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CHECK report for microbiomeDASim on malbec1

This page was generated on 2021-01-25 11:49:03 -0500 (Mon, 25 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE microbiomeDASim PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1094/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
microbiomeDASim 1.4.0
Justin Williams
Snapshot Date: 2021-01-24 14:40:16 -0500 (Sun, 24 Jan 2021)
URL: https://git.bioconductor.org/packages/microbiomeDASim
Branch: RELEASE_3_12
Last Commit: 55fb35a
Last Changed Date: 2020-10-27 11:49:06 -0500 (Tue, 27 Oct 2020)
malbec1 Linux (Ubuntu 18.04.5 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: microbiomeDASim
Version: 1.4.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:microbiomeDASim.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings microbiomeDASim_1.4.0.tar.gz
StartedAt: 2021-01-25 04:09:33 -0500 (Mon, 25 Jan 2021)
EndedAt: 2021-01-25 04:13:21 -0500 (Mon, 25 Jan 2021)
EllapsedTime: 227.5 seconds
RetCode: 0
Status:  OK 
CheckDir: microbiomeDASim.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:microbiomeDASim.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings microbiomeDASim_1.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/microbiomeDASim.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘microbiomeDASim/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘microbiomeDASim’ version ‘1.4.0’
* 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 ‘microbiomeDASim’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
gen_norm_microbiome_obs 22.156  0.028  22.211
simulate2MRexperiment    8.604  0.004   8.626
simulate2phyloseq        7.800  0.000   7.840
gen_norm_microbiome      5.612  0.008   5.643
* 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

microbiomeDASim.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL microbiomeDASim
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘microbiomeDASim’ ...
** using staged installation
** R
** 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 (microbiomeDASim)

Tests output

microbiomeDASim.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-pc-linux-gnu (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(microbiomeDASim)
> 
> test_check("microbiomeDASim")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 33 ]
> 
> proc.time()
   user  system elapsed 
 12.236   0.296  12.563 

Example timings

microbiomeDASim.Rcheck/microbiomeDASim-Ex.timings

nameusersystemelapsed
gen_norm_microbiome5.6120.0085.643
gen_norm_microbiome_obs22.156 0.02822.211
ggplot_spaghetti3.0840.0123.097
mean_trend0.4800.0000.483
mvrnorm_corr_gen0.2120.0000.215
mvrnorm_sim2.7960.0122.812
mvrnorm_sim_obs3.8400.0363.883
simulate2MRexperiment8.6040.0048.626
simulate2phyloseq7.800.007.84