Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-28 12:04 -0400 (Thu, 28 Aug 2025).
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" | 4822 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4613 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4556 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4539 |
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 144/2319 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BatchQC 2.5.0 (landing page) Jessica Anderson
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
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. |
Package: BatchQC |
Version: 2.5.0 |
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_2.5.0.tar.gz |
StartedAt: 2025-08-27 19:14:05 -0400 (Wed, 27 Aug 2025) |
EndedAt: 2025-08-27 19:21:29 -0400 (Wed, 27 Aug 2025) |
EllapsedTime: 444.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BatchQC.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_2.5.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/BatchQC.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 ‘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 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 30.858 0.484 31.560 DE_analyze 23.471 0.560 24.173 pval_plotter 19.850 0.331 20.306 pval_summary 19.818 0.314 20.222 batch_correct 16.486 0.261 16.798 PCA_plotter 13.475 0.229 13.750 goodness_of_fit_DESeq2 4.945 0.055 5.021 * 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
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-x86_64/Resources/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)
BatchQC.Rcheck/tests/spelling.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. > if (requireNamespace('spelling', quietly = TRUE)) + spelling::spell_check_test(vignettes = TRUE, error = FALSE, + skip_on_cran = TRUE) All Done! > > proc.time() user system elapsed 0.220 0.086 0.315
BatchQC.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. > 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 13.359 0.786 14.256
BatchQC.Rcheck/BatchQC-Ex.timings
name | user | system | elapsed | |
BatchQC | 0.000 | 0.000 | 0.001 | |
DE_analyze | 23.471 | 0.560 | 24.173 | |
EV_plotter | 1.380 | 0.038 | 1.430 | |
EV_table | 1.081 | 0.037 | 1.125 | |
PCA_plotter | 13.475 | 0.229 | 13.750 | |
batch_correct | 16.486 | 0.261 | 16.798 | |
batch_design | 0.688 | 0.025 | 0.716 | |
batchqc_explained_variation | 1.067 | 0.118 | 1.189 | |
bladder_data_upload | 0.293 | 0.050 | 0.347 | |
color_palette | 0.314 | 0.019 | 0.335 | |
confound_metrics | 0.644 | 0.022 | 0.669 | |
cor_props | 0.629 | 0.022 | 0.653 | |
covariates_not_confounded | 0.655 | 0.023 | 0.681 | |
cramers_v | 0.640 | 0.027 | 0.669 | |
dendrogram_alpha_numeric_check | 0.525 | 0.020 | 0.548 | |
dendrogram_color_palette | 0.846 | 0.026 | 0.874 | |
dendrogram_plotter | 1.706 | 0.053 | 1.765 | |
goodness_of_fit_DESeq2 | 4.945 | 0.055 | 5.021 | |
heatmap_num_to_char_converter | 0.567 | 0.023 | 0.596 | |
heatmap_plotter | 1.548 | 0.038 | 1.589 | |
normalize_SE | 0.890 | 0.036 | 0.931 | |
process_dendrogram | 0.858 | 0.054 | 0.917 | |
pval_plotter | 19.850 | 0.331 | 20.306 | |
pval_summary | 19.818 | 0.314 | 20.222 | |
ratio_plotter | 1.414 | 0.045 | 1.471 | |
std_pearson_corr_coef | 0.655 | 0.024 | 0.683 | |
summarized_experiment | 0.023 | 0.002 | 0.027 | |
umap | 2.391 | 0.090 | 2.498 | |
variation_ratios | 1.093 | 0.046 | 1.148 | |
volcano_plot | 30.858 | 0.484 | 31.560 | |