Multiple platform build/check report for BioC 3.11 - CHECK report for proBatch on machv2

##############################################################################
##############################################################################
###
### Running command:
###
###   /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_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/proBatch.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.4.0’
* 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
calculate_PVCA              25.234  0.183  25.446
plot_PVCA.df                24.964  0.046  25.066
plot_PVCA                   24.715  0.077  24.842
prepare_PVCA_df             24.561  0.041  24.635
correct_batch_effects        8.200  0.138   8.351
plot_sample_mean_or_boxplot  5.243  0.063   5.311
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL proBatch
###
##############################################################################
##############################################################################


* 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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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 
  0.317   0.071   0.363


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 159 | SKIPPED: 0 | WARNINGS: 30 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 44.137   0.871  45.012

Example timings

name	user	system	elapsed
calculate_PVCA	25.234	0.183	25.446
calculate_feature_CV	0.540	0.019	0.561
calculate_peptide_corr_distr	0.044	0.001	0.045
calculate_sample_corr_distr	0.956	0.029	0.990
check_sample_consistency	0.471	0.006	0.478
correct_batch_effects	8.200	0.138	8.351
create_peptide_annotation	0.011	0.000	0.011
date_to_sample_order	0.326	0.002	0.328
dates_to_posix	0.017	0.000	0.016
define_sample_order	0.020	0.003	0.023
feature_level_diagnostics	4.805	0.052	4.860
fit_nonlinear	0.013	0.001	0.013
long_to_matrix	0.057	0.007	0.064
matrix_to_long	0.020	0.002	0.021
normalize	0.114	0.002	0.116
plot_CV_distr	0.806	0.015	0.822
plot_PCA	1.069	0.032	1.103
plot_PVCA	24.715	0.077	24.842
plot_PVCA.df	24.964	0.046	25.066
plot_corr_matrix	0.066	0.002	0.067
plot_heatmap_diagnostic	1.802	0.094	1.899
plot_heatmap_generic	0.852	0.056	0.912
plot_hierarchical_clustering	0.635	0.027	0.666
plot_peptide_corr_distribution	2.181	0.037	2.225
plot_protein_corrplot	0.239	0.003	0.244
plot_sample_corr_distribution	1.626	0.023	1.651
plot_sample_corr_heatmap	0.697	0.031	0.727
plot_sample_mean_or_boxplot	5.243	0.063	5.311
prepare_PVCA_df	24.561	0.041	24.635
sample_annotation_to_colors	0.048	0.001	0.049
transform_raw_data	0.015	0.001	0.016

CHECK report for proBatch on machv2

Summary

Command output

Installation output

Tests output

Example timings