Multiple platform build/check report for BioC 3.12 - CHECK report for proBatch on merida1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:proBatch.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings proBatch_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/proBatch.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘proBatch/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘proBatch’ version ‘1.6.0’
* 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 ‘proBatch’ 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 R 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
plot_PVCA.df          21.996  0.050  22.070
calculate_PVCA        21.794  0.136  21.960
plot_PVCA             21.786  0.088  21.913
prepare_PVCA_df       21.369  0.053  21.447
correct_batch_effects  6.548  0.123   6.687
* 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL proBatch
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘proBatch’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (proBatch)

Tests output


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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 
  0.238   0.059   0.273


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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(proBatch)

> 
> test_check("proBatch")
[ FAIL 0 | WARN 30 | SKIP 0 | PASS 159 ]
> 
> proc.time()
   user  system elapsed 
 37.651   0.705  38.665

Example timings

name	user	system	elapsed
calculate_PVCA	21.794	0.136	21.960
calculate_feature_CV	0.433	0.016	0.450
calculate_peptide_corr_distr	0.038	0.000	0.038
calculate_sample_corr_distr	1.096	0.025	1.123
check_sample_consistency	0.023	0.002	0.025
correct_batch_effects	6.548	0.123	6.687
create_peptide_annotation	0.006	0.000	0.006
date_to_sample_order	0.183	0.000	0.183
dates_to_posix	0.011	0.000	0.011
define_sample_order	0.014	0.004	0.017
feature_level_diagnostics	4.070	0.030	4.104
fit_nonlinear	0.013	0.001	0.013
long_to_matrix	0.051	0.001	0.051
matrix_to_long	0.015	0.001	0.016
normalize	0.097	0.004	0.102
plot_CV_distr	0.665	0.017	0.686
plot_PCA	1.205	0.026	1.240
plot_PVCA	21.786	0.088	21.913
plot_PVCA.df	21.996	0.050	22.070
plot_corr_matrix	0.047	0.002	0.049
plot_heatmap_diagnostic	1.645	0.066	1.717
plot_heatmap_generic	0.528	0.039	0.571
plot_hierarchical_clustering	0.412	0.020	0.436
plot_peptide_corr_distribution	1.741	0.024	1.767
plot_protein_corrplot	0.258	0.004	0.263
plot_sample_corr_distribution	1.415	0.022	1.442
plot_sample_corr_heatmap	0.591	0.029	0.623
plot_sample_mean_or_boxplot	4.237	0.045	4.287
prepare_PVCA_df	21.369	0.053	21.447
sample_annotation_to_colors	0.039	0.000	0.039
transform_raw_data	0.009	0.000	0.009

CHECK report for proBatch on merida1

Summary

Command output

Installation output

Tests output

Example timings