| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-09 11:40:34 -0400 (Thu, 09 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" | 4748 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4484 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4514 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4480 |
| 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 | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: BatchQC |
| Version: 2.0.0 |
| Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:BatchQC.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings BatchQC_2.0.0.tar.gz |
| StartedAt: 2024-05-09 04:59:44 -0000 (Thu, 09 May 2024) |
| EndedAt: 2024-05-09 05:07:56 -0000 (Thu, 09 May 2024) |
| EllapsedTime: 491.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BatchQC.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:BatchQC.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --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 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* 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 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 32.971 0.171 33.207
DE_analyze 25.393 0.228 25.671
pval_plotter 22.842 0.092 22.977
pval_summary 22.069 0.032 22.139
PCA_plotter 21.036 0.075 21.151
batch_correct 17.515 0.051 17.596
* 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: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL BatchQC ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/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 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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
0.196 0.039 0.224
BatchQC.Rcheck/tests/testthat.Rout
R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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
15.186 0.542 15.756
BatchQC.Rcheck/BatchQC-Ex.timings
| name | user | system | elapsed | |
| BatchQC | 0 | 0 | 0 | |
| DE_analyze | 25.393 | 0.228 | 25.671 | |
| EV_plotter | 1.504 | 0.048 | 1.555 | |
| EV_table | 1.175 | 0.020 | 1.197 | |
| PCA_plotter | 21.036 | 0.075 | 21.151 | |
| batch_correct | 17.515 | 0.051 | 17.596 | |
| batch_design | 0.883 | 0.004 | 0.889 | |
| batchqc_explained_variation | 0.741 | 0.008 | 0.750 | |
| bladder_data_upload | 0.306 | 0.004 | 0.311 | |
| color_palette | 0.269 | 0.008 | 0.278 | |
| confound_metrics | 0.868 | 0.040 | 0.911 | |
| cor_props | 0.822 | 0.024 | 0.847 | |
| covariates_not_confounded | 0.907 | 0.004 | 0.913 | |
| cramers_v | 0.806 | 0.000 | 0.809 | |
| dendrogram_alpha_numeric_check | 0.768 | 0.008 | 0.778 | |
| dendrogram_color_palette | 1.212 | 0.000 | 1.214 | |
| dendrogram_plotter | 2.372 | 0.016 | 2.396 | |
| heatmap_num_to_char_converter | 0.792 | 0.000 | 0.793 | |
| heatmap_plotter | 2.306 | 0.008 | 2.320 | |
| normalize_SE | 1.175 | 0.000 | 1.178 | |
| process_dendrogram | 1.210 | 0.024 | 1.236 | |
| pval_plotter | 22.842 | 0.092 | 22.977 | |
| pval_summary | 22.069 | 0.032 | 22.139 | |
| std_pearson_corr_coef | 0.798 | 0.000 | 0.799 | |
| summarized_experiment | 0.020 | 0.000 | 0.021 | |
| volcano_plot | 32.971 | 0.171 | 33.207 | |