Jessica McClintock
| Snapshot Date: 2025-03-31 13:00 -0400 (Mon, 31 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/BatchQC |
| git_branch: RELEASE_3_20 |
| git_last_commit: 71f8bea |
| git_last_commit_date: 2024-10-29 10:09:55 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-04-02 19:29 -0400 (Wed, 02 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4764 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4495 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4522 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4449 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4426 |
| 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 142/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BatchQC 2.2.0 (landing page) Jessica McClintock
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 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: 2.2.0 |
| Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BatchQC.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BatchQC_2.2.0.tar.gz |
| StartedAt: 2025-03-31 23:07:57 -0400 (Mon, 31 Mar 2025) |
| EndedAt: 2025-03-31 23:15:53 -0400 (Mon, 31 Mar 2025) |
| EllapsedTime: 476.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BatchQC.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BatchQC.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BatchQC_2.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/BatchQC.Rcheck'
* using R version 4.4.3 (2025-02-28 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.3.0
GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'BatchQC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BatchQC' version '2.2.0'
* 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 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 34.94 0.46 37.18
DE_analyze 26.28 0.44 26.72
pval_summary 25.54 0.42 26.00
pval_plotter 23.74 0.28 24.01
PCA_plotter 19.28 0.42 19.70
batch_correct 18.17 0.29 18.48
goodness_of_fit_DESeq2 5.09 0.11 5.21
* 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: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL BatchQC ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'BatchQC' ... ** 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 4.4.3 (2025-02-28 ucrt) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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)
NULL
>
> proc.time()
user system elapsed
0.21 0.09 0.32
BatchQC.Rcheck/tests/testthat.Rout
R version 4.4.3 (2025-02-28 ucrt) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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
13.93 1.10 15.18
BatchQC.Rcheck/BatchQC-Ex.timings
| name | user | system | elapsed | |
| BatchQC | 0 | 0 | 0 | |
| DE_analyze | 26.28 | 0.44 | 26.72 | |
| EV_plotter | 2.47 | 0.06 | 2.53 | |
| EV_table | 1.00 | 0.06 | 1.07 | |
| PCA_plotter | 19.28 | 0.42 | 19.70 | |
| batch_correct | 18.17 | 0.29 | 18.48 | |
| batch_design | 0.86 | 0.06 | 0.92 | |
| batchqc_explained_variation | 1.17 | 0.11 | 1.28 | |
| bladder_data_upload | 0.25 | 0.06 | 0.43 | |
| color_palette | 0.20 | 0.06 | 0.26 | |
| confound_metrics | 0.55 | 0.02 | 0.56 | |
| cor_props | 0.68 | 0.01 | 0.71 | |
| covariates_not_confounded | 0.68 | 0.07 | 0.73 | |
| cramers_v | 0.56 | 0.09 | 0.66 | |
| dendrogram_alpha_numeric_check | 0.53 | 0.05 | 0.57 | |
| dendrogram_color_palette | 1.32 | 0.08 | 1.39 | |
| dendrogram_plotter | 2.17 | 0.06 | 2.23 | |
| goodness_of_fit_DESeq2 | 5.09 | 0.11 | 5.21 | |
| heatmap_num_to_char_converter | 0.60 | 0.06 | 0.65 | |
| heatmap_plotter | 1.55 | 0.08 | 1.62 | |
| normalize_SE | 0.92 | 0.08 | 1.00 | |
| process_dendrogram | 1.50 | 0.03 | 1.53 | |
| pval_plotter | 23.74 | 0.28 | 24.01 | |
| pval_summary | 25.54 | 0.42 | 26.00 | |
| ratio_plotter | 1.18 | 0.06 | 1.24 | |
| std_pearson_corr_coef | 0.57 | 0.07 | 0.64 | |
| summarized_experiment | 0.01 | 0.00 | 0.02 | |
| variation_ratios | 1.19 | 0.04 | 1.23 | |
| volcano_plot | 34.94 | 0.46 | 37.18 | |