Package: microbiome

Version: 1.5.31

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_1.5.31.tar.gz

StartedAt: 2019-04-09 02:12:40 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:16:30 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 229.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: microbiome.Rcheck

Warnings: 1

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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_1.5.31.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/microbiome.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.5.31’
* 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 ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                       old_size new_size compress
  atlas1006.rda           233Kb    127Kb       xz
  dietswap.rda             45Kb     28Kb       xz
  hitchip.taxonomy.rda    402Kb    124Kb       xz
  peerj32.rda             113Kb     87Kb       xz
* 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: 1 WARNING
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/microbiome.Rcheck/00check.log’
for details.

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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/3.6/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 Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
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) 2011-2019 Leo Lahti, 
    Sudarshan Shetty et al. <microbiome.github.io>


Attaching package: 'microbiome'

The following object is masked from 'package:ggplot2':

    alpha

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

    transform

══ testthat results  ═══════════════════════════════════════════════════════════
OK: 72 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 12.142   0.797  12.988 

name	user	system	elapsed
abundances	0.015	0.001	0.017
aggregate_taxa	0.644	0.007	0.653
aggregate_top_taxa	0.330	0.017	0.353
alpha	0.015	0.003	0.018
associate	0.050	0.007	0.056
baseline	0.032	0.005	0.038
bfratio	0.213	0.026	0.241
bimodality	0.020	0.002	0.022
bimodality_sarle	0	0	0
boxplot_abundance	0.086	0.014	0.100
chunk_reorder	0	0	0
cmat2table	0.140	0.023	0.168
collapse_replicates	0.073	0.008	0.082
core	0.030	0.002	0.032
core_abundance	0.043	0.003	0.045
core_matrix	0.000	0.000	0.001
core_members	0.005	0.001	0.006
coverage	0.041	0.003	0.045
default_colors	0.000	0.000	0.001
densityplot	0	0	0
divergence	0.809	0.009	0.831
diversities	0.015	0.003	0.018
diversity	0.032	0.004	0.037
dominance	0.012	0.002	0.014
dominant	0.011	0.002	0.013
estimate_stability	0.001	0.000	0.000
evenness	0.007	0.002	0.008
find_optima	0	0	0
gktau	0.006	0.001	0.007
global	0.008	0.001	0.010
group_age	0.014	0.001	0.015
group_bmi	0.001	0.000	0.001
heat	0.094	0.003	0.098
hotplot	0.169	0.007	0.177
inequality	0.030	0.005	0.035
intermediate_stability	0.931	0.009	0.951
log_modulo_skewness	0.165	0.020	0.187
low_abundance	0.034	0.003	0.038
map_levels	0.078	0.004	0.084
merge_taxa2	0.040	0.002	0.043
meta	0.006	0.001	0.008
microbiome-package	0.012	0.001	0.012
multimodality	0	0	0
neat	0.088	0.002	0.091
neatsort	0.210	0.005	0.217
noncore_abundance	0.059	0.003	0.061
noncore_members	0.018	0.001	0.019
plot_atlas	0.078	0.002	0.082
plot_composition	0.306	0.008	0.316
plot_core	0.114	0.009	0.124
plot_density	0.037	0.001	0.038
plot_frequencies	0.018	0.002	0.019
plot_landscape	1.760	0.042	1.819
plot_regression	0.211	0.009	0.221
plot_taxa_prevalence	0.531	0.014	0.547
plot_tipping	0.131	0.014	0.145
potential_analysis	0.058	0.006	0.064
potential_univariate	0	0	0
prevalence	0.005	0.001	0.005
quiet	0.000	0.000	0.001
rare_members	0.006	0.002	0.007
rarity	0.100	0.006	0.105
read_biom2phyloseq	0	0	0
read_csv2phyloseq	0	0	0
read_mothur2phyloseq	0.000	0.000	0.001
read_phyloseq	0.000	0.000	0.001
readcount	0.006	0.001	0.008
remove_samples	0.017	0.003	0.020
remove_taxa	0.024	0.002	0.027
richness	0.033	0.004	0.036
summarize_phyloseq	0.020	0.001	0.021
taxa	0.005	0.001	0.007
time_normalize	0.040	0.001	0.042
time_sort	0.226	0.002	0.232
timesplit	0.161	0.003	0.164
top_taxa	0.007	0.002	0.008
transform	0.024	0.001	0.025
variable_members	0.053	0.002	0.055
write_phyloseq	0.001	0.001	0.001
ztransform	0	0	0