color: chr [1:1500] "#EE3B3B" "#EE3B3B" "#EE3B3B" "#EE3B3B" ... $ steps : num 0 $ status : num 5 $ dirty : logi TRUE $ version : chr "2.0.0" $ params :List of 3 ..$ GENERAL :List of 5 .. ..$ X_VAR_ONE : chr "Time" .. ..$ X_VAR_TWO : chr "Cycle_Number" .. ..$ Y_VAR : chr "FLUORESCENCE" .. ..$ X_VAR_ONE_LABEL: chr "TIME" .. ..$ X_VAR_TWO_LABEL: chr "CYCLE NUMBER" ..$ THRESHOLDS:List of 4 .. ..$ MAX_FLUOR : num 65536 .. ..$ MIN_FLUOR : num 128 .. ..$ CUTOFF_UPPER_LIMIT: num 32768 .. ..$ CUTOFF_LOWER_LIMIT: num 4096 ..$ COLORS :List of 4 .. ..$ POS : chr "#7FFFD4" .. ..$ TEST : chr "#0000CD" .. ..$ NEG : chr "#EE3B3B" .. ..$ NEUTRAL: chr "#BF3EFF" $ dataset_name: chr "dat_1" $ data_summary: chr "36 Wells Used" - attr(*, "class")= chr [1:3] "96well_plate" "normfluodbf_plate" "list" The upload_data step needs to be completed Initializing Data ... [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)" [[1]] [1] "C9" Data Initialized step DONE... DONE (2 seconds) [1] "Steps left:4" [1] "Next step function: format_plate_data" Formating Plate Data ... Data Formatted step DONE... DONE (0 seconds) [1] "Next step function: normalize_by_well" Normalizing Data ... Data Normalized step DONE... DONE (0 seconds) [1] "Next step function: modify_plate_data" [1] "Next step function: analyze_ready" Process complete The upload_data step needs to be completed Initializing Data ... [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)" [[1]] [1] "C9" Data Initialized step DONE... DONE (1 seconds) [1] "Steps left:4" [1] "Next step function: format_plate_data" Formating Plate Data ... Data Formatted step DONE... DONE (0 seconds) [1] "Next step function: normalize_by_well" Normalizing Data ... Data Normalized step DONE... DONE (0 seconds) [1] "Next step function: modify_plate_data" [1] "Next step function: analyze_ready" Process complete Crikee, some values in your original data violate thresholds 🐷 🐫 [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)" [[1]] [1] "C9" The upload_data step needs to be completed Initializing Data ... [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)" [[1]] [1] "C9" Data Initialized step DONE... DONE (1 seconds) [1] "Steps left:5" [1] "Next step function: format_plate_data" Formating Plate Data ... Data Formatted step DONE... DONE (0 seconds) [1] "Next step function: remove_outliers" [1] "Next step function: normalize_by_well" Normalizing Data ... Data Normalized step DONE... DONE (0 seconds) [1] "Next step function: modify_plate_data" [1] "Next step function: analyze_ready" Process complete [ FAIL 1 | WARN 617 | SKIP 0 | PASS 23 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test_plot.R:21:3'): test normfluodbf plot ───────────────────────── "gg" (`actual`) not equal to class(plt.obj)[1] (`expected`). `actual`: "gg" `expected`: "ggplot2::ggplot" [ FAIL 1 | WARN 617 | SKIP 0 | PASS 23 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [13s] OK * checking PDF version of manual ... [21s] OK * checking HTML version of manual ... [15s] OK * DONE Status: 1 ERROR