Leo Lahti
| Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/microbiome |
| git_branch: RELEASE_3_21 |
| git_last_commit: 1d04e67 |
| git_last_commit_date: 2025-04-15 11:13:38 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-16 11:40 -0400 (Thu, 16 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
| 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 1278/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| microbiome 1.30.0 (landing page) Leo Lahti
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
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. |
| Package: microbiome |
| Version: 1.30.0 |
| 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_1.30.0.tar.gz |
| StartedAt: 2025-10-15 03:32:52 -0400 (Wed, 15 Oct 2025) |
| EndedAt: 2025-10-15 03:36:38 -0400 (Wed, 15 Oct 2025) |
| EllapsedTime: 225.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: microbiome.Rcheck |
| Warnings: NA |
##############################################################################
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###
### 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_1.30.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/microbiome.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘microbiome/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘microbiome’ version ‘1.30.0’
* 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 ... NOTE
Problems with news in ‘NEWS’:
Cannot process chunk/lines:
CHANGES IN VERSION 0.1.2
# New features
o Added plot_abundances function
o Added Chao1 index in richness function
o In atlas1006 data set, pseudocount of +1 in otu table has been
removed to facilitate comparison with sequencing data sets and to
avoid confusion
o In atlas1006 data set, only a single replicate per subject-time
combination is chosen (at random)
o New function collapse_replicates has been added
# Major changes
o Abundance matrices (otu tables) for all example data sets now
starting from 0 without pseudocount
# Minor changes
o Changed the default for the detection argument in the richness function to
detection=0
o Color order in plot_landscape legend now follows the factor levels
of the col argument
o Various minor fixes; see github commits for many more details
* 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 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 18.207 2.29 20.557
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
[ FAIL 1 | WARN 3 | SKIP 1 | PASS 82 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On Bioconductor (1): 'test_divergence.R:5:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_transformations.R:47:3'): transform works correctly ──────────
... < 1e-15 is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 1 | WARN 3 | SKIP 1 | PASS 82 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.21-bioc/meat/microbiome.Rcheck/00check.log’
for details.
microbiome.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL microbiome ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘microbiome’ ... ** this is package ‘microbiome’ version ‘1.30.0’ ** 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)
microbiome.Rcheck/tests/testthat.Rout.fail
R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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 1 | WARN 3 | SKIP 1 | PASS 82 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On Bioconductor (1): 'test_divergence.R:5:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_transformations.R:47:3'): transform works correctly ──────────
... < 1e-15 is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 1 | WARN 3 | SKIP 1 | PASS 82 ]
Error: Test failures
Execution halted
microbiome.Rcheck/microbiome-Ex.timings
| name | user | system | elapsed | |
| TibbleUtilites | 0.166 | 0.022 | 0.189 | |
| abundances | 0.008 | 0.003 | 0.011 | |
| add_besthit | 0.000 | 0.001 | 0.001 | |
| add_refseq | 0 | 0 | 0 | |
| aggregate_rare | 0.296 | 0.030 | 0.325 | |
| aggregate_taxa | 0.083 | 0.004 | 0.086 | |
| alpha | 0.013 | 0.003 | 0.017 | |
| associate | 0.037 | 0.003 | 0.040 | |
| baseline | 0.045 | 0.004 | 0.049 | |
| bimodality | 0.001 | 0.000 | 0.002 | |
| bimodality_sarle | 0 | 0 | 0 | |
| boxplot_abundance | 0.245 | 0.012 | 0.257 | |
| boxplot_alpha | 0.607 | 0.020 | 0.631 | |
| chunk_reorder | 0.000 | 0.000 | 0.001 | |
| cmat2table | 0.061 | 0.007 | 0.068 | |
| collapse_replicates | 0.054 | 0.007 | 0.060 | |
| core | 0.044 | 0.007 | 0.050 | |
| core_abundance | 0.055 | 0.005 | 0.058 | |
| core_matrix | 0 | 0 | 0 | |
| core_members | 0.009 | 0.002 | 0.013 | |
| coverage | 0.029 | 0.002 | 0.031 | |
| default_colors | 0 | 0 | 0 | |
| densityplot | 0 | 0 | 0 | |
| divergence | 0.415 | 0.005 | 0.420 | |
| diversity | 0.013 | 0.004 | 0.016 | |
| dominance | 0.011 | 0.003 | 0.014 | |
| dominant | 0.011 | 0.002 | 0.014 | |
| estimate_stability | 0 | 0 | 0 | |
| evