Package: microbiome

Version: 1.0.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings microbiome_1.0.2.tar.gz

StartedAt: 2018-04-12 06:25:49 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 06:28:39 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 170.6 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 --no-vignettes --timings microbiome_1.0.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/microbiome.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.0.2’
* 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... 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

* installing *source* package ‘microbiome’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (microbiome)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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 
  9.387   0.314   9.817 

name	user	system	elapsed
abundances	0.041	0.003	0.045
aggregate_taxa	0.418	0.007	0.432
associate	0.104	0.001	0.105
baseline	0.034	0.002	0.037
bimodality	0.155	0.001	0.157
bimodality_sarle	0.001	0.000	0.001
boxplot_abundance	0.229	0.002	0.241
chunk_reorder	0.001	0.000	0.001
cmat2table	0.287	0.002	0.293
core	0.015	0.002	0.017
core_abundance	0.263	0.004	0.270
core_matrix	0.001	0.000	0.000
core_members	0.008	0.002	0.011
coverage	0.089	0.005	0.100
densityplot	0.000	0.000	0.001
divergence	0.637	0.030	0.672
diversities	0.014	0.006	0.019
dominance	0.046	0.009	0.059
estimate_stability	0.001	0.000	0.001
evenness	0.010	0.008	0.018
find_optima	0.000	0.000	0.001
gktau	0.007	0.000	0.007
global	0.091	0.012	0.104
group_age	0.032	0.008	0.040
group_bmi	0.001	0.000	0.001
heat	0.094	0.001	0.100
hotplot	0.182	0.021	0.213
inequality	0.032	0.004	0.036
intermediate_stability	0.814	0.016	0.837
log_modulo_skewness	0.123	0.006	0.129
low_abundance	0.019	0.005	0.024
map_levels	0.074	0.003	0.079
merge_taxa2	0.032	0.002	0.035
meta	0.011	0.003	0.014
microbiome-package	0.011	0.000	0.011
multimodality	0.000	0.000	0.001
neat	0.458	0.002	0.461
neatsort	0.168	0.002	0.170
noncore_abundance	0.015	0.003	0.020
noncore_members	0.020	0.001	0.021
plot_atlas	0.090	0.004	0.094
plot_composition	0.212	0.005	0.218
plot_core	0.427	0.024	0.455
plot_density	0.046	0.004	0.051
plot_frequencies	0.054	0.002	0.056
plot_landscape	0.053	0.004	0.056
plot_regression	3.621	0.042	3.704
plot_taxa_prevalence	1.515	0.016	1.549
plot_tipping	0.127	0.011	0.139
potential_analysis	0.035	0.001	0.036
potential_univariate	0.000	0.000	0.001
prevalence	0.007	0.001	0.007
quiet	0.000	0.000	0.001
rare_members	0.012	0.004	0.016
rarity	0.111	0.012	0.127
read_biom2phyloseq	0	0	0
read_csv2phyloseq	0.001	0.000	0.001
read_mothur2phyloseq	0.001	0.000	0.001
read_phyloseq	0.000	0.000	0.001
remove_samples	0.014	0.004	0.018
remove_taxa	0.019	0.006	0.026
richness	0.010	0.006	0.016
summarize_phyloseq	0.026	0.009	0.034
taxa	0.008	0.002	0.009
time_normalize	0.028	0.001	0.030
time_sort	0.181	0.011	0.192
top_taxa	0.008	0.002	0.011
transform	0.032	0.004	0.036
variable_members	0.060	0.006	0.071
write_phyloseq	0.001	0.000	0.001
ztransform	0.001	0.000	0.000