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CHECK report for ALDEx2 on merida1

This page was generated on 2020-08-07 12:31:11 -0400 (Fri, 07 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE ALDEx2 PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 40/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ALDEx2 1.21.1
Greg Gloor
Snapshot Date: 2020-08-06 14:50:46 -0400 (Thu, 06 Aug 2020)
URL: https://git.bioconductor.org/packages/ALDEx2
Branch: master
Last Commit: 93c54f9
Last Changed Date: 2020-07-07 15:59:33 -0400 (Tue, 07 Jul 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ALDEx2
Version: 1.21.1
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_1.21.1.tar.gz
StartedAt: 2020-08-07 00:49:28 -0400 (Fri, 07 Aug 2020)
EndedAt: 2020-08-07 00:56:22 -0400 (Fri, 07 Aug 2020)
EllapsedTime: 413.9 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_1.21.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/ALDEx2.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.21.1’
* 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 (user + system) or elapsed time > 5s
                    user system elapsed
aldex.corr       130.598  4.512 135.697
aldex.glm.effect   7.820  0.032   7.859
* 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/4.0/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 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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)
Loading required package: zCompositions
Loading required package: MASS
Loading required package: NADA
Loading required package: survival

Attaching package: 'NADA'

The following object is masked from 'package:stats':

    cor

Loading required package: truncnorm
> 
> test_check("ALDEx2")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 22 | SKIPPED: 0 | WARNINGS: 4 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 63.189   1.441  64.688 

Example timings

ALDEx2.Rcheck/ALDEx2-Ex.timings

nameusersystemelapsed
ALDEx2m-package0.0000.0010.001
aldex2.2960.4632.806
aldex.clr-class0.0790.0070.086
aldex.clr.function-methods0.0790.0060.085
aldex.corr130.598 4.512135.697
aldex.effect3.9790.0174.051
aldex.glm1.7260.0151.746
aldex.glm.effect7.8200.0327.859
aldex.kw3.0160.0173.037
aldex.plotFeature0.1350.0060.142
aldex.set.mode0.0690.0020.071
aldex.ttest0.2410.0030.245
expectedDistance0.4780.0180.496
getDenom-method0.1500.0050.156
getFeatureNames-method0.0800.0030.084
getFeatures-method0.0790.0020.080
getMonteCarloInstances-method0.0730.0030.076
getMonteCarloReplicate-method0.0730.0030.076
getMonteCarloSample-method0.0760.0030.079
getReads-method0.0740.0030.077
getSampleIDs-method0.0810.0030.085
numConditions-method0.0690.0020.072
numFeatures-method0.0640.0020.066
numMCInstances-method0.0680.0020.070
plot.aldex000