Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-10-02 12:03 -0400 (Thu, 02 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4844
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4631
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4576
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4576
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

Package 1283/2337HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
microbiome 1.31.4  (landing page)
Leo Lahti
Snapshot Date: 2025-10-01 13:45 -0400 (Wed, 01 Oct 2025)
git_url: https://git.bioconductor.org/packages/microbiome
git_branch: devel
git_last_commit: 7c4e0e86
git_last_commit_date: 2025-07-24 17:36:09 -0400 (Thu, 24 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for microbiome on nebbiolo2

To the developers/maintainers of the microbiome package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: microbiome
Version: 1.31.4
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:microbiome.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings microbiome_1.31.4.tar.gz
StartedAt: 2025-10-02 01:56:35 -0400 (Thu, 02 Oct 2025)
EndedAt: 2025-10-02 02:00:09 -0400 (Thu, 02 Oct 2025)
EllapsedTime: 213.2 seconds
RetCode: 0
Status:   OK  
CheckDir: microbiome.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:microbiome.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings microbiome_1.31.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/microbiome.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘microbiome/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘microbiome’ version ‘1.31.4’
* 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 code 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 ... NOTE
checkRd: (-1) bimodality.Rd:51-52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bimodality.Rd:53-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bimodality.Rd:55-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bimodality.Rd:38-39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) bimodality.Rd:40-41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) bimodality.Rd:42-43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) bimodality.Rd:91-93: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bimodality.Rd:94-95: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bimodality.Rd:96: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bimodality.Rd:97: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bimodality.Rd:98: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bimodality.Rd:99: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bimodality_sarle.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bimodality_sarle.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bimodality_sarle.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bimodality_sarle.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diversity.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diversity.Rd:30-32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diversity.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diversity.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diversity.Rd:35-36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dominance.Rd:39-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dominance.Rd:44-45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dominance.Rd:46-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dominance.Rd:49-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dominance.Rd:52-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dominance.Rd:59-60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dominance.Rd:61-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) multimodality.Rd:33-34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) multimodality.Rd:35-36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) multimodality.Rd:37-38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) multimodality.Rd:55-57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) multimodality.Rd:58-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) potential_analysis.Rd:30-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) potential_analysis.Rd:32-33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) potential_analysis.Rd:34-35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) potential_analysis.Rd:36-37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) potential_analysis.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) potential_analysis.Rd:61-63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) potential_analysis.Rd:64-65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) potential_univariate.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) potential_univariate.Rd:51-52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) potential_univariate.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) potential_univariate.Rd:54-55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) potential_univariate.Rd:56-57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) potential_univariate.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) potential_univariate.Rd:59-60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) potential_univariate.Rd:61-62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) potential_univariate.Rd:73-75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) potential_univariate.Rd:76-78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rarity.Rd:35-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rarity.Rd:42-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rarity.Rd:45-48: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  TibbleUtilites.Rd: phyloseq-class
  abundances.Rd: phyloseq-class
  add_besthit.Rd: phyloseq-class
  add_refseq.Rd: phyloseq-class
  aggregate_rare.Rd: phyloseq-class
  aggregate_taxa.Rd: phyloseq-class
  alpha.Rd: phyloseq-class, estimate_richness
  atlas1006.Rd: phyloseq-class
  baseline.Rd: phyloseq
  boxplot_abundance.Rd: phyloseq-class, ggplot
  boxplot_alpha.Rd: phyloseq-class, ggplot
  collapse_replicates.Rd: phyloseq-class
  core.Rd: phyloseq-class
  core_abundance.Rd: phyloseq-class
  core_matrix.Rd: phyloseq
  core_members.Rd: phyloseq-class
  coverage.Rd: phyloseq-class
  dietswap.Rd: phyloseq-class
  diversity.Rd: phyloseq-class
  dominance.Rd: phyloseq-class
  dominant.Rd: phyloseq-class
  evenness.Rd: phyloseq-class
  hotplot.Rd: phyloseq-class, ggplot
  inequality.Rd: phyloseq-class
  is_compositional.Rd: phyloseq-class
  low_abundance.Rd: phyloseq-class
  map_levels.Rd: phyloseq, taxonomyTable-class
  merge_taxa2.Rd: phyloseq-class
  meta.Rd: sample_data
  neat.Rd: vegdist
  neatsort.Rd: phyloseq-class, ordinate
  overlap.Rd: phyloseq-class
  peerj32.Rd: phyloseq-class
  plot_composition.Rd: phyloseq-class, ggplot
  plot_core.Rd: phyloseq
  plot_density.Rd: phyloseq-class, ggplot
  plot_frequencies.Rd: ggplot
  plot_landscape.Rd: phyloseq-class, ggplot
  plot_taxa_prevalence.Rd: phyloseq-class, ggplot
  plot_tipping.Rd: phyloseq-class, ggplot
  prevalence.Rd: phyloseq
  psmelt2.Rd: phyloseq-class
  rare.Rd: phyloseq-class
  rare_abundance.Rd: phyloseq-class
  rare_members.Rd: phyloseq-class
  rarity.Rd: phyloseq-class
  read_biom2phyloseq.Rd: phyloseq-class
  read_csv2phyloseq.Rd: phyloseq-class
  read_mothur2phyloseq.Rd: phyloseq-class
  read_phyloseq.Rd: phyloseq-class
  readcount.Rd: phyloseq-class
  remove_samples.Rd: phyloseq-class
  remove_taxa.Rd: phyloseq-class
  richness.Rd: phyloseq-class
  spreadplot.Rd: phyloseq-class
  summarize_phyloseq.Rd: phyloseq-class
  taxa.Rd: phyloseq-class
  transform.Rd: phyloseq-class, phyloseq
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 14.699  0.166  14.867
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/microbiome.Rcheck/00check.log’
for details.


