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CHECK report for ANCOMBC on merida1

This page was generated on 2020-11-27 11:59:18 -0500 (Fri, 27 Nov 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE ANCOMBC PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 55/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ANCOMBC 1.0.1
Huang Lin
Snapshot Date: 2020-11-26 14:42:42 -0500 (Thu, 26 Nov 2020)
URL: https://git.bioconductor.org/packages/ANCOMBC
Branch: RELEASE_3_12
Last Commit: aa55bbc
Last Changed Date: 2020-11-20 10:41:08 -0500 (Fri, 20 Nov 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
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: ANCOMBC
Version: 1.0.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ANCOMBC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ANCOMBC_1.0.1.tar.gz
StartedAt: 2020-11-26 23:04:14 -0500 (Thu, 26 Nov 2020)
EndedAt: 2020-11-26 23:08:08 -0500 (Thu, 26 Nov 2020)
EllapsedTime: 234.9 seconds
RetCode: 0
Status:  OK 
CheckDir: ANCOMBC.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ANCOMBC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ANCOMBC_1.0.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/ANCOMBC.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ANCOMBC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ANCOMBC’ 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 ‘ANCOMBC’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘microbiome’
A package should be listed in only one of these fields.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
ancombc 30.839   0.27  31.162
* 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-3.12-bioc/meat/ANCOMBC.Rcheck/00check.log’
for details.



Installation output

ANCOMBC.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘ANCOMBC’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
Loading required namespace: ANCOMBC
*** 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 (ANCOMBC)

Tests output

ANCOMBC.Rcheck/tests/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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")
> packageVersion("ANCOMBC")
[1] '1.0.1'
> test_check("ANCOMBC")
Loading required package: ANCOMBC
── Warning (test-data_prep.R:64:7): `data_prep` function should only activate th
The multi-group comparison will be deactivated as the group variable has < 3 categories.

══ testthat results  ═══════════════════════════════════════════════════════════
Warning (test-data_prep.R:64:7): `data_prep` function should only activate the global test when the
          number of categories for the group variable is greater than or equal
          to 3

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 6 ]
> 
> proc.time()
   user  system elapsed 
 22.379   0.657  23.050 

Example timings

ANCOMBC.Rcheck/ANCOMBC-Ex.timings

nameusersystemelapsed
ancombc30.839 0.27031.162