Package: microbiome

Version: 1.0.2

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings microbiome_1.0.2.tar.gz

StartedAt: 2018-04-12 01:06:07 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:08:31 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 144.0 seconds

RetCode: 0

Status:  OK

CheckDir: microbiome.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings microbiome_1.0.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/microbiome.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (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-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)
> 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 
  8.776   0.120   8.904 

name	user	system	elapsed
abundances	0.036	0.000	0.034
aggregate_taxa	0.372	0.000	0.371
associate	0.088	0.000	0.088
baseline	0.036	0.000	0.038
bimodality	0.124	0.000	0.122
bimodality_sarle	0	0	0
boxplot_abundance	0.164	0.000	0.162
chunk_reorder	0.000	0.000	0.001
cmat2table	0.244	0.004	0.250
core	0.016	0.000	0.017
core_abundance	0.012	0.000	0.015
core_matrix	0.000	0.000	0.001
core_members	0.012	0.000	0.010
coverage	0.072	0.004	0.078
densityplot	0.004	0.000	0.000
divergence	0.540	0.004	0.546
diversities	0.016	0.000	0.014
dominance	0.044	0.004	0.048
estimate_stability	0.000	0.000	0.001
evenness	0.004	0.004	0.010
find_optima	0	0	0
gktau	0.004	0.000	0.006
global	0.076	0.000	0.076
group_age	0.040	0.000	0.038
group_bmi	0.000	0.000	0.001
heat	0.096	0.000	0.094
hotplot	0.448	0.000	0.448
inequality	0.304	0.000	0.305
intermediate_stability	0.656	0.004	0.662
log_modulo_skewness	0.100	0.000	0.098
low_abundance	0.016	0.004	0.020
map_levels	0.052	0.004	0.056
merge_taxa2	0.028	0.000	0.027
meta	0.008	0.000	0.009
microbiome-package	0.008	0.000	0.010
multimodality	0	0	0
neat	0.372	0.000	0.376
neatsort	0.16	0.00	0.16
noncore_abundance	0.008	0.004	0.014
noncore_members	0.016	0.000	0.016
plot_atlas	0.088	0.008	0.097
plot_composition	0.18	0.00	0.18
plot_core	0.444	0.004	0.449
plot_density	0.040	0.004	0.043
plot_frequencies	0.048	0.000	0.047
plot_landscape	0.048	0.000	0.048
plot_regression	3.048	0.008	3.058
plot_taxa_prevalence	1.308	0.012	1.321
plot_tipping	0.408	0.000	0.408
potential_analysis	0.036	0.000	0.034
potential_univariate	0	0	0
prevalence	0.008	0.000	0.006
quiet	0.000	0.000	0.001
rare_members	0.008	0.004	0.011
rarity	0.092	0.000	0.089
read_biom2phyloseq	0.000	0.000	0.001
read_csv2phyloseq	0.000	0.000	0.001
read_mothur2phyloseq	0.000	0.000	0.001
read_phyloseq	0	0	0
remove_samples	0.016	0.000	0.012
remove_taxa	0.020	0.000	0.021
richness	0.012	0.000	0.010
summarize_phyloseq	0.020	0.000	0.021
taxa	0.008	0.000	0.007
time_normalize	0.024	0.000	0.026
time_sort	0.148	0.000	0.147
top_taxa	0.012	0.000	0.010
transform	0.028	0.004	0.032
variable_members	0.056	0.000	0.054
write_phyloseq	0.000	0.000	0.001
ztransform	0.000	0.000	0.001