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This page was generated on 2025-10-06 11:40 -0400 (Mon, 06 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4832
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4613
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4554
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4585
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 143/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BatchQC 2.4.0  (landing page)
Jessica Anderson
Snapshot Date: 2025-10-02 13:40 -0400 (Thu, 02 Oct 2025)
git_url: https://git.bioconductor.org/packages/BatchQC
git_branch: RELEASE_3_21
git_last_commit: b31f36a
git_last_commit_date: 2025-04-15 11:00:59 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for BatchQC on kjohnson1

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.

raw results


Summary

Package: BatchQC
Version: 2.4.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BatchQC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BatchQC_2.4.0.tar.gz
StartedAt: 2025-10-03 13:27:20 -0400 (Fri, 03 Oct 2025)
EndedAt: 2025-10-03 13:35:01 -0400 (Fri, 03 Oct 2025)
EllapsedTime: 461.2 seconds
RetCode: 0
Status:   OK  
CheckDir: BatchQC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BatchQC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BatchQC_2.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/BatchQC.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BatchQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BatchQC’ version ‘2.4.0’
* 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 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  29.305  0.405  30.733
DE_analyze    22.889  0.549  24.251
pval_plotter  20.994  0.509  22.167
pval_summary  19.245  0.440  20.190
batch_correct 18.614  0.425  19.755
PCA_plotter   12.759  0.557  13.891
* 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:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BatchQC
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘BatchQC’ ...
** this is package ‘BatchQC’ version ‘2.4.0’
** 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 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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.

> if (requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                              skip_on_cran = TRUE)
All Done!
> 
> proc.time()
   user  system elapsed 
  0.203   0.063   0.270 

BatchQC.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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.

> 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 
 12.772   0.885  14.564 

Example timings

BatchQC.Rcheck/BatchQC-Ex.timings

nameusersystemelapsed
BatchQC000
DE_analyze22.889 0.54924.251
EV_plotter1.4490.0511.531
EV_table1.1890.0491.271
PCA_plotter12.759 0.55713.891
batch_correct18.614 0.42519.755
batch_design0.6740.0300.736
batchqc_explained_variation1.2240.1291.399
bladder_data_upload0.3300.0270.365
color_palette0.3030.0180.327
confound_metrics0.6390.0220.715
cor_props0.6090.0250.706
covariates_not_confounded0.5920.0180.627
cramers_v0.6000.0220.642
dendrogram_alpha_numeric_check0.6140.0290.703
dendrogram_color_palette0.9730.0421.091
dendrogram_plotter1.9000.0482.053
goodness_of_fit_DESeq24.6150.0524.765
heatmap_num_to_char_converter0.6020.0250.659
heatmap_plotter1.5840.0561.665
normalize_SE0.7830.0490.843
process_dendrogram1.0850.0871.206
pval_plotter20.994 0.50922.167
pval_summary19.245 0.44020.190
ratio_plotter1.3830.0461.489
std_pearson_corr_coef0.6200.0240.657
summarized_experiment0.0180.0030.024
umap2.2490.1552.446
variation_ratios1.1620.0621.258
volcano_plot29.305 0.40530.733