Multiple platform build/check report for BioC 3.13 - CHECK results for microbiome on machv2

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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_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/microbiome.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.14.0’
* 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 ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
overlap 23.751  1.774  25.544
* 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: OK

Installation output

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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/4.1/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)

Tests output


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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) 2011-2020 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

══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Bioconductor (1)

[ FAIL 0 | WARN 2 | SKIP 1 | PASS 75 ]
> 
> proc.time()
   user  system elapsed 
 15.528   0.749  16.262

Example timings

name	user	system	elapsed
abundances	0.021	0.003	0.024
aggregate_rare	0.349	0.014	0.363
aggregate_taxa	0.111	0.002	0.113
alpha	0.015	0.002	0.018
associate	0.060	0.002	0.062
baseline	0.100	0.003	0.102
bfratio	0.193	0.002	0.196
bimodality	0.002	0.000	0.002
bimodality_sarle	0	0	0
boxplot_abundance	0.071	0.003	0.075
chunk_reorder	0.000	0.000	0.001
cmat2table	0.087	0.003	0.090
collapse_replicates	0.511	0.005	0.515
core	0.039	0.001	0.041
core_abundance	0.042	0.003	0.045
core_matrix	0.000	0.001	0.000
core_members	0.011	0.002	0.013
coverage	0.045	0.003	0.047
default_colors	0	0	0
densityplot	0	0	0
divergence	0.807	0.031	0.839
diversities	0.015	0.003	0.018
diversity	0.015	0.004	0.018
dominance	0.011	0.002	0.012
dominant	0.015	0.003	0.018
estimate_stability	0.000	0.000	0.001
evenness	0.009	0.001	0.011
find_optima	0	0	0
gktau	0.016	0.002	0.018
global	0.012	0.002	0.015
group_age	0.025	0.002	0.026
group_bmi	0.000	0.000	0.001
heat	0.078	0.009	0.088
hotplot	0.177	0.005	0.182
inequality	0.041	0.006	0.048
intermediate_stability	0.657	0.005	0.662
is_compositional	0.089	0.003	0.092
log_modulo_skewness	0.205	0.005	0.210
low_abundance	0.018	0.002	0.022
map_levels	0.046	0.002	0.048
merge_taxa2	0.025	0.001	0.027
meta	0.006	0.001	0.007
microbiome-package	0.012	0.001	0.014
multimodality	0.000	0.001	0.000
neat	0.100	0.003	0.104
neatsort	0.249	0.005	0.254
overlap	23.751	1.774	25.544
plot_atlas	0.059	0.002	0.062
plot_composition	0.246	0.003	0.248
plot_core	0.082	0.005	0.086
plot_density	0.040	0.002	0.043
plot_frequencies	0.031	0.002	0.033
plot_landscape	1.271	0.016	1.290
plot_regression	0.197	0.004	0.201
plot_taxa_prevalence	0.408	0.006	0.413
plot_tipping	0.132	0.004	0.135
potential_analysis	0.057	0.002	0.058
potential_univariate	0	0	0
prevalence	0.013	0.001	0.015
quiet	0.000	0.000	0.001
rare	0.032	0.002	0.034
rare_abundance	0.037	0.001	0.038
rare_members	0.015	0.002	0.017
rarity	0.126	0.003	0.129
read_biom2phyloseq	0.000	0.000	0.001
read_csv2phyloseq	0.000	0.001	0.001
read_mothur2phyloseq	0.001	0.001	0.000
read_phyloseq	0.000	0.000	0.001
readcount	0.032	0.003	0.034
remove_samples	0.019	0.002	0.020
remove_taxa	0.024	0.001	0.025
richness	0.015	0.002	0.016
spreadplot	0.074	0.002	0.077
summarize_phyloseq	0.026	0.003	0.028
taxa	0.007	0.002	0.009
time_normalize	0.045	0.002	0.047
time_sort	0.188	0.003	0.191
timesplit	0.189	0.002	0.192
top	0.012	0.002	0.014
top_taxa	0.009	0.001	0.010
transform	0.094	0.003	0.096
write_phyloseq	0	0	0
ztransform	0	0	0

CHECK results for microbiome on machv2

Summary

Command output

Installation output

Tests output

Example timings