Package: microbiome

Version: 1.8.0

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_1.8.0.tar.gz

StartedAt: 2020-04-15 03:51:28 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 03:55:31 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 242.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: microbiome.Rcheck

Warnings: 3

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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_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/microbiome.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.8.0’
* 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 ... WARNING
Documented arguments not in \usage in documentation object 'core':
  ‘...’

Documented arguments not in \usage in documentation object 'rare':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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    128Kb       xz
  dietswap.rda             45Kb     28Kb       xz
  hitchip.taxonomy.rda    402Kb    115Kb       xz
  peerj32.rda             113Kb     87Kb       xz
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:

  Warning: 'noncore_abundance' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* 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: 3 WARNINGs
See
  ‘/Users/biocbuild/bbs-3.10-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’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (microbiome)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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: 74 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 15.831   1.006  16.995 

name	user	system	elapsed
abundances	0.017	0.002	0.018
aggregate_taxa	0.693	0.013	0.713
aggregate_top_taxa	0.399	0.033	0.438
alpha	0.015	0.004	0.019
associate	0.066	0.010	0.076
baseline	0.057	0.005	0.064
bfratio	0.210	0.001	0.216
bimodality	0.015	0.001	0.015
bimodality_sarle	0	0	0
boxplot_abundance	0.070	0.004	0.076
chunk_reorder	0.000	0.000	0.001
cmat2table	0.120	0.002	0.124
collapse_replicates	0.066	0.004	0.070
core	0.052	0.002	0.054
core_abundance	0.050	0.003	0.053
core_matrix	0	0	0
core_members	0.407	0.004	0.414
coverage	0.049	0.003	0.053
default_colors	0.001	0.000	0.000
densityplot	0.000	0.000	0.001
divergence	0.759	0.029	0.796
diversities	0.013	0.003	0.016
diversity	0.016	0.002	0.018
dominance	0.011	0.002	0.013
dominant	0.012	0.004	0.016
estimate_stability	0.001	0.000	0.000
evenness	0.008	0.001	0.010
find_optima	0	0	0
gktau	0.009	0.002	0.011
global	0.008	0.002	0.010
group_age	0.018	0.003	0.022
group_bmi	0.001	0.000	0.001
heat	0.090	0.013	0.103
hotplot	0.156	0.024	0.180
inequality	0.034	0.009	0.043
intermediate_stability	0.875	0.008	0.885
is.compositional	0.031	0.001	0.032
log_modulo_skewness	0.162	0.007	0.172
low_abundance	0.017	0.003	0.021
map_levels	0.065	0.003	0.071
merge_taxa2	0.043	0.007	0.050
meta	0.006	0.002	0.008
microbiome-package	0.010	0.002	0.013
multimodality	0	0	0
neat	0.099	0.010	0.113
neatsort	0.271	0.019	0.290
noncore_abundance	0.042	0.002	0.045
noncore_members	0.000	0.000	0.001
plot_atlas	0.038	0.003	0.043
plot_composition	0.286	0.007	0.299
plot_core	0.094	0.009	0.103
plot_density	0.044	0.001	0.046
plot_frequencies	0.017	0.001	0.018
plot_landscape	1.079	0.025	1.118
plot_regression	0.168	0.003	0.171
plot_taxa_prevalence	0.539	0.006	0.556
plot_tipping	0.145	0.006	0.151
potential_analysis	0.040	0.001	0.042
potential_univariate	0	0	0
prevalence	0.007	0.001	0.009
quiet	0.001	0.001	0.001
rare	0.018	0.001	0.019
rare_abundance	0.047	0.002	0.049
rare_members	0.011	0.002	0.013
rarity	0.092	0.005	0.098
read_biom2phyloseq	0.001	0.000	0.000
read_csv2phyloseq	0	0	0
read_mothur2phyloseq	0	0	0
read_phyloseq	0.000	0.001	0.000
readcount	0.004	0.001	0.006
remove_samples	0.019	0.002	0.021
remove_taxa	0.023	0.002	0.025
richness	0.014	0.002	0.017
spreadplot	0.093	0.005	0.098
summarize_phyloseq	0.020	0.001	0.022
taxa	0.006	0.002	0.007
time_normalize	0.043	0.002	0.045
time_sort	0.168	0.003	0.173
timesplit	0.108	0.001	0.109
top_taxa	0.004	0.001	0.006
transform	0.029	0.001	0.030
write_phyloseq	0.000	0.001	0.001
ztransform	0.000	0.000	0.001