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This page was generated on 2022-05-16 11:07:59 -0400 (Mon, 16 May 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4379
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4153
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4220
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 merida1


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 1171/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
microbiome 1.18.0  (landing page)
Leo Lahti
Snapshot Date: 2022-05-15 13:55:12 -0400 (Sun, 15 May 2022)
git_url: https://git.bioconductor.org/packages/microbiome
git_branch: RELEASE_3_15
git_last_commit: 4887f83
git_last_commit_date: 2022-04-26 11:42:45 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: microbiome
Version: 1.18.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:microbiome.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings microbiome_1.18.0.tar.gz
StartedAt: 2022-05-16 04:33:47 -0400 (Mon, 16 May 2022)
EndedAt: 2022-05-16 04:39:46 -0400 (Mon, 16 May 2022)
EllapsedTime: 359.6 seconds
RetCode: 0
Status:   OK  
CheckDir: microbiome.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:microbiome.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings microbiome_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/microbiome.Rcheck’
* using R version 4.2.0 (2022-04-22)
* 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 ‘1.18.0’
* 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 34.774  2.215  37.105
* 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/Resources/bin/R CMD INSTALL microbiome
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/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 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 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) 2011-2022 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 3 | SKIP 1 | PASS 83 ]

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

[ FAIL 0 | WARN 3 | SKIP 1 | PASS 83 ]
> 
> proc.time()
   user  system elapsed 
 22.585   0.850  23.480 

Example timings

microbiome.Rcheck/microbiome-Ex.timings

nameusersystemelapsed
TibbleUtilites0.3450.0090.355
abundances0.0110.0020.013
add_besthit0.0010.0010.001
add_refseq0.0000.0000.001
aggregate_rare1.0570.0111.071
aggregate_taxa0.1930.0010.196
alpha0.0230.0020.024
associate0.0700.0020.072
baseline0.0560.0020.058
bimodality0.0020.0010.002
bimodality_sarle000
boxplot_abundance0.1000.0060.105
boxplot_alpha0.6570.0080.670
chunk_reorder0.0010.0000.001
cmat2table0.1400.0030.143
collapse_replicates0.0880.0060.095
core0.0670.0030.070
core_abundance0.0610.0050.066
core_matrix0.0000.0000.001
core_members0.0140.0020.016
coverage0.0930.0040.097
default_colors000
densityplot000
divergence1.0820.0141.099
diversity0.0200.0030.023
dominance0.0170.0020.018
dominant0.0170.0020.019
estimate_stability0.0000.0000.001
evenness0.0120.0030.016
find_optima0.0010.0000.000
gktau0.0200.0020.022
group_age0.0360.0030.038
group_bmi0.0010.0000.001
heat0.1060.0090.116
hotplot0.2490.0120.262
inequality0.0480.0070.054
intermediate_stability0.9490.0050.955
is_compositional0.1050.0020.107
log_modulo_skewness0.2040.0050.211
low_abundance0.0970.0050.101
map_levels0.0810.0020.083
merge_taxa20.0450.0020.047
meta0.0110.0020.012
microbiome-package0.0130.0000.015
multimodality0.0010.0000.000
neat0.1240.0040.126
neatsort0.3030.0050.308
overlap34.774 2.21537.105
plot_atlas0.0770.0020.080
plot_composition0.3920.0050.398
plot_core0.1140.0070.122
plot_density0.0740.0020.076
plot_frequencies0.0450.0020.048
plot_landscape1.4690.0151.487
plot_regression0.3670.0030.371
plot_taxa_prevalence0.5020.0060.508
plot_tipping0.1770.0040.181
potential_analysis0.0630.0030.067
potential_univariate000
prevalence0.0180.0020.020
psmelt20.1740.0050.179
quiet0.0010.0000.001
rare0.0360.0010.037
rare_abundance0.0580.0010.060
rare_members0.0150.0020.018
rarity0.1410.0020.142
read_biom2phyloseq0.0010.0000.001
read_csv2phyloseq000
read_mothur2phyloseq0.0000.0000.001
read_phyloseq000
readcount0.0100.0020.013
remove_samples0.0240.0020.026
remove_taxa0.0310.0010.033
richness0.0190.0020.021
spreadplot0.1120.0020.115
summarize_phyloseq0.0280.0020.030
taxa0.0100.0020.012
time_normalize0.0560.0020.058
time_sort0.2740.0030.278
timesplit0.2080.0030.212
top0.0120.0020.014
top_taxa0.0120.0020.014
transform0.5670.0210.599
ztransform000