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 03:33:14 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:38:17 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 303.2 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) (2019-03-18 r76245)
* 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’ ...
** 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) (2019-03-18 r76245) -- "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: 72 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 16.902   1.686  18.547 

name	user	system	elapsed
abundances	0.019	0.003	0.022
aggregate_taxa	0.847	0.009	0.910
aggregate_top_taxa	0.514	0.033	0.548
alpha	0.023	0.005	0.027
associate	0.081	0.019	0.099
baseline	0.045	0.009	0.054
bfratio	0.281	0.053	0.336
bimodality	0.020	0.005	0.025
bimodality_sarle	0	0	0
boxplot_abundance	0.110	0.027	0.137
chunk_reorder	0.000	0.000	0.001
cmat2table	0.119	0.029	0.148
collapse_replicates	0.069	0.010	0.079
core	0.026	0.002	0.028
core_abundance	0.038	0.004	0.042
core_matrix	0.000	0.000	0.001
core_members	0.005	0.002	0.007
coverage	0.047	0.010	0.056
default_colors	0.000	0.000	0.001
densityplot	0	0	0
divergence	0.759	0.011	0.770
diversities	0.024	0.007	0.031
diversity	0.044	0.010	0.054
dominance	0.013	0.002	0.015
dominant	0.013	0.003	0.016
estimate_stability	0.001	0.000	0.001
evenness	0.009	0.003	0.012
find_optima	0.000	0.001	0.000
gktau	0.012	0.002	0.014
global	0.013	0.003	0.015
group_age	0.015	0.004	0.019
group_bmi	0.001	0.000	0.001
heat	0.083	0.003	0.087
hotplot	0.143	0.009	0.152
inequality	0.046	0.007	0.053
intermediate_stability	1.033	0.015	1.049
log_modulo_skewness	0.206	0.043	0.250
low_abundance	0.021	0.004	0.024
map_levels	0.088	0.004	0.092
merge_taxa2	0.046	0.003	0.049
meta	0.008	0.003	0.011
microbiome-package	0.017	0.002	0.020
multimodality	0.000	0.001	0.000
neat	0.128	0.006	0.134
neatsort	0.288	0.015	0.303
noncore_abundance	0.090	0.006	0.096
noncore_members	0.029	0.002	0.030
plot_atlas	0.085	0.004	0.089
plot_composition	0.381	0.012	0.394
plot_core	0.166	0.018	0.184
plot_density	0.070	0.003	0.073
plot_frequencies	0.018	0.002	0.021
plot_landscape	1.596	0.077	1.673
plot_regression	0.289	0.016	0.305
plot_taxa_prevalence	0.768	0.051	0.819
plot_tipping	0.150	0.012	0.162
potential_analysis	0.063	0.007	0.069
potential_univariate	0.001	0.000	0.001
prevalence	0.010	0.003	0.013
quiet	0.001	0.000	0.001
rare_members	0.013	0.006	0.019
rarity	0.168	0.014	0.182
read_biom2phyloseq	0.000	0.000	0.001
read_csv2phyloseq	0.001	0.000	0.001
read_mothur2phyloseq	0.001	0.001	0.001
read_phyloseq	0.000	0.001	0.001
readcount	0.009	0.002	0.010
remove_samples	0.022	0.003	0.025
remove_taxa	0.026	0.002	0.028
richness	0.016	0.004	0.020
summarize_phyloseq	0.028	0.004	0.032
taxa	0.006	0.003	0.009
time_normalize	0.052	0.003	0.054
time_sort	0.275	0.003	0.277
timesplit	0.209	0.005	0.214
top_taxa	0.007	0.002	0.008
transform	0.045	0.003	0.049
variable_members	0.070	0.007	0.077
write_phyloseq	0	0	0
ztransform	0.000	0.000	0.001