| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-18 11:37:35 -0400 (Sat, 18 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4751 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4485 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4515 |
| 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 137/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BatchQC 2.0.0 (landing page) Jessica McClintock
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 2.0.0 |
| 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_2.0.0.tar.gz |
| StartedAt: 2024-05-17 19:14:01 -0400 (Fri, 17 May 2024) |
| EndedAt: 2024-05-17 19:21:04 -0400 (Fri, 17 May 2024) |
| EllapsedTime: 423.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BatchQC.Rcheck |
| Warnings: 0 |
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### Running command:
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### /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_2.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/BatchQC.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BatchQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BatchQC’ version ‘2.0.0’
* 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 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 29.087 0.537 29.894
DE_analyze 21.851 0.561 22.559
pval_plotter 20.502 0.445 21.094
pval_summary 18.218 0.403 18.752
PCA_plotter 14.292 0.372 14.777
batch_correct 11.490 0.299 11.857
* 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/4.4-x86_64/Resources/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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 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)
NULL
>
> proc.time()
user system elapsed
0.215 0.089 0.297
BatchQC.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 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
13.253 0.813 14.194
BatchQC.Rcheck/BatchQC-Ex.timings
| name | user | system | elapsed | |
| BatchQC | 0.000 | 0.001 | 0.001 | |
| DE_analyze | 21.851 | 0.561 | 22.559 | |
| EV_plotter | 1.550 | 0.049 | 1.616 | |
| EV_table | 1.215 | 0.035 | 1.259 | |
| PCA_plotter | 14.292 | 0.372 | 14.777 | |
| batch_correct | 11.490 | 0.299 | 11.857 | |
| batch_design | 0.798 | 0.030 | 0.835 | |
| batchqc_explained_variation | 0.668 | 0.027 | 0.702 | |
| bladder_data_upload | 0.250 | 0.034 | 0.286 | |
| color_palette | 0.280 | 0.022 | 0.306 | |
| confound_metrics | 0.793 | 0.038 | 0.839 | |
| cor_props | 0.749 | 0.028 | 0.785 | |
| covariates_not_confounded | 0.799 | 0.039 | 0.845 | |
| cramers_v | 0.751 | 0.024 | 0.782 | |
| dendrogram_alpha_numeric_check | 0.682 | 0.026 | 0.714 | |
| dendrogram_color_palette | 0.972 | 0.036 | 1.016 | |
| dendrogram_plotter | 1.934 | 0.056 | 2.021 | |
| heatmap_num_to_char_converter | 0.716 | 0.026 | 0.748 | |
| heatmap_plotter | 1.786 | 0.070 | 1.870 | |
| normalize_SE | 1.104 | 0.034 | 1.149 | |
| process_dendrogram | 1.135 | 0.071 | 1.221 | |
| pval_plotter | 20.502 | 0.445 | 21.094 | |
| pval_summary | 18.218 | 0.403 | 18.752 | |
| std_pearson_corr_coef | 0.722 | 0.026 | 0.753 | |
| summarized_experiment | 0.015 | 0.003 | 0.017 | |
| volcano_plot | 29.087 | 0.537 | 29.894 | |