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This page was generated on 2022-06-27 11:10:00 -0400 (Mon, 27 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
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 nebbiolo1


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: 2022-06-26 13:55:11 -0400 (Sun, 26 Jun 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

Summary

Package: microbiome
Version: 1.18.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:microbiome.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings microbiome_1.18.0.tar.gz
StartedAt: 2022-06-26 20:41:30 -0400 (Sun, 26 Jun 2022)
EndedAt: 2022-06-26 20:44:30 -0400 (Sun, 26 Jun 2022)
EllapsedTime: 180.1 seconds
RetCode: 0
Status:   OK  
CheckDir: microbiome.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:microbiome.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings microbiome_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/microbiome.Rcheck’
* using R version 4.2.0 (2022-04-22)
* 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 ‘1.18.0’
* 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 14.543  0.072  14.616
* 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

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##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL microbiome
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-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 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
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) 2011-2022 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 
 12.899   0.457  13.341 

Example timings

microbiome.Rcheck/microbiome-Ex.timings

nameusersystemelapsed
TibbleUtilites0.1760.0000.175
abundances0.0020.0040.007
add_besthit0.0000.0000.001
add_refseq000
aggregate_rare0.8780.0040.882
aggregate_taxa0.080.000.08
alpha0.0120.0000.012
associate0.0290.0040.033
baseline0.040.000.04
bimodality0.0000.0010.002
bimodality_sarle000
boxplot_abundance0.0590.0020.061
boxplot_alpha0.3260.0000.327
chunk_reorder0.0000.0000.001
cmat2table0.0580.0000.058
collapse_replicates0.0420.0000.043
core0.0370.0000.036
core_abundance0.030.000.03
core_matrix000
core_members0.0080.0000.008
coverage0.0370.0040.041
default_colors000
densityplot0.0000.0000.001
divergence0.4220.0000.423
diversity0.0100.0000.011
dominance0.0090.0000.009
dominant0.0080.0000.009
estimate_stability000
evenness0.0040.0030.007
find_optima0.0000.0010.000
gktau0.0090.0030.012
group_age0.0210.0000.022
group_bmi000
heat0.0400.0110.051
hotplot0.1110.0080.119
inequality0.0150.0040.018
intermediate_stability0.3720.0040.376
is_compositional0.0460.0000.046
log_modulo_skewness0.7300.0000.731
low_abundance0.0130.0000.012
map_levels0.0370.0000.037
merge_taxa20.0170.0040.021
meta0.0020.0040.006
microbiome-package0.0080.0000.009
multimodality000
neat0.0540.0040.057
neatsort0.1440.0000.144
overlap14.543 0.07214.616
plot_atlas0.0500.0040.054
plot_composition0.2280.0040.233
plot_core0.0570.0000.057
plot_density0.0360.0000.036
plot_frequencies0.0240.0000.024
plot_landscape0.7470.0080.755
plot_regression0.1870.0000.187
plot_taxa_prevalence0.2360.0000.236
plot_tipping0.0920.0000.092
potential_analysis0.0300.0040.034
potential_univariate0.0000.0000.001
prevalence0.0080.0040.012
psmelt20.0720.0030.076
quiet0.0010.0000.000
rare0.020.000.02
rare_abundance0.0490.0000.049
rare_members0.0090.0000.009
rarity0.0620.0000.062
read_biom2phyloseq0.0010.0000.000
read_csv2phyloseq0.0010.0000.001
read_mothur2phyloseq0.0010.0000.001
read_phyloseq0.0010.0000.001
readcount0.0080.0000.008
remove_samples0.0140.0000.014
remove_taxa0.0160.0000.016
richness0.0090.0000.010
spreadplot0.0550.0000.055
summarize_phyloseq0.0170.0000.017
taxa0.0060.0000.006
time_normalize0.0310.0000.031
time_sort0.1020.0040.106
timesplit0.0960.0000.096
top0.0030.0040.007
top_taxa0.0030.0040.007
transform0.3010.0040.304
ztransform000