R Under development (unstable) (2024-07-03 r86870 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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.

> # 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(PCAPAM50)

========================================
PCAPAM50 version 1.0.0
Documentation: https://www.wriwindber.org/tools-portal/pca-pam50/

If you use it in published research, please cite:
PCAPAM50: Raj-Kumar PK, et al.Scientific reports. 2019 May 28;9(1):7956.
PAM50: Parker JS, et al. Journal of clinical oncology. 2009 Mar 3;27(8):1160.

This message can be suppressed by:
  suppressPackageStartupMessages(library(PCAPAM50))

========================================

> 
> test_check("PCAPAM50")
inputDir: D:\temp\RtmpUvBD3h/Call.PC1
Directory already exists: D:\temp\RtmpUvBD3h/Call.PC1
All necessary input data are correctly formatted and present. Grab a cup of coffee while we do the heavy lifting for you!
paramater Dir path: D:/RCompile/CRANincoming/R-devel/lib/PCAPAM50/PAM50/bioclassifier_R

Input File path: D:\temp\RtmpUvBD3h/Call.PC1/TEST_pam_mat.txt

Output Median File path: D:\temp\RtmpUvBD3h/Call.PC1/Mdns.PC1ihcPAM50.txt

Reading file: D:/RCompile/CRANincoming/R-devel/lib/PCAPAM50/PAM50/bioclassifier_R/mediansPerDataset_v2.txt
Sourcing: D:/RCompile/CRANincoming/R-devel/lib/PCAPAM50/PAM50/bioclassifier_R/subtypePrediction_distributed_PNmodified.R
Sourcing: D:/RCompile/CRANincoming/R-devel/lib/PCAPAM50/PAM50/bioclassifier_R/subtypePrediction_functions_PNmodified.R
[1] "calibration to: Mdns.PC1ihcPAM50"
[1] "Number of genes used: 50"
[1] "ER range: 3.92325182503492"
Expected output file: D:\temp\RtmpUvBD3h/Call.PC1/PC1ihc.Mdns_pam50scores.txt
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 9 ]
> 
> proc.time()
   user  system elapsed 
   7.92    0.50    9.07