Package: proBatch

Version: 1.0.0

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_1.0.0.tar.gz

StartedAt: 2019-10-16 05:44:19 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 05:52:04 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 464.6 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_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/proBatch.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.0.0’
* 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 ‘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
adjust_batch_trend      54.548 23.815  78.385
plot_with_fitting_curve 51.836 25.026  76.882
correct_batch_effects   50.975 24.962  75.955
plot_PVCA                6.901  0.058   6.964
* 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’ ...
** 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)

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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 | WARNINGS: 2 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 23.192   1.478  24.632 

name	user	system	elapsed
adjust_batch_trend	54.548	23.815	78.385
center_peptide_batch_medians	1.416	0.096	1.513
correct_batch_effects	50.975	24.962	75.955
correct_with_ComBat	2.446	0.149	2.599
create_peptide_annotation	0.018	0.001	0.019
date_to_sample_order	0.191	0.000	0.191
dates_to_posix	0.009	0.000	0.009
log_transform	0.005	0.003	0.007
long_to_matrix	0.119	0.028	0.147
matrix_to_long	0.587	0.059	0.645
normalize_data	0.036	0.005	0.040
normalize_sample_medians	0.097	0.016	0.113
plot_PCA	0.340	0.042	0.382
plot_PVCA	6.901	0.058	6.964
plot_corr_matrix	0.021	0.002	0.023
plot_heatmap	1.629	0.096	1.727
plot_hierarchical_clustering	0.374	0.016	0.391
plot_iRT	0.129	0.007	0.137
plot_peptide_corr_distribution	4.526	0.288	4.815
plot_peptides_of_one_protein	0.071	0.013	0.083
plot_protein_corrplot	0.084	0.002	0.085
plot_sample_corr_distribution	0.597	0.047	0.645
plot_sample_corr_heatmap	0.065	0.001	0.066
plot_sample_mean_or_boxplot	1.016	0.070	1.088
plot_single_feature	0.042	0.004	0.046
plot_spike_in	0.128	0.007	0.135
plot_with_fitting_curve	51.836	25.026	76.882
quantile_normalize	0.032	0.002	0.033
sample_annotation_to_colors	0.054	0.000	0.055