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CHECK report for ALDEx2 on celaya2

This page was generated on 2019-10-16 12:54:07 -0400 (Wed, 16 Oct 2019).

Package 41/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ALDEx2 1.16.0
Greg Gloor
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/ALDEx2
Branch: RELEASE_3_9
Last Commit: bd698a8
Last Changed Date: 2019-05-02 11:53:49 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ALDEx2
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ALDEx2.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ALDEx2_1.16.0.tar.gz
StartedAt: 2019-10-16 00:28:02 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 00:32:54 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 292.3 seconds
RetCode: 0
Status:  OK 
CheckDir: ALDEx2.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:ALDEx2.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ALDEx2_1.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/ALDEx2.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 ‘ALDEx2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ALDEx2’ version ‘1.16.0’
* 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 ‘ALDEx2’ 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
aldex.corr 15.259  0.338  15.598
* 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

ALDEx2.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ALDEx2
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘ALDEx2’ ...
** using staged installation
** R
** data
** 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 (ALDEx2)

Tests output

ALDEx2.Rcheck/tests/testthat.Rout


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(ALDEx2)
> 
> test_check("ALDEx2")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 22 | SKIPPED: 0 | WARNINGS: 4 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 59.961   2.441  62.477 

Example timings

ALDEx2.Rcheck/ALDEx2-Ex.timings

nameusersystemelapsed
ALDEx2m-package000
aldex2.0690.4462.515
aldex.clr-class0.6430.0040.648
aldex.clr.function-methods0.0890.0070.096
aldex.corr15.259 0.33815.598
aldex.effect3.7460.0613.807
aldex.glm1.5000.0231.524
aldex.kw3.3510.0213.372
aldex.set.mode0.0790.0070.085
aldex.ttest0.2600.0130.273
getDenom-method0.1330.0080.141
getFeatureNames-method0.0840.0070.091
getFeatures-method0.0820.0060.088
getMonteCarloInstances-method0.0760.0040.079
getMonteCarloReplicate-method0.0850.0070.093
getReads-method0.0870.0080.096
getSampleIDs-method0.0910.0100.100
numConditions-method0.0860.0070.093
numFeatures-method0.0570.0040.061
numMCInstances-method0.0550.0030.058
plot.aldex000