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This page was generated on 2021-10-15 15:06:42 -0400 (Fri, 15 Oct 2021).

CHECK results for microbiome on machv2

To the developers/maintainers of the microbiome package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/microbiome.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1127/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
microbiome 1.14.0  (landing page)
Leo Lahti
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/microbiome
git_branch: RELEASE_3_13
git_last_commit: bd8313a
git_last_commit_date: 2021-05-19 12:29:45 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: microbiome
Version: 1.14.0
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_1.14.0.tar.gz
StartedAt: 2021-10-14 21:06:30 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 21:10:47 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 256.4 seconds
RetCode: 0
Status:   OK  
CheckDir: microbiome.Rcheck
Warnings: 0

Command output

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###
### Running 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_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* 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

microbiome.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL microbiome
###
##############################################################################
##############################################################################


* 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

microbiome.Rcheck/tests/testthat.Rout


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

microbiome.Rcheck/microbiome-Ex.timings

nameusersystemelapsed
abundances0.0210.0030.024
aggregate_rare0.3490.0140.363
aggregate_taxa0.1110.0020.113
alpha0.0150.0020.018
associate0.0600.0020.062
baseline0.1000.0030.102
bfratio0.1930.0020.196
bimodality0.0020.0000.002
bimodality_sarle000
boxplot_abundance0.0710.0030.075
chunk_reorder0.0000.0000.001
cmat2table0.0870.0030.090
collapse_replicates0.5110.0050.515
core0.0390.0010.041
core_abundance0.0420.0030.045
core_matrix0.0000.0010.000
core_members0.0110.0020.013
coverage0.0450.0030.047
default_colors000
densityplot000
divergence0.8070.0310.839
diversities0.0150.0030.018
diversity0.0150.0040.018
dominance0.0110.0020.012
dominant0.0150.0030.018
estimate_stability0.0000.0000.001
evenness0.0090.0010.011
find_optima000
gktau0.0160.0020.018
global0.0120.0020.015
group_age0.0250.0020.026
group_bmi0.0000.0000.001
heat0.0780.0090.088
hotplot0.1770.0050.182
inequality0.0410.0060.048
intermediate_stability0.6570.0050.662
is_compositional0.0890.0030.092
log_modulo_skewness0.2050.0050.210
low_abundance0.0180.0020.022
map_levels0.0460.0020.048
merge_taxa20.0250.0010.027
meta0.0060.0010.007
microbiome-package0.0120.0010.014
multimodality0.0000.0010.000
neat0.1000.0030.104
neatsort0.2490.0050.254
overlap23.751 1.77425.544
plot_atlas0.0590.0020.062
plot_composition0.2460.0030.248
plot_core0.0820.0050.086
plot_density0.0400.0020.043
plot_frequencies0.0310.0020.033
plot_landscape1.2710.0161.290
plot_regression0.1970.0040.201
plot_taxa_prevalence0.4080.0060.413
plot_tipping0.1320.0040.135
potential_analysis0.0570.0020.058
potential_univariate000
prevalence0.0130.0010.015
quiet0.0000.0000.001
rare0.0320.0020.034
rare_abundance0.0370.0010.038
rare_members0.0150.0020.017
rarity0.1260.0030.129
read_biom2phyloseq0.0000.0000.001
read_csv2phyloseq0.0000.0010.001
read_mothur2phyloseq0.0010.0010.000
read_phyloseq0.0000.0000.001
readcount0.0320.0030.034
remove_samples0.0190.0020.020
remove_taxa0.0240.0010.025
richness0.0150.0020.016
spreadplot0.0740.0020.077
summarize_phyloseq0.0260.0030.028
taxa0.0070.0020.009
time_normalize0.0450.0020.047
time_sort0.1880.0030.191
timesplit0.1890.0020.192
top0.0120.0020.014
top_taxa0.0090.0010.010
transform0.0940.0030.096
write_phyloseq000
ztransform000