Multiple platform build/check report for BioC 3.23 - CHECK results for treeclimbR on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"	4875
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"	4593
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*

CHECK results for treeclimbR on nebbiolo1

To the developers/maintainers of the treeclimbR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/treeclimbR.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: treeclimbR

Version: 1.7.0

Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:treeclimbR.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings treeclimbR_1.7.0.tar.gz

StartedAt: 2025-12-19 04:28:29 -0500 (Fri, 19 Dec 2025)

EndedAt: 2025-12-19 04:35:23 -0500 (Fri, 19 Dec 2025)

EllapsedTime: 414.6 seconds

RetCode: 0

Status: OK

CheckDir: treeclimbR.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:treeclimbR.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings treeclimbR_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/treeclimbR.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘treeclimbR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘treeclimbR’ version ‘1.7.0’
* 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 ‘treeclimbR’ can be installed ... OK
* 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 loading without being on the library search path ... 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 ... 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 ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
diffcyt_workflow 9.900  0.263  10.163
TreeHeatmap      6.442  0.219   6.662
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

treeclimbR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL treeclimbR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘treeclimbR’ ...
** this is package ‘treeclimbR’ version ‘1.7.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (treeclimbR)

Tests output

treeclimbR.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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(treeclimbR)
> 
> test_check("treeclimbR")

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |========                                                              |  11%
  |                                                                            
  |================                                                      |  22%
  |                                                                            
  |=======================                                               |  33%
  |                                                                            
  |===============================                                       |  44%
  |                                                                            
  |=======================================                               |  56%
  |                                                                            
  |===============================================                       |  67%
  |                                                                            
  |======================================================                |  78%
  |                                                                            
  |==============================================================        |  89%
  |                                                                            
  |======================================================================| 100%
  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |========                                                              |  11%
  |                                                                            
  |================                                                      |  22%
  |                                                                            
  |=======================                                               |  33%
  |                                                                            
  |===============================                                       |  44%
  |                                                                            
  |=======================================                               |  56%
  |                                                                            
  |===============================================                       |  67%
  |                                                                            
  |======================================================                |  78%
  |                                                                            
  |==============================================================        |  89%
  |                                                                            
  |======================================================================| 100%[ FAIL 0 | WARN 0 | SKIP 0 | PASS 2095 ]
> 
> proc.time()
   user  system elapsed 
 74.999   1.630  76.630

Example timings

treeclimbR.Rcheck/treeclimbR-Ex.timings

name	user	system	elapsed
TreeHeatmap	6.442	0.219	6.662
aggDS	0.843	0.015	0.858
diffcyt_workflow	9.900	0.263	10.163
edgerWrp	0.319	0.007	0.326
evalCand	0.932	0.007	0.939
fdr	0.547	0.004	0.551
findChild	0.501	0.006	0.506
findExcl	0.502	0.006	0.508
getCand	0.563	0.011	0.574
getData	1.979	0.023	2.002
getLevel	0.563	0.006	0.570
infoCand	0.971	0.014	0.984
isConnect	0.509	0.017	0.526
medianByClusterMarker	0.268	0.008	0.276
nodeResult	1.166	0.014	1.179
parEstimate	0.507	0.005	0.513
runDA	0.819	0.011	0.830
runDS	1.832	0.066	1.899
selNode	0.568	0.004	0.573
simData	0.775	0.008	0.783
topNodes	0.883	0.048	0.931
tpr	0.583	0.026	0.608
treeScore	0.783	0.013	0.796