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> # 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: Call.PC1
Directory created: 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:  Call.PC1/TEST_pam_mat.txt 
Output Median File path:  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: Call.PC1/PC1ihc.Mdns_pam50scores.txt
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 9 ]
> 
> proc.time()
   user  system elapsed 
   7.26    0.46    7.71