Package: proBatch

Version: 0.99.25

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_0.99.25.tar.gz

StartedAt: 2019-04-09 03:00:07 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:03:29 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 201.9 seconds

RetCode: 0

Status:  OK

CheckDir: proBatch.Rcheck

Warnings: 0

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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_0.99.25.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/proBatch.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘0.99.25’
* 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 or elapsed time > 5s
                         user system elapsed
correct_batch_effects   9.455  0.187   9.676
adjust_batch_trend      8.854  0.262   9.146
plot_with_fitting_curve 8.919  0.112   9.050
plot_PVCA               5.749  0.040   5.813
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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

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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/3.6/Resources/library’
* installing *source* package ‘proBatch’ ...
** 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
* DONE (proBatch)

R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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")
Standardizing Data across genes
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 144 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 17.967   0.764  18.760 

name	user	system	elapsed
adjust_batch_trend	8.854	0.262	9.146
center_peptide_batch_medians	1.321	0.060	1.387
correct_batch_effects	9.455	0.187	9.676
correct_with_ComBat	1.034	0.054	1.092
create_peptide_annotation	0.014	0.001	0.015
date_to_sample_order	0.162	0.006	0.170
dates_to_posix	0.007	0.000	0.007
log_transform	0.004	0.001	0.004
long_to_matrix	0.106	0.009	0.117
matrix_to_long	0.549	0.016	0.567
normalize_data	0.035	0.000	0.036
normalize_sample_medians	0.087	0.008	0.098
plot_PCA	0.28	0.01	0.29
plot_PVCA	5.749	0.040	5.813
plot_corr_matrix	0.021	0.001	0.021
plot_heatmap	2.014	0.053	2.074
plot_hierarchical_clustering	0.289	0.009	0.301
plot_iRT	0.138	0.004	0.142
plot_peptide_corr_distribution	3.761	0.104	3.878
plot_peptides_of_one_protein	0.060	0.004	0.064
plot_protein_corrplot	0.080	0.001	0.080
plot_sample_corr_distribution	0.592	0.027	0.621
plot_sample_corr_heatmap	0.045	0.001	0.046
plot_sample_mean_or_boxplot	0.771	0.027	0.801
plot_single_feature	0.034	0.002	0.037
plot_spike_in	0.084	0.003	0.088
plot_with_fitting_curve	8.919	0.112	9.050
quantile_normalize	0.030	0.000	0.031
sample_annotation_to_colors	0.037	0.000	0.037