Package: MSstatsSampleSize

Version: 1.0.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MSstatsSampleSize.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MSstatsSampleSize_1.0.1.tar.gz

StartedAt: 2020-04-15 04:07:03 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 04:10:23 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 199.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: MSstatsSampleSize.Rcheck

Warnings: 2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MSstatsSampleSize.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MSstatsSampleSize_1.0.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/MSstatsSampleSize.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSstatsSampleSize/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MSstatsSampleSize’ version ‘1.0.1’
* 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 ‘MSstatsSampleSize’ 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 ... WARNING
Functions or methods with usage in documentation object '.classification' but not in code:
  ‘.classification’

* 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 ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                             old_size new_size compress
  classification_results.rda    1.8Mb    1.3Mb       xz
  simulated_datasets.rda        656Kb    511Kb       xz
  variance_estimation.rda       690Kb    320Kb       xz
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                      user system elapsed
designSampleSizeClassificationPlots 69.370  9.281  26.640
designSampleSizeClassification      15.109  0.132  15.473
* 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: 2 WARNINGs
See
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/MSstatsSampleSize.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MSstatsSampleSize
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘MSstatsSampleSize’ ...
** 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 (MSstatsSampleSize)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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(MSstatsSampleSize)
> 
> test_check("MSstatsSampleSize")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 7 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 20.893   0.525  21.603 

name	user	system	elapsed
OV_SRM_train	0.007	0.007	0.015
OV_SRM_train_annotation	0.006	0.000	0.006
classification_results	0.062	0.014	0.076
designSampleSizeClassification	15.109	0.132	15.473
designSampleSizeClassificationPlots	69.370	9.281	26.640
designSampleSizeHypothesisTestingPlot	0.403	0.015	0.420
designSampleSizePCAplot	3.927	0.104	4.081
estimateVar	0.354	0.011	0.370
meanSDplot	2.299	0.181	2.505
simulateDataset	0.470	0.023	0.506
simulated_datasets	0.033	0.007	0.041
variance_estimation	0.029	0.004	0.033