Installation output

microbiome.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL microbiome
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘microbiome’ ...
** this is package ‘microbiome’ version ‘1.31.4’
** 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 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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) 2011-2025 Leo Lahti, 
    Sudarshan Shetty et al. <microbiome.github.io>
    
 
    Note: we recommend switching to the SummarizedExperiment
    framework, see microbiome.github.io/OMA and the mia package.
    Minimum maintenance is provided microbiome R package but the
    development efforts have switched to mia.

Attaching package: 'microbiome'

The following object is masked from 'package:ggplot2':

    alpha

The following object is masked from 'package:base':

    transform

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 75 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On Bioconductor (1): 'test_divergence.R:5:3'

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 75 ]
> 
> proc.time()
   user  system elapsed 
 10.799   0.456  11.249 

Example timings

microbiome.Rcheck/microbiome-Ex.timings

nameusersystemelapsed
TibbleUtilites0.1550.0330.187
abundances0.0060.0000.007
add_besthit000
add_refseq000
aggregate_rare0.2520.0210.273
aggregate_taxa0.0940.0010.093
alpha0.0120.0000.012
associate0.0330.0000.034
baseline0.0360.0000.036
bimodality0.0010.0000.001
bimodality_sarle000
boxplot_abundance0.2330.0010.236
boxplot_alpha0.5740.0130.588
chunk_reorder000
cmat2table0.0590.0130.074
collapse_replicates0.0420.0070.049
core0.0550.0000.055
core_abundance0.0300.0010.033
core_matrix000
core_members0.0080.0010.009
coverage0.0260.0000.027
default_colors000
densityplot0.0000.0000.001
divergence0.4730.0000.473
diversity0.0200.0020.022
dominance0.0080.0000.009
dominant0.0090.0000.009
estimate_stability000
evenness0.0080.0000.007
find_optima000
gktau0.0110.0010.011
group_age0.0190.0030.022
group_bmi0.0010.0000.001
heat0.0650.0110.076
hotplot0.1830.0100.192
inequality0.1050.0120.117
intermediate_stability0.4130.0010.415
is_compositional0.0640.0020.065
log_modulo_skewness0.0920.0000.092
low_abundance0.0110.0000.011
map_levels0.0380.0010.039
merge_taxa20.0230.0000.023
meta0.0060.0010.006
microbiome-package0.0090.0010.010
multimodality000
neat0.0680.0010.068
neatsort0.1260.0000.125
overlap14.699 0.16614.867
plot_atlas0.0720.0070.078
plot_composition0.2290.0070.236
plot_core0.0710.0090.080
plot_density0.0460.0040.050
plot_frequencies0.0290.0020.032
plot_landscape0.8370.0280.865
plot_regression0.1530.0020.155
plot_taxa_prevalence0.5390.0220.561
plot_tipping0.1340.0030.138
potential_analysis0.0330.0000.033
potential_univariate000
prevalence0.0110.0010.012
psmelt20.0740.0110.084
quiet0.0000.0010.000
rare0.0190.0010.020
rare_abundance0.0310.0020.033
rare_members0.0080.0010.010
rarity0.0670.0030.070
read_biom2phyloseq000
read_csv2phyloseq000
read_mothur2phyloseq000
read_phyloseq000
readcount0.0070.0000.007
remove_samples0.0110.0030.014
remove_taxa0.0130.0040.017
richness0.0110.0000.010
spreadplot0.0650.0050.070
summarize_phyloseq0.0140.0020.016
taxa0.0050.0010.006
time_normalize0.0300.0020.032
time_sort0.1220.0070.129
timesplit0.0960.0010.096
top0.0070.0000.007
top_taxa0.0060.0010.007
transform0.2730.0040.277
ztransform000