Package: microbiome

Version: 1.6.0

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_1.6.0.tar.gz

StartedAt: 2019-10-16 04:36:10 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:40:51 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 280.6 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_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/microbiome.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.6.0’
* 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 ... 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    123Kb       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’ ...
** 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 3.6.1 (2019-07-05) -- "Action of the Toes"
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. 


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 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 17.407   1.776  19.211 

name	user	system	elapsed
abundances	0.013	0.002	0.016
aggregate_taxa	0.771	0.013	0.783
aggregate_top_taxa	0.561	0.058	0.618
alpha	0.027	0.008	0.034
associate	0.083	0.021	0.104
baseline	0.052	0.013	0.064
bfratio	0.306	0.058	0.364
bimodality	0.023	0.006	0.029
bimodality_sarle	0.000	0.000	0.001
boxplot_abundance	0.094	0.030	0.125
chunk_reorder	0.000	0.000	0.001
cmat2table	0.192	0.042	0.235
collapse_replicates	0.10	0.01	0.11
core	0.045	0.003	0.048
core_abundance	0.048	0.005	0.052
core_matrix	0.001	0.000	0.000
core_members	0.009	0.002	0.012
coverage	0.069	0.014	0.082
default_colors	0.001	0.000	0.001
densityplot	0	0	0
divergence	1.073	0.010	1.083
diversities	0.050	0.008	0.058
diversity	0.018	0.003	0.021
dominance	0.012	0.002	0.013
dominant	0.012	0.003	0.014
estimate_stability	0.001	0.000	0.001
evenness	0.007	0.002	0.009
find_optima	0	0	0
gktau	0.010	0.003	0.013
global	0.010	0.002	0.013
group_age	0.017	0.004	0.021
group_bmi	0.001	0.000	0.002
heat	0.112	0.003	0.116
hotplot	0.204	0.015	0.218
inequality	0.076	0.013	0.090
intermediate_stability	1.080	0.018	1.099
log_modulo_skewness	0.237	0.026	0.264
low_abundance	0.025	0.007	0.032
map_levels	0.063	0.003	0.065
merge_taxa2	0.049	0.004	0.053
meta	0.007	0.003	0.010
microbiome-package	0.016	0.001	0.018
multimodality	0	0	0
neat	0.100	0.005	0.105
neatsort	0.322	0.017	0.339
noncore_abundance	0.058	0.002	0.062
noncore_members	0.032	0.003	0.035
plot_atlas	0.082	0.003	0.084
plot_composition	0.381	0.009	1.052
plot_core	0.162	0.017	0.178
plot_density	0.073	0.005	0.077
plot_frequencies	0.024	0.003	0.027
plot_landscape	1.499	0.042	1.541
plot_regression	0.307	0.009	0.315
plot_taxa_prevalence	1.068	0.083	1.151
plot_tipping	0.119	0.010	0.128
potential_analysis	0.044	0.005	0.048
potential_univariate	0.000	0.000	0.001
prevalence	0.007	0.002	0.010
quiet	0.001	0.000	0.002
rare_members	0.009	0.004	0.013
rarity	0.086	0.006	0.093
read_biom2phyloseq	0.001	0.000	0.001
read_csv2phyloseq	0.001	0.000	0.001
read_mothur2phyloseq	0	0	0
read_phyloseq	0.001	0.000	0.001
readcount	0.006	0.003	0.008
remove_samples	0.017	0.003	0.020
remove_taxa	0.025	0.002	0.027
richness	0.012	0.004	0.016
summarize_phyloseq	0.022	0.005	0.027
taxa	0.006	0.003	0.009
time_normalize	0.058	0.005	0.064
time_sort	0.423	0.074	0.497
timesplit	0.161	0.006	0.167
top_taxa	0.005	0.002	0.007
transform	0.027	0.002	0.029
variable_members	0.051	0.004	0.054
write_phyloseq	0	0	0
ztransform	0.000	0.000	0.001