Multiple platform build/check report for BioC 3.22 - CHECK results for treeclimbR on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.2 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4796
palomino8	Windows Server 2022 Datacenter	x64	4.5.1 (2025-06-13 ucrt) -- "Great Square Root"	4535
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4578
kjohnson3	macOS 13.7.1 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4519
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4516
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 nebbiolo2

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: 1.5.1

Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:treeclimbR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings treeclimbR_1.5.1.tar.gz

StartedAt: 2025-07-29 03:41:11 -0400 (Tue, 29 Jul 2025)

EndedAt: 2025-07-29 03:47:26 -0400 (Tue, 29 Jul 2025)

EllapsedTime: 375.5 seconds

RetCode: 0

Status: OK

CheckDir: treeclimbR.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:treeclimbR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings treeclimbR_1.5.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/treeclimbR.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘treeclimbR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘treeclimbR’ version ‘1.5.1’
* 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 9.567  0.252   9.819
TreeHeatmap      5.268  0.170   5.440
* 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-3.22-bioc/R/bin/R CMD INSTALL treeclimbR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘treeclimbR’ ...
** this is package ‘treeclimbR’ version ‘1.5.1’
** 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 version 4.5.1 (2025-06-13) -- "Great Square Root"
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")

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  |======================================================================| 100%[ FAIL 0 | WARN 0 | SKIP 0 | PASS 2095 ]
> 
> proc.time()
   user  system elapsed 
 72.423   1.436  73.911

Example timings

treeclimbR.Rcheck/treeclimbR-Ex.timings

name	user	system	elapsed
TreeHeatmap	5.268	0.170	5.440
aggDS	0.647	0.029	0.676
diffcyt_workflow	9.567	0.252	9.819
edgerWrp	0.278	0.005	0.283
evalCand	0.739	0.005	0.743
fdr	0.350	0.001	0.351
findChild	0.305	0.005	0.311
findExcl	0.339	0.004	0.343
getCand	0.413	0.001	0.414
getData	1.602	0.018	1.621
getLevel	0.356	0.004	0.361
infoCand	0.694	0.009	0.702
isConnect	0.302	0.003	0.305
medianByClusterMarker	0.244	0.002	0.247
nodeResult	1.095	0.008	1.104
parEstimate	0.433	0.013	0.446
runDA	0.724	0.020	0.745
runDS	1.741	0.008	1.749
selNode	0.491	0.007	0.498
simData	0.693	0.014	0.707
topNodes	0.750	0.025	0.775
tpr	0.352	0.015	0.367
treeScore	0.497	0.017	0.513