* using log directory 'd:/RCompile/CRANincoming/R-devel/viralmodels.Rcheck'
* using R version 4.4.0 alpha (2024-03-26 r86209 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'viralmodels/DESCRIPTION' ... OK
* this is package 'viralmodels' version '1.3.0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... Note_to_CRAN_maintainers
Maintainer: 'Juan Pablo Acuña González <22253567@uagro.mx>'
* 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 serialization versions ... OK
* checking whether package 'viralmodels' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... 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 examples ... ERROR
Running examples in 'viralmodels-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: viralmodel
> ### Title: Select best model
> ### Aliases: viralmodel
>
> ### ** Examples
>
> library(tidyverse)
── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
✔ dplyr 1.1.4 ✔ readr 2.1.5
✔ forcats 1.0.0 ✔ stringr 1.5.1
✔ ggplot2 3.5.0 ✔ tibble 3.2.1
✔ lubridate 1.9.3 ✔ tidyr 1.3.1
✔ purrr 1.0.2
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag() masks stats::lag()
ℹ Use the conflicted package () to force all conflicts to become errors
> library(baguette)
Loading required package: parsnip
> library(kernlab)
Attaching package: 'kernlab'
The following object is masked from 'package:purrr':
cross
The following object is masked from 'package:ggplot2':
alpha
> library(kknn)
> library(ranger)
> library(rules)
> library(glmnet)
Loading required package: Matrix
Attaching package: 'Matrix'
The following objects are masked from 'package:tidyr':
expand, pack, unpack
Loaded glmnet 4.1-8
> # Define the function to impute values in the undetectable range
> impute_undetectable <- function(column) {
+ ifelse(column <= 40,
+ rexp(sum(column <= 40), rate = 1/13) + 1,
+ column)
+ }
> # Apply the function to all vl columns using purrr's map_dfc
> library(viraldomain)
> data("viral", package = "viraldomain")
> viral_imputed <- viral |>
+ mutate(across(starts_with("vl"), ~impute_undetectable(.x)))
> traindata <- viral_imputed
> semilla <- 123
> target <- "cd_2022"
> viralvars <- c("vl_2019", "vl_2021", "vl_2022")
> logbase <- 10
> pliegues <- 2
> repeticiones <- 1
> rejilla <- 1
> modelo <- "simple_rf"
> viralmodel(traindata, semilla, target, viralvars, logbase, pliegues, repeticiones, rejilla, modelo)
i Creating pre-processing data to finalize unknown parameter: mtry
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... ERROR
Running 'testthat.R'
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(viralmodels)
>
> test_check("viralmodels")
-- Attaching core tidyverse packages ------------------------ tidyverse 2.0.0 --
v dplyr 1.1.4 v readr 2.1.5
v forcats 1.0.0 v stringr 1.5.1
v ggplot2 3.5.0 v tibble 3.2.1
v lubridate 1.9.3 v tidyr 1.3.1
v purrr 1.0.2
-- Conflicts ------------------------------------------ tidyverse_conflicts() --
x readr::edition_get() masks testthat::edition_get()
x dplyr::filter() masks stats::filter()
x purrr::is_null() masks testthat::is_null()
x dplyr::lag() masks stats::lag()
x readr::local_edition() masks testthat::local_edition()
x dplyr::matches() masks tidyr::matches(), testthat::matches()
i Use the conflicted package () to force all conflicts to become errors
Loading required package: parsnip
Attaching package: 'kernlab'
The following object is masked from 'package:purrr':
cross
The following object is masked from 'package:ggplot2':
alpha
Loading required package: Matrix
Attaching package: 'Matrix'
The following objects are masked from 'package:tidyr':
expand, pack, unpack
Loaded glmnet 4.1-8
* checking PDF version of manual ... [13s] OK
* checking HTML version of manual ... OK
* DONE
Status: 2 ERRORs