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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BreastSubtypeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BreastSubtypeR_1.1.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/BreastSubtypeR.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BreastSubtypeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BreastSubtypeR’ version ‘1.1.2’
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BreastSubtypeR’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘e1071::element’ by ‘ggplot2::element’ when loading ‘BreastSubtypeR’
See ‘/Users/biocbuild/bbs-3.22-bioc/meat/BreastSubtypeR.Rcheck/00install.out’ for details.
* 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 ... 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 dependencies in R code ... WARNING
'loadNamespace' or 'requireNamespace' call not declared from: ‘tidyverse’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'iBreastSubtypeR.Rd':
iBreastSubtypeR
  Code: function(attach = c("shiny", "bslib"), attach_tidyverse =
                 FALSE, max_upload_mb = 1000)
  Docs: function()
  Argument names in code not in docs:
    attach attach_tidyverse max_upload_mb

* 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/BreastSubtypeR.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BreastSubtypeR
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘BreastSubtypeR’ ...
** this is package ‘BreastSubtypeR’ version ‘1.1.2’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘e1071::element’ by ‘ggplot2::element’ when loading ‘BreastSubtypeR’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘e1071::element’ by ‘ggplot2::element’ when loading ‘BreastSubtypeR’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘e1071::element’ by ‘ggplot2::element’ when loading ‘BreastSubtypeR’
** testing if installed package keeps a record of temporary installation path
* DONE (BreastSubtypeR)

R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(BreastSubtypeR)
Warning message:
replacing previous import 'e1071::element' by 'ggplot2::element' when loading 'BreastSubtypeR' 
> 
> test_that("BS_Multi performs subtyping correctly", {
+     # Load required dataset
+     data("OSLO2EMIT0obj")
+ 
+     # Define methods to use for subtyping
+     methods <- c("genefu.robust", "PCAPAM50", "ssBC", "AIMS")
+ 
+     # Perform subtyping
+     res.test <- BS_Multi(
+         data_input = OSLO2EMIT0obj$data_input,
+         methods = methods,
+         Subtype = FALSE,
+         hasClinical = FALSE
+     )
+ 
+     # Validate results
+     expect_true(identical(res.test$res_subtypes[, methods], OSLO2EMIT0obj$res$res_subtypes[, methods])) # Validate results
+ })
Test passed 😀
> 
> proc.time()
   user  system elapsed 
 12.134   0.656  12.841