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This page was generated on 2025-09-20 12:04 -0400 (Sat, 20 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4814
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4603
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4547
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4553
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 243/2333HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BreastSubtypeR 1.1.2  (landing page)
Qiao Yang
Snapshot Date: 2025-09-19 13:45 -0400 (Fri, 19 Sep 2025)
git_url: https://git.bioconductor.org/packages/BreastSubtypeR
git_branch: devel
git_last_commit: ab53da2
git_last_commit_date: 2025-09-12 14:40:07 -0400 (Fri, 12 Sep 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    WARNINGS  


CHECK results for BreastSubtypeR on lconway

To the developers/maintainers of the BreastSubtypeR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BreastSubtypeR.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: BreastSubtypeR
Version: 1.1.2
Command: /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
StartedAt: 2025-09-19 19:41:47 -0400 (Fri, 19 Sep 2025)
EndedAt: 2025-09-19 19:46:22 -0400 (Fri, 19 Sep 2025)
EllapsedTime: 274.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: BreastSubtypeR.Rcheck
Warnings: 3

Command output

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###
### Running command:
###
###   /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
###
##############################################################################
##############################################################################


* 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.


Installation output

BreastSubtypeR.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BreastSubtypeR
###
##############################################################################
##############################################################################


* 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)

Tests output

BreastSubtypeR.Rcheck/tests/testthat.Rout


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 
 12.105   0.652  12.810 

Example timings

BreastSubtypeR.Rcheck/BreastSubtypeR-Ex.timings

nameusersystemelapsed
AIMSmodel0.0030.0020.004
BS_AIMS0.2510.0170.271
BS_Multi1.2430.0301.277
BS_PCAPAM500.4750.0520.532
BS_cIHC0.1830.0040.187
BS_cIHC.itr1.6220.0431.670
BS_parker0.1970.0040.201
BS_ssBC0.3700.0080.378
BS_sspbc0.5410.0170.560
BreastSubtypeRobj0.0040.0010.006
Gene.ID.ann0.1710.0020.174
Mapping1.0810.0121.098
OSLO2EMIT0obj0.0190.0020.020
Vis_Multi1.2090.0201.240
Vis_PCA1.2050.0301.244
Vis_boxplot0.4550.0050.462
Vis_heatmap4.5670.0664.662
Vis_pie0.6750.0080.688
iBreastSubtypeR0.0010.0000.001
sspbc.models0.0140.0010.015
sspbc.models.fullname0.0140.0010.015