Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-31 17:02:50 -0400 (Fri, 31 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" | 4753 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
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 | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | 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: 2.0.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:BatchQC.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings BatchQC_2.0.0.tar.gz |
StartedAt: 2024-05-31 01:27:20 -0400 (Fri, 31 May 2024) |
EndedAt: 2024-05-31 01:33:59 -0400 (Fri, 31 May 2024) |
EllapsedTime: 398.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BatchQC.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:BatchQC.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings BatchQC_2.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/BatchQC.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * 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 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 22.984 0.064 23.047 DE_analyze 17.833 0.219 18.053 pval_plotter 16.046 0.112 16.158 pval_summary 15.200 0.208 15.408 batch_correct 12.219 0.096 12.315 PCA_plotter 11.958 0.167 12.127 * 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-3.19-bioc/R/bin/R CMD INSTALL BatchQC ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-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 version 4.4.0 (2024-04-24) -- "Puppy Cup" 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 0.146 0.038 0.175
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-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 11.152 0.652 11.795
BatchQC.Rcheck/BatchQC-Ex.timings
name | user | system | elapsed | |
BatchQC | 0 | 0 | 0 | |
DE_analyze | 17.833 | 0.219 | 18.053 | |
EV_plotter | 1.217 | 0.021 | 1.238 | |
EV_table | 0.978 | 0.032 | 1.011 | |
PCA_plotter | 11.958 | 0.167 | 12.127 | |
batch_correct | 12.219 | 0.096 | 12.315 | |
batch_design | 0.559 | 0.008 | 0.567 | |
batchqc_explained_variation | 0.510 | 0.013 | 0.524 | |
bladder_data_upload | 0.206 | 0.024 | 0.231 | |
color_palette | 0.186 | 0.004 | 0.191 | |
confound_metrics | 0.561 | 0.012 | 0.572 | |
cor_props | 0.547 | 0.000 | 0.546 | |
covariates_not_confounded | 0.609 | 0.008 | 0.616 | |
cramers_v | 0.530 | 0.000 | 0.531 | |
dendrogram_alpha_numeric_check | 0.523 | 0.012 | 0.535 | |
dendrogram_color_palette | 0.768 | 0.012 | 0.779 | |
dendrogram_plotter | 1.507 | 0.020 | 1.527 | |
heatmap_num_to_char_converter | 0.504 | 0.004 | 0.508 | |
heatmap_plotter | 1.334 | 0.020 | 1.355 | |
normalize_SE | 0.840 | 0.028 | 0.869 | |
process_dendrogram | 0.837 | 0.044 | 0.880 | |
pval_plotter | 16.046 | 0.112 | 16.158 | |
pval_summary | 15.200 | 0.208 | 15.408 | |
std_pearson_corr_coef | 0.504 | 0.016 | 0.519 | |
summarized_experiment | 0.014 | 0.000 | 0.014 | |
volcano_plot | 22.984 | 0.064 | 23.047 | |