* using log directory ‘/srv/hornik/tmp/CRAN/PCAPAM50.Rcheck’
* using R Under development (unstable) (2024-06-30 r86854)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 18.1.8 (1)
    Debian flang-new version 18.1.8 (1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘PCAPAM50/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PCAPAM50’ version ‘1.0.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/3s] NOTE
Maintainer: ‘Praveen-Kumar Raj-Kumar <p.rajkumar@wriwindber.org>’

New submission

Possibly misspelled words in DESCRIPTION:
  PCAPAM (4:10, 12:14, 12:102, 12:351)
  Subtyping (3:59, 4:34)
  subtyping (12:52, 12:379)

The Description field should not start with the package name,
  'This package' or similar.
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘PCAPAM50’ can be installed ... [5s/5s] OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [2s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [2s/2s] OK
* checking whether startup messages can be suppressed ... [1s/1s] 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 ... [8s/8s] OK
* checking Rd files ... [0s/0s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [2s/2s] OK
* checking for unstated dependencies in ‘tests’ ... WARNING
'library' or 'require' call not declared from: ‘circlize’
* checking tests ... [2s/2s] ERROR
  Running ‘testthat.R’ [2s/2s]
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(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")
  ========================================
  circlize version 0.4.16
  CRAN page: https://cran.r-project.org/package=circlize
  Github page: https://github.com/jokergoo/circlize
  Documentation: https://jokergoo.github.io/circlize_book/book/
  
  If you use it in published research, please cite:
  Gu, Z. circlize implements and enhances circular visualization
    in R. Bioinformatics 2014.
  
  This message can be suppressed by:
    suppressPackageStartupMessages(library(circlize))
  ========================================
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-functions_PCA-PAM50.R:9:3'): makeCalls.PC1ihc works correctly with test data ──
  Error in `readChar(con, 5L, useBytes = TRUE)`: cannot open the connection
  Backtrace:
      ▆
   1. └─base::load(data_path) at test-functions_PCA-PAM50.R:9:3
   2.   └─base::readChar(con, 5L, useBytes = TRUE)
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [1s/1s] OK
* checking PDF version of manual ... [3s/2s] OK
* checking HTML version of manual ... [0s/0s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 1 WARNING, 1 NOTE