Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:05:36 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for microbiome on nebbiolo2


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? 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 1141/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
microbiome 1.16.0  (landing page)
Leo Lahti
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/microbiome
git_branch: RELEASE_3_14
git_last_commit: a7b74b7
git_last_commit_date: 2021-10-26 12:37:27 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: 1.16.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:microbiome.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings microbiome_1.16.0.tar.gz
StartedAt: 2022-04-12 08:13:16 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 08:16:08 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 171.3 seconds
RetCode: 0
Status:   OK  
CheckDir: microbiome.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:microbiome.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings microbiome_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/microbiome.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (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 ‘1.16.0’
* 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 15.407   0.22  15.628
* 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:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL microbiome
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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) 2011-2021 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

[ FAIL 0 | WARN 5 | SKIP 1 | PASS 82 ]

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

[ FAIL 0 | WARN 5 | SKIP 1 | PASS 82 ]
> 
> proc.time()
   user  system elapsed 
 12.477   0.534  12.995 

Example timings

microbiome.Rcheck/microbiome-Ex.timings

nameusersystemelapsed
abundances0.0140.0000.014
aggregate_rare0.5030.0280.531
aggregate_taxa0.0980.0000.099
alpha0.0120.0000.012
associate0.0360.0000.036
baseline0.0370.0000.036
bfratio0.6440.0840.727
bimodality0.0010.0000.001
bimodality_sarle000
boxplot_abundance0.0620.0000.062
chunk_reorder000
cmat2table0.0570.0000.057
collapse_replicates0.040.000.04
core0.0350.0000.035
core_abundance0.0280.0000.028
core_matrix0.0000.0000.001
core_members0.0080.0000.008
coverage0.0220.0040.025
default_colors000
densityplot000
divergence0.4950.0200.515
diversity0.0110.0000.012
dominance0.010.000.01
dominant0.0090.0000.009
estimate_stability000
evenness0.0040.0040.007
find_optima000
gktau0.0120.0000.012
group_age0.0240.0000.023
group_bmi0.0010.0000.000
heat0.0490.0000.048
hotplot0.1020.0040.106
inequality0.0190.0000.019
intermediate_stability0.3960.0040.399
is_compositional0.0470.0000.046
log_modulo_skewness0.0990.0000.099
low_abundance0.0080.0040.012
map_levels0.040.000.04
merge_taxa20.0220.0000.023
meta0.0060.0000.007
microbiome-package0.0090.0000.010
multimodality000
neat0.0610.0000.061
neatsort0.1780.0000.179
overlap15.407 0.22015.628
plot_atlas0.0430.0000.043
plot_composition0.1940.0080.201
plot_core0.0610.0000.061
plot_density0.0320.0040.035
plot_frequencies0.0280.0000.027
plot_landscape0.7450.0040.748
plot_regression0.1920.0040.195
plot_taxa_prevalence0.2560.0080.264
plot_tipping0.0850.0000.086
potential_analysis0.0310.0000.032
potential_univariate0.0000.0000.001
prevalence0.0120.0000.012
quiet0.0000.0000.001
rare0.0190.0000.019
rare_abundance0.0290.0000.028
rare_members0.0090.0000.008
rarity0.0780.0040.081
read_biom2phyloseq0.0010.0000.000
read_csv2phyloseq000
read_mothur2phyloseq000
read_phyloseq000
readcount0.0070.0000.007
remove_samples0.0130.0000.013
remove_taxa0.0160.0000.015
richness0.0100.0000.009
spreadplot0.0550.0000.054
summarize_phyloseq0.0160.0000.016
taxa0.0060.0000.006
time_normalize0.0300.0000.029
time_sort0.1040.0000.104
timesplit0.0940.0000.094
top0.0060.0000.007
top_taxa0.0070.0000.007
transform0.0510.0000.050
ztransform000