Package: microbiome

Version: 1.9.19

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_1.9.19.tar.gz

StartedAt: 2020-01-16 06:28:01 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 06:33:34 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 333.3 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_1.9.19.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/microbiome.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.9.19’
* 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    129Kb       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-3.11-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/4.0/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 Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
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) 2011-2019 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: 76 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 22.244   2.105  24.376 

name	user	system	elapsed
abundances	0.013	0.002	0.015
aggregate_taxa	0.729	0.011	0.740
aggregate_top_taxa	0.589	0.061	0.656
alpha	0.030	0.011	0.043
associate	0.081	0.019	0.100
baseline	0.099	0.014	0.114
bfratio	0.265	0.003	0.268
bimodality	0.018	0.003	0.020
bimodality_sarle	0.000	0.001	0.000
boxplot_abundance	0.080	0.009	0.090
chunk_reorder	0.000	0.001	0.001
cmat2table	0.136	0.005	0.141
collapse_replicates	0.100	0.013	0.113
core	0.071	0.005	0.076
core_abundance	0.065	0.005	0.071
core_matrix	0.001	0.000	0.001
core_members	0.011	0.003	0.014
coverage	0.107	0.005	0.112
default_colors	0.000	0.000	0.001
densityplot	0	0	0
divergence	1.217	0.061	1.278
diversities	0.020	0.007	0.028
diversity	0.021	0.004	0.025
dominance	0.013	0.003	0.016
dominant	0.012	0.003	0.015
estimate_stability	0.000	0.000	0.001
evenness	0.010	0.004	0.014
find_optima	0.000	0.000	0.001
gktau	0.013	0.005	0.018
global	0.013	0.004	0.019
group_age	0.056	0.011	0.067
group_bmi	0.002	0.000	0.001
heat	0.097	0.003	0.100
hotplot	0.214	0.019	0.233
inequality	0.054	0.010	0.065
intermediate_stability	0.936	0.010	0.947
is_compositional	0.107	0.004	0.111
log_modulo_skewness	0.244	0.013	0.256
low_abundance	0.018	0.004	0.021
map_levels	0.059	0.003	0.062
merge_taxa2	0.035	0.002	0.037
meta	0.004	0.002	0.007
microbiome-package	0.018	0.003	0.021
multimodality	0.001	0.000	0.000
neat	0.098	0.006	0.105
neatsort	0.793	0.023	0.816
noncore_members	0.000	0.001	0.000
plot_atlas	0.045	0.004	0.049
plot_composition	0.400	0.011	0.412
plot_core	0.098	0.021	0.118
plot_density	0.077	0.005	0.082
plot_frequencies	0.024	0.003	0.026
plot_landscape	1.808	0.052	1.861
plot_regression	0.276	0.005	0.281
plot_taxa_prevalence	0.726	0.047	0.773
plot_tipping	0.227	0.040	0.267
potential_analysis	0.073	0.003	0.075
potential_univariate	0.000	0.001	0.001
prevalence	0.008	0.002	0.010
quiet	0.001	0.000	0.002
rare	0.032	0.002	0.034
rare_abundance	0.062	0.004	0.066
rare_members	0.013	0.003	0.016
rarity	0.148	0.010	0.159
read_biom2phyloseq	0	0	0
read_csv2phyloseq	0.001	0.001	0.001
read_mothur2phyloseq	0.000	0.000	0.001
read_phyloseq	0.001	0.000	0.000
readcount	0.007	0.004	0.010
remove_samples	0.025	0.003	0.028
remove_taxa	0.021	0.003	0.025
richness	0.012	0.005	0.017
spreadplot	0.066	0.007	0.073
summarize_phyloseq	0.018	0.003	0.020
taxa	0.006	0.002	0.009
time_normalize	0.041	0.001	0.043
time_sort	0.248	0.004	0.251
timesplit	0.184	0.002	0.186
top	0.009	0.002	0.011
top_taxa	0.009	0.003	0.012
transform	0.123	0.019	0.142
write_phyloseq	0	0	0
ztransform	0.000	0.000	0.001