Jessica McClintock
| Snapshot Date: 2024-11-17 13:40 -0500 (Sun, 17 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/BatchQC |
| git_branch: devel |
| git_last_commit: 8029628 |
| git_last_commit_date: 2024-10-29 10:09:55 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-11-18 11:34 -0500 (Mon, 18 Nov 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" | 4740 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4454 |
| 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 141/2268 | 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 | | ||||||||
|
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: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BatchQC.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings BatchQC_2.3.0.tar.gz |
| StartedAt: 2024-11-17 22:23:02 -0500 (Sun, 17 Nov 2024) |
| EndedAt: 2024-11-17 22:30:49 -0500 (Sun, 17 Nov 2024) |
| EllapsedTime: 467.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BatchQC.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BatchQC.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings BatchQC_2.3.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/BatchQC.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* 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 '2.3.0'
* 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 35.56 0.50 38.08
DE_analyze 27.97 0.48 28.45
pval_plotter 23.75 0.29 24.05
pval_summary 21.14 0.25 21.37
PCA_plotter 19.39 0.29 19.67
batch_correct 17.44 0.15 17.60
goodness_of_fit_DESeq2 5.06 0.09 5.15
* 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: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL BatchQC ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-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 Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 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
0.18 0.07 0.50
BatchQC.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 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
12.06 0.84 13.23
BatchQC.Rcheck/BatchQC-Ex.timings
| name | user | system | elapsed | |
| BatchQC | 0 | 0 | 0 | |
| DE_analyze | 27.97 | 0.48 | 28.45 | |
| EV_plotter | 1.25 | 0.13 | 1.37 | |
| EV_table | 1.17 | 0.07 | 1.25 | |
| PCA_plotter | 19.39 | 0.29 | 19.67 | |
| batch_correct | 17.44 | 0.15 | 17.60 | |
| batch_design | 1.75 | 0.06 | 1.81 | |
| batchqc_explained_variation | 1.25 | 0.11 | 1.36 | |
| bladder_data_upload | 0.22 | 0.05 | 0.38 | |
| color_palette | 0.33 | 0.01 | 0.34 | |
| confound_metrics | 0.66 | 0.06 | 0.71 | |
| cor_props | 0.61 | 0.05 | 0.66 | |
| covariates_not_confounded | 0.59 | 0.03 | 0.63 | |
| cramers_v | 0.61 | 0.03 | 0.64 | |
| dendrogram_alpha_numeric_check | 0.53 | 0.00 | 0.53 | |
| dendrogram_color_palette | 1.05 | 0.03 | 1.08 | |
| dendrogram_plotter | 2.12 | 0.10 | 2.22 | |
| goodness_of_fit_DESeq2 | 5.06 | 0.09 | 5.15 | |
| heatmap_num_to_char_converter | 0.46 | 0.05 | 0.51 | |
| heatmap_plotter | 1.93 | 0.08 | 2.00 | |
| normalize_SE | 1.04 | 0.08 | 1.13 | |
| process_dendrogram | 1.16 | 0.06 | 1.22 | |
| pval_plotter | 23.75 | 0.29 | 24.05 | |
| pval_summary | 21.14 | 0.25 | 21.37 | |
| ratio_plotter | 1.39 | 0.02 | 1.41 | |
| std_pearson_corr_coef | 0.60 | 0.01 | 0.61 | |
| summarized_experiment | 0.01 | 0.00 | 0.02 | |
| variation_ratios | 2.02 | 0.05 | 2.06 | |
| volcano_plot | 35.56 | 0.50 | 38.08 | |