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CHECK report for BEclear on merida1

This page was generated on 2019-04-16 11:58:41 -0400 (Tue, 16 Apr 2019).

Package 118/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BEclear 1.14.0
David Rasp
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/BEclear
Branch: RELEASE_3_8
Last Commit: e124e81
Last Changed Date: 2018-10-30 11:41:58 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: BEclear
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BEclear.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BEclear_1.14.0.tar.gz
StartedAt: 2019-04-15 22:32:52 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 22:34:11 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 79.0 seconds
RetCode: 0
Status:  OK 
CheckDir: BEclear.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BEclear.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BEclear_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/BEclear.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BEclear/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BEclear’ version ‘1.14.0’
* 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 ‘BEclear’ 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
BEclear-package    18.131  2.750   6.190
imputeMissingData   5.433  2.213   1.718
correctBatchEffect  4.056  2.458   1.935
clearBEgenes        3.988  1.285   0.942
* 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


Installation output

BEclear.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BEclear
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘BEclear’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
Loading required namespace: BEclear
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BEclear)

Tests output

BEclear.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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(BEclear)
Loading required package: BiocParallel
> 
> test_check("BEclear")
INFO [2019-04-15 22:34:04] Calculating the medians for 2 batches
INFO [2019-04-15 22:34:04] Calculating the medians for 3 batches
INFO [2019-04-15 22:34:05] Calculating the p-values for 2 batches
INFO [2019-04-15 22:34:05] Calculating the p-values for 3 batches
INFO [2019-04-15 22:34:05] Calculating the p-values for 3 batches
INFO [2019-04-15 22:34:05] Adjusting p-values
INFO [2019-04-15 22:34:05] 3 wrong values found
INFO [2019-04-15 22:34:06] Replacing values below 0 or above 1:
INFO [2019-04-15 22:34:06] 3 values replaced
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 71 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  7.010   3.996   4.487 

Example timings

BEclear.Rcheck/BEclear-Ex.timings

nameusersystemelapsed
BEclear-package18.131 2.750 6.190
calcMedians0.4260.4130.167
calcPvalues2.2741.2420.831
calcScore3.4691.4060.997
calcSummary2.6461.6471.016
clearBEgenes3.9881.2850.942
correctBatchEffect4.0562.4581.935
countValuesToPredict2.8712.1111.040
findWrongValues0.4710.0260.498
imputeMissingData5.4332.2131.718
makeBoxplot2.6872.0661.020
replaceWrongValues0.5930.0280.624