Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-23 11:40 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4372 |
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 141/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BatchQC 2.3.0 (landing page) Jessica McClintock
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: 2.3.0 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:BatchQC.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings BatchQC_2.3.0.tar.gz |
StartedAt: 2024-12-22 20:04:48 -0500 (Sun, 22 Dec 2024) |
EndedAt: 2024-12-22 20:11:29 -0500 (Sun, 22 Dec 2024) |
EllapsedTime: 400.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BatchQC.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:BatchQC.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings BatchQC_2.3.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/BatchQC.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘BatchQC/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BatchQC’ version ‘2.3.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 23 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 27.494 0.164 27.660 DE_analyze 20.197 0.494 20.692 pval_summary 17.244 0.273 17.517 pval_plotter 16.763 0.115 16.878 PCA_plotter 11.186 0.145 11.330 batch_correct 9.879 0.117 9.996 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
BatchQC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL BatchQC ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-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 Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-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) NULL > > proc.time() user system elapsed 0.143 0.030 0.163
BatchQC.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-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 10.837 0.708 11.535
BatchQC.Rcheck/BatchQC-Ex.timings
name | user | system | elapsed | |
BatchQC | 0 | 0 | 0 | |
DE_analyze | 20.197 | 0.494 | 20.692 | |
EV_plotter | 1.949 | 0.101 | 2.051 | |
EV_table | 0.823 | 0.018 | 0.841 | |
PCA_plotter | 11.186 | 0.145 | 11.330 | |
batch_correct | 9.879 | 0.117 | 9.996 | |
batch_design | 0.496 | 0.013 | 0.514 | |
batchqc_explained_variation | 0.904 | 0.130 | 1.044 | |
bladder_data_upload | 0.243 | 0.021 | 0.265 | |
color_palette | 0.177 | 0.009 | 0.187 | |
confound_metrics | 0.484 | 0.013 | 0.498 | |
cor_props | 0.426 | 0.011 | 0.437 | |
covariates_not_confounded | 0.493 | 0.006 | 0.500 | |
cramers_v | 0.424 | 0.009 | 0.434 | |
dendrogram_alpha_numeric_check | 0.403 | 0.007 | 0.411 | |
dendrogram_color_palette | 0.702 | 0.008 | 0.710 | |
dendrogram_plotter | 1.509 | 0.010 | 1.519 | |
goodness_of_fit_DESeq2 | 3.878 | 0.011 | 3.889 | |
heatmap_num_to_char_converter | 0.445 | 0.007 | 0.452 | |
heatmap_plotter | 1.273 | 0.011 | 1.285 | |
normalize_SE | 1.583 | 0.054 | 1.636 | |
process_dendrogram | 0.664 | 0.033 | 0.697 | |
pval_plotter | 16.763 | 0.115 | 16.878 | |
pval_summary | 17.244 | 0.273 | 17.517 | |
ratio_plotter | 1.012 | 0.006 | 1.018 | |
std_pearson_corr_coef | 0.448 | 0.010 | 0.457 | |
summarized_experiment | 0.016 | 0.000 | 0.015 | |
variation_ratios | 0.891 | 0.031 | 0.921 | |
volcano_plot | 27.494 | 0.164 | 27.660 | |