* using log directory 'd:/Rcompile/CRANpkg/local/4.3/viraldomain.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'viraldomain/DESCRIPTION' ... OK
* this is package 'viraldomain' version '0.0.3'
* 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 'viraldomain' can be installed ... OK
* checking installed package size ... OK
* checking package 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [5s] OK
* checking whether the package can be loaded with stated dependencies ... [4s] OK
* checking whether the package can be unloaded cleanly ... [4s] OK
* checking whether the namespace can be loaded with stated dependencies ... [5s] OK
* checking whether the namespace can be unloaded cleanly ... [5s] OK
* checking loading without being on the library search path ... [5s] 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 ... [11s] OK
* checking Rd files ... [1s] 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 ... [0s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [7s] ERROR
Running examples in 'viraldomain-Ex.R' failed
The error most likely occurred in:

> ### Name: normalized_domain_plot
> ### Title: Create a Normalized Domain Plot
> ### Aliases: normalized_domain_plot
> 
> ### ** Examples
> 
> data(viral)
> data(sero)
>  # Adding "jitter_" prefix to original variable
> features <- list(
+   featured_col = "jittered_cd_2022",
+   features_vl = "vl_2022",
+   features_cd = "cd_2022"
+   )
> train_data = viral |>
+ dplyr::select("cd_2022", "vl_2022")
> test_data = sero
> treshold_value = 0.99
> impute_hyperparameters = list(indetect = 40, tasa_exp = 1/13, semi = 123)
> normalized_domain_plot(features, train_data, test_data, treshold_value, impute_hyperparameters)
Error in `recipes::prep()`:
✖ The following variables have the wrong attributes:
  `jittered_log10_imputed_vl_2022` and `jittered_cd_2022`.
Run `lapply(recipes_ptype(rec), attributes)` to see expected attributes. For
`rec` being the name of your recipe.
Backtrace:
     ▆
  1. └─viraldomain::normalized_domain_plot(...)
  2.   ├─applicable::autoplot.apd_pca(...)
  3.   ├─applicable::apd_pca(...)
  4.   └─applicable:::apd_pca.recipe(...)
  5.     ├─hardhat::mold(x, data)
  6.     └─hardhat:::mold.recipe(x, data)
  7.       ├─hardhat::run_mold(blueprint, data = data)
  8.       └─hardhat:::run_mold.default_recipe_blueprint(blueprint, data = data)
  9.         └─hardhat:::mold_recipe_default_process(...)
 10.           ├─recipes::prep(...)
 11.           └─recipes:::prep.recipe(...)
 12.             └─recipes:::check_training_set(training, x, fresh)
 13.               └─recipes::recipes_ptype_validate(...)
 14.                 └─cli::cli_abort(msg, call = call)
 15.                   └─rlang::abort(...)
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [7s] ERROR
  Running 'testthat.R' [7s]
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(viraldomain)
  > 
  > test_check("viraldomain")
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  [ FAIL 2 | WARN 0 | SKIP 3 | PASS 0 ]
  
  ══ Skipped tests (3) ═══════════════════════════════════════════════════════════
  • On CRAN (3): 'test-knn_domain_score.R:12:3', 'test-mars_domain_score.R:80:3',
    'test-nn_domain_score.R:80:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-normalized_domain_plot.R:18:3'): `normalized_domain_plot()` plots as expected ──
  Error in `recipes::prep(blueprint$recipe, training = training, fresh = blueprint$fresh, 
      strings_as_factors = blueprint_strings_as_factors(blueprint))`: x The following variables have the wrong attributes: `jittered_log10_imputed_vl_2022` and `jittered_cd_2022`.
  Run `lapply(recipes_ptype(rec), attributes)` to see expected attributes. For `rec` being the name of your recipe.
  Backtrace:
       ▆
    1. ├─vdiffr::expect_doppelganger(...) at test-normalized_domain_plot.R:18:3
    2. │ └─vdiffr (local) writer(fig, testcase, title)
    3. │   └─vdiffr:::print_plot(plot, title)
    4. └─viraldomain::normalized_domain_plot(...)
    5.   ├─applicable::autoplot.apd_pca(...)
    6.   ├─applicable::apd_pca(...)
    7.   └─applicable:::apd_pca.recipe(...)
    8.     ├─hardhat::mold(x, data)
    9.     └─hardhat:::mold.recipe(x, data)
   10.       ├─hardhat::run_mold(blueprint, data = data)
   11.       └─hardhat:::run_mold.default_recipe_blueprint(blueprint, data = data)
   12.         └─hardhat:::mold_recipe_default_process(...)
   13.           ├─recipes::prep(...)
   14.           └─recipes:::prep.recipe(...)
   15.             └─recipes:::check_training_set(training, x, fresh)
   16.               └─recipes::recipes_ptype_validate(...)
   17.                 └─cli::cli_abort(msg, call = call)
   18.                   └─rlang::abort(...)
  ── Error ('test-simple_domain_plot.R:18:3'): `simple_domain_plot()` plots as expected ──
  Error in `recipes::prep(blueprint$recipe, training = training, fresh = blueprint$fresh, 
      strings_as_factors = blueprint_strings_as_factors(blueprint))`: x The following variables have the wrong attributes: `jittered_log10_imputed_vl_2022` and `jittered_cd_2022`.
  Run `lapply(recipes_ptype(rec), attributes)` to see expected attributes. For `rec` being the name of your recipe.
  Backtrace:
       ▆
    1. ├─vdiffr::expect_doppelganger(...) at test-simple_domain_plot.R:18:3
    2. │ └─vdiffr (local) writer(fig, testcase, title)
    3. │   └─vdiffr:::print_plot(plot, title)
    4. └─viraldomain::simple_domain_plot(...)
    5.   ├─applicable::autoplot.apd_pca(...)
    6.   ├─applicable::apd_pca(...)
    7.   └─applicable:::apd_pca.recipe(...)
    8.     ├─hardhat::mold(x, data)
    9.     └─hardhat:::mold.recipe(x, data)
   10.       ├─hardhat::run_mold(blueprint, data = data)
   11.       └─hardhat:::run_mold.default_recipe_blueprint(blueprint, data = data)
   12.         └─hardhat:::mold_recipe_default_process(...)
   13.           ├─recipes::prep(...)
   14.           └─recipes:::prep.recipe(...)
   15.             └─recipes:::check_training_set(training, x, fresh)
   16.               └─recipes::recipes_ptype_validate(...)
   17.                 └─cli::cli_abort(msg, call = call)
   18.                   └─rlang::abort(...)
  
  [ FAIL 2 | WARN 0 | SKIP 3 | PASS 0 ]
  Error: Test failures
  Execution halted
* checking PDF version of manual ... [16s] OK
* checking HTML version of manual ... [1s] OK
* DONE
Status: 2 ERRORs