Package: microbiome

Version: 1.2.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:microbiome.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings microbiome_1.2.1.tar.gz

StartedAt: 2018-10-16 22:37:55 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 22:40:59 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 183.7 seconds

RetCode: 0

Status:  OK

CheckDir: microbiome.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:microbiome.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings microbiome_1.2.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/microbiome.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘microbiome/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘microbiome’ version ‘1.2.1’
* 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 ‘microbiome’ 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
* 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

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL microbiome
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘microbiome’ ...
** 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
* DONE (microbiome)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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)
> test_check("microbiome")
Loading required package: microbiome
Loading required package: phyloseq
Loading required package: ggplot2

microbiome R package (microbiome.github.com)
    


 Copyright (C) 2011-2018 Leo Lahti et al. <microbiome.github.io>


Attaching package: 'microbiome'

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

    transform

══ testthat results  ═══════════════════════════════════════════════════════════
OK: 69 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  9.869   0.528  10.475 

name	user	system	elapsed
abundances	0.016	0.002	0.018
aggregate_taxa	1.531	0.096	1.641
associate	0.045	0.008	0.053
baseline	0.060	0.008	0.069
bimodality	0.021	0.003	0.025
bimodality_sarle	0.001	0.000	0.002
boxplot_abundance	0.081	0.013	0.093
chunk_reorder	0.003	0.000	0.003
cmat2table	0.130	0.011	0.142
core	0.017	0.002	0.018
core_abundance	0.016	0.003	0.019
core_matrix	0.000	0.000	0.001
core_members	0.011	0.002	0.013
coverage	0.041	0.006	0.048
densityplot	0.001	0.000	0.001
divergence	0.728	0.008	0.745
diversities	0.037	0.007	0.045
dominance	0.015	0.002	0.018
estimate_stability	0.001	0.001	0.001
evenness	0.014	0.004	0.018
find_optima	0.002	0.000	0.002
gktau	0.011	0.002	0.012
global	0.048	0.009	0.056
group_age	0.040	0.005	0.047
group_bmi	0.001	0.000	0.001
heat	0.083	0.002	0.085
hotplot	0.194	0.025	0.220
inequality	0.458	0.028	0.489
intermediate_stability	0.841	0.034	0.879
log_modulo_skewness	0.181	0.017	0.203
low_abundance	0.021	0.003	0.025
map_levels	0.053	0.003	0.056
merge_taxa2	0.040	0.004	0.045
meta	0.010	0.002	0.013
microbiome-package	0.011	0.001	0.011
multimodality	0.002	0.000	0.002
neat	0.081	0.002	0.086
neatsort	0.179	0.004	0.185
noncore_abundance	0.017	0.004	0.022
noncore_members	0.017	0.001	0.020
plot_atlas	0.100	0.006	0.110
plot_composition	3.278	0.016	3.307
plot_core	0.221	0.032	0.255
plot_density	0.064	0.008	0.072
plot_frequencies	0.023	0.003	0.025
plot_landscape	0.061	0.005	0.069
plot_regression	4.016	0.057	4.093
plot_taxa_prevalence	0.583	0.013	0.609
plot_tipping	0.176	0.030	0.209
potential_analysis	0.017	0.001	0.019
potential_univariate	0.001	0.000	0.001
prevalence	0.006	0.001	0.007
quiet	0.001	0.000	0.002
rare_members	0.013	0.003	0.016
rarity	0.103	0.011	0.114
read_biom2phyloseq	0.001	0.000	0.001
read_csv2phyloseq	0.002	0.000	0.002
read_mothur2phyloseq	0.002	0.000	0.002
read_phyloseq	0.001	0.000	0.001
remove_samples	0.013	0.003	0.016
remove_taxa	0.026	0.003	0.031
richness	0.012	0.004	0.015
summarize_phyloseq	0.022	0.002	0.024
taxa	0.008	0.001	0.010
time_normalize	0.032	0.001	0.033
time_sort	0.264	0.018	0.282
top_taxa	0.010	0.002	0.012
transform	0.068	0.004	0.073
variable_members	0.059	0.006	0.065
write_phyloseq	0.002	0.000	0.001
ztransform	0.001	0.000	0.001