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This page was generated on 2022-06-24 12:07:46 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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: 2022-06-23 13:55:15 -0400 (Thu, 23 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
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: 2022-06-24 05:11:11 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 05:17:32 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 381.5 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 35.875  1.681  39.694
* 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 
 23.310   0.807  25.043 

Example timings

microbiome.Rcheck/microbiome-Ex.timings

nameusersystemelapsed
TibbleUtilites0.3630.0070.390
abundances0.0110.0020.013
add_besthit0.0000.0000.001
add_refseq0.0010.0000.000
aggregate_rare1.1160.0091.175
aggregate_taxa0.2010.0030.219
alpha0.0250.0030.028
associate0.0760.0020.082
baseline0.0630.0030.070
bimodality0.0020.0000.002
bimodality_sarle000
boxplot_abundance0.1050.0040.114
boxplot_alpha1.2100.0111.294
chunk_reorder0.0010.0000.000
cmat2table0.1430.0020.154
collapse_replicates0.0960.0060.110
core0.0680.0040.077
core_abundance0.0640.0050.069
core_matrix000
core_members0.0150.0020.018
coverage0.0700.0080.082
default_colors000
densityplot000
divergence1.1370.0321.236
diversity0.0220.0020.025
dominance0.0170.0020.019
dominant0.0170.0020.021
estimate_stability0.0000.0010.000
evenness0.0120.0020.016
find_optima0.0010.0000.001
gktau0.0200.0030.023
group_age0.0380.0020.043
group_bmi0.0010.0010.001
heat0.1130.0020.118
hotplot0.2270.0050.241
inequality0.0500.0070.061
intermediate_stability0.9790.0051.011
is_compositional0.1150.0030.124
log_modulo_skewness0.2070.0060.226
low_abundance0.0260.0030.029
map_levels0.0900.0030.095
merge_taxa20.0500.0020.059
meta0.0110.0010.014
microbiome-package0.0170.0000.020
multimodality000
neat0.1310.0040.152
neatsort0.3610.0070.406
overlap35.875 1.68139.694
plot_atlas0.0800.0030.087
plot_composition0.4070.0040.437
plot_core0.1130.0040.128
plot_density0.0730.0020.080
plot_frequencies0.0480.0020.052
plot_landscape1.5360.0131.665
plot_regression0.3810.0040.406
plot_taxa_prevalence0.5050.0040.534
plot_tipping0.1800.0030.186
potential_analysis0.0640.0020.068
potential_univariate0.0000.0000.001
prevalence0.0190.0020.021
psmelt20.1740.0040.194
quiet0.0010.0000.001
rare0.0360.0010.039
rare_abundance0.0610.0020.069
rare_members0.0150.0020.018
rarity0.1580.0030.171
read_biom2phyloseq0.0000.0000.001
read_csv2phyloseq0.0010.0000.000
read_mothur2phyloseq0.0000.0000.001
read_phyloseq000
readcount0.0120.0010.014
remove_samples0.0260.0020.027
remove_taxa0.0290.0010.031
richness0.0190.0020.021
spreadplot0.1160.0050.127
summarize_phyloseq0.0290.0020.036
taxa0.0100.0010.012
time_normalize0.0580.0010.063
time_sort0.3040.0030.324
timesplit0.2140.0030.221
top0.0120.0020.013
top_taxa0.0120.0020.014
transform0.5810.0170.634
ztransform000