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This page was generated on 2025-07-28 12:06 -0400 (Mon, 28 Jul 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4796
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4536
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4578
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4519
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4512
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 2210/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
treeclimbR 1.5.1  (landing page)
Charlotte Soneson
Snapshot Date: 2025-07-27 13:25 -0400 (Sun, 27 Jul 2025)
git_url: https://git.bioconductor.org/packages/treeclimbR
git_branch: devel
git_last_commit: 88e3b05
git_last_commit_date: 2025-07-18 05:35:35 -0400 (Fri, 18 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


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: 2025-07-28 03:24:05 -0400 (Mon, 28 Jul 2025)
EndedAt: 2025-07-28 03:30:20 -0400 (Mon, 28 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 9.540  0.201   9.741
TreeHeatmap      5.006  0.078   5.085
* 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 
 71.014   1.641  72.693 

Example timings

treeclimbR.Rcheck/treeclimbR-Ex.timings

nameusersystemelapsed
TreeHeatmap5.0060.0785.085
aggDS0.6440.0050.648
diffcyt_workflow9.5400.2019.741
edgerWrp0.2940.0060.300
evalCand0.7540.0060.760
fdr0.3650.0130.378
findChild0.3240.0130.337
findExcl0.3610.0080.369
getCand0.4230.0030.427
getData1.5190.0051.524
getLevel0.3820.0030.386
infoCand0.7590.0240.783
isConnect0.3470.0040.350
medianByClusterMarker0.2250.0010.225
nodeResult1.1040.0091.113
parEstimate0.4020.0060.409
runDA0.7510.0050.757
runDS1.7660.0491.815
selNode0.5030.0040.508
simData0.7090.0070.717
topNodes0.7260.0070.734
tpr0.3560.0150.371
treeScore0.5100.0320.542