Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-09-23 12:06 -0400 (Tue, 23 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4816
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4605
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4549
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4560
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 144/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BatchQC 2.5.0  (landing page)
Jessica Anderson
Snapshot Date: 2025-09-22 13:45 -0400 (Mon, 22 Sep 2025)
git_url: https://git.bioconductor.org/packages/BatchQC
git_branch: devel
git_last_commit: 3ab9c73
git_last_commit_date: 2025-04-15 11:00:59 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  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 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for BatchQC on taishan

To the developers/maintainers of the BatchQC package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BatchQC.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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: BatchQC
Version: 2.5.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:BatchQC.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BatchQC_2.5.0.tar.gz
StartedAt: 2025-09-23 04:41:06 -0000 (Tue, 23 Sep 2025)
EndedAt: 2025-09-23 04:49:30 -0000 (Tue, 23 Sep 2025)
EllapsedTime: 504.2 seconds
RetCode: 0
Status:   OK  
CheckDir: BatchQC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:BatchQC.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BatchQC_2.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BatchQC.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BatchQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BatchQC’ version ‘2.5.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 24 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘BatchQC’ 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 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
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
volcano_plot           33.673  0.199  33.961
DE_analyze             25.900  0.929  26.900
pval_plotter           22.986  0.108  23.150
pval_summary           22.203  0.068  22.328
batch_correct          19.242  0.140  19.431
PCA_plotter            18.594  0.391  19.039
goodness_of_fit_DESeq2  6.213  0.008   6.238
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  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

BatchQC.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL BatchQC
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘BatchQC’ ...
** this is package ‘BatchQC’ version ‘2.5.0’
** using staged installation
** R
** data
** 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 (BatchQC)

Tests output

BatchQC.Rcheck/tests/spelling.Rout


R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.

> if (requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                              skip_on_cran = TRUE)
All Done!
> 
> proc.time()
   user  system elapsed 
  0.215   0.028   0.235 

BatchQC.Rcheck/tests/testthat.Rout


R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.

> library(testthat)
> library(BatchQC)
> 
> test_check("BatchQC")
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 0 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On CRAN (1): 'test-lintr.R:3:5'

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
 14.478   0.643  15.193 

Example timings

BatchQC.Rcheck/BatchQC-Ex.timings

nameusersystemelapsed
BatchQC000
DE_analyze25.900 0.92926.900
EV_plotter1.2870.0721.362
EV_table0.8550.0640.922
PCA_plotter18.594 0.39119.039
batch_correct19.242 0.14019.431
batch_design0.7120.0120.731
batchqc_explained_variation0.9070.0150.926
bladder_data_upload0.2920.0040.297
color_palette0.3150.0000.316
confound_metrics0.7220.0040.728
cor_props0.6630.0040.670
covariates_not_confounded0.7300.0040.736
cramers_v0.6430.0040.649
dendrogram_alpha_numeric_check0.5900.0120.603
dendrogram_color_palette1.2630.0081.274
dendrogram_plotter2.7040.0002.717
goodness_of_fit_DESeq26.2130.0086.238
heatmap_num_to_char_converter0.7010.0000.703
heatmap_plotter1.9570.0121.976
normalize_SE1.0110.0081.022
process_dendrogram1.2780.0121.293
pval_plotter22.986 0.10823.150
pval_summary22.203 0.06822.328
ratio_plotter1.1680.0041.176
std_pearson_corr_coef0.6570.0000.658
summarized_experiment0.0230.0000.023
umap2.3730.0082.391
variation_ratios0.8840.0160.903
volcano_plot33.673 0.19933.961