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

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4824
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4615
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4562
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4541
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 lconway

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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:treeclimbR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings treeclimbR_1.5.1.tar.gz

StartedAt: 2025-08-30 00:26:52 -0400 (Sat, 30 Aug 2025)

EndedAt: 2025-08-30 00:33:42 -0400 (Sat, 30 Aug 2025)

EllapsedTime: 410.1 seconds

RetCode: 0

Status: OK

CheckDir: treeclimbR.Rcheck

Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:treeclimbR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings treeclimbR_1.5.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/treeclimbR.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘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 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 11.111  0.161  11.342
TreeHeatmap       5.764  0.107   5.906
* 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: OK

Installation output

treeclimbR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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-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.

> # 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 
 86.773   2.998  90.809

Example timings

treeclimbR.Rcheck/treeclimbR-Ex.timings

name	user	system	elapsed
TreeHeatmap	5.764	0.107	5.906
aggDS	0.893	0.032	0.934
diffcyt_workflow	11.111	0.161	11.342
edgerWrp	0.437	0.023	0.462
evalCand	0.995	0.031	1.032
fdr	0.541	0.024	0.568
findChild	0.441	0.024	0.468
findExcl	0.506	0.025	0.534
getCand	0.581	0.026	0.611
getData	1.780	0.036	1.824
getLevel	0.517	0.025	0.544
infoCand	0.895	0.026	0.924
isConnect	0.467	0.021	0.490
medianByClusterMarker	0.333	0.015	0.349
nodeResult	1.358	0.031	1.400
parEstimate	0.534	0.023	0.561
runDA	0.997	0.028	1.030
runDS	2.206	0.041	2.263
selNode	0.669	0.029	0.702
simData	0.946	0.032	0.984
topNodes	0.893	0.028	0.923
tpr	0.536	0.025	0.564
treeScore	0.685	0.026	0.714