Package: microbiome

Version: 1.4.2

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_1.4.2.tar.gz

StartedAt: 2019-04-16 01:15:56 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 01:19:12 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 195.3 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_1.4.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/microbiome.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.4.2’
* 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 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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 
 10.239   0.551  10.869 

name	user	system	elapsed
abundances	0.017	0.003	0.019
aggregate_taxa	1.469	0.091	1.585
associate	0.059	0.010	0.069
baseline	0.028	0.004	0.033
bimodality	0.012	0.002	0.015
bimodality_sarle	0.001	0.000	0.000
boxplot_abundance	0.060	0.010	0.071
chunk_reorder	0.000	0.000	0.001
cmat2table	0.138	0.011	0.149
core	0.016	0.003	0.019
core_abundance	0.015	0.004	0.019
core_matrix	0	0	0
core_members	0.010	0.004	0.013
coverage	0.041	0.008	0.049
densityplot	0	0	0
divergence	0.792	0.010	0.808
diversities	0.030	0.006	0.038
dominance	0.016	0.004	0.019
estimate_stability	0	0	0
evenness	0.011	0.004	0.014
find_optima	0	0	0
gktau	0.006	0.001	0.006
global	0.035	0.009	0.044
group_age	0.040	0.006	0.046
group_bmi	0.001	0.000	0.001
heat	0.094	0.002	0.096
hotplot	0.191	0.020	0.213
inequality	0.471	0.028	0.503
intermediate_stability	0.923	0.050	0.975
log_modulo_skewness	0.187	0.017	0.204
low_abundance	0.024	0.006	0.029
map_levels	0.061	0.005	0.067
merge_taxa2	0.031	0.004	0.035
meta	0.012	0.004	0.017
microbiome-package	0.012	0.001	0.012
multimodality	0	0	0
neat	0.087	0.002	0.093
neatsort	0.182	0.004	0.186
noncore_abundance	0.016	0.005	0.021
noncore_members	0.025	0.002	0.026
plot_atlas	0.088	0.006	0.095
plot_composition	4.035	0.026	4.096
plot_core	0.214	0.032	0.247
plot_density	0.072	0.010	0.082
plot_frequencies	0.016	0.005	0.019
plot_landscape	0.052	0.005	0.058
plot_regression	4.494	0.071	4.620
plot_taxa_prevalence	0.524	0.015	0.544
plot_tipping	0.200	0.029	0.232
potential_analysis	0.023	0.002	0.026
potential_univariate	0	0	0
prevalence	0.006	0.002	0.007
quiet	0.001	0.000	0.000
rare_members	0.016	0.005	0.021
rarity	0.135	0.012	0.149
read_biom2phyloseq	0	0	0
read_csv2phyloseq	0.001	0.000	0.000
read_mothur2phyloseq	0.000	0.001	0.000
read_phyloseq	0.001	0.000	0.000
remove_samples	0.012	0.003	0.015
remove_taxa	0.029	0.004	0.033
richness	0.012	0.004	0.016
summarize_phyloseq	0.020	0.003	0.024
taxa	0.008	0.003	0.010
time_normalize	0.029	0.001	0.029
time_sort	0.244	0.014	0.260
top_taxa	0.013	0.003	0.016
transform	0.045	0.007	0.053
variable_members	0.066	0.009	0.074
write_phyloseq	0	0	0
ztransform	0.000	0.000	0.001