• using R Under development (unstable) (2025-09-13 r88827)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-15 (Debian 15.2.0-3) 15.2.0     GNU Fortran (Debian 15.2.0-3) 15.2.0
• running under: Debian GNU/Linux forky/sid
• 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 CRAN incoming feasibility ... [1s/2s] OK
• 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 whether package ‘normfluodbf’ 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/2s] OK
• checking whether the package can be unloaded cleanly ... [2s/2s] OK
• checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
• checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
• checking loading without being on the library search path ... [2s/2s] OK
• checking whether startup messages can be suppressed ... [2s/2s] 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 ... [24s/28s] 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 contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... [0s/0s] 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 ... [2s/2s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [21s/27s] ERROR   Running ‘testthat.R’ [20s/27s] 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 (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   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 ... [6s/10s] OK
• checking PDF version of manual ... [8s/11s] OK
• checking HTML version of manual ... [2s/3s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR