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This page was generated on 2021-09-24 15:06:33 -0400 (Fri, 24 Sep 2021).

CHECK results for ALDEx2 on machv2

To the developers/maintainers of the ALDEx2 package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ALDEx2.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 42/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ALDEx2 1.24.0  (landing page)
Greg Gloor
Snapshot Date: 2021-09-23 04:50:12 -0400 (Thu, 23 Sep 2021)
git_url: https://git.bioconductor.org/packages/ALDEx2
git_branch: RELEASE_3_13
git_last_commit: a41b778
git_last_commit_date: 2021-05-19 12:08:00 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ALDEx2
Version: 1.24.0
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_1.24.0.tar.gz
StartedAt: 2021-09-23 16:06:55 -0400 (Thu, 23 Sep 2021)
EndedAt: 2021-09-23 16:12:51 -0400 (Thu, 23 Sep 2021)
EllapsedTime: 355.8 seconds
RetCode: 0
Status:   OK  
CheckDir: ALDEx2.Rcheck
Warnings: 0

Command output

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### Running 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_1.24.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/ALDEx2.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.24.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
aldex.corr 109.705  4.209 114.278
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/ALDEx2.Rcheck/00check.log’
for details.



Installation output

ALDEx2.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ALDEx2
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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
Loading required package: Rfast
Loading required package: Rcpp
Loading required package: RcppZiggurat
> 
> test_check("ALDEx2")
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 22 ]
> 
> proc.time()
   user  system elapsed 
 51.600   1.360  52.985 

Example timings

ALDEx2.Rcheck/ALDEx2-Ex.timings

nameusersystemelapsed
ALDEx2m-package000
aldex2.3020.4692.772
aldex.clr-class0.0970.0160.180
aldex.clr.function-methods0.1070.0060.113
aldex.corr109.705 4.209114.278
aldex.effect0.3830.0090.393
aldex.glm1.4950.0061.501
aldex.glm.effect0.6790.0230.702
aldex.kw2.9460.0152.978
aldex.plotFeature0.1580.0050.204
aldex.set.mode0.0820.0040.086
aldex.ttest0.1990.0060.204
expectedDistance1.0740.0431.117
getDenom-method0.1450.0060.151
getDirichletInstances-method0.0600.0040.064
getDirichletReplicate-method0.0860.0040.090
getDirichletSample-method0.0560.0030.060
getFeatureNames-method0.0690.0060.075
getFeatures-method0.0920.0020.095
getMonteCarloInstances-method0.0650.0030.067
getMonteCarloReplicate-method0.0750.0020.078
getMonteCarloSample-method0.0880.0020.091
getReads-method0.0570.0030.060
getSampleIDs-method0.0700.0030.073
numConditions-method0.0870.0020.090
numFeatures-method0.0700.0040.074
numMCInstances-method0.0820.0030.084
plot.aldex0.0000.0000.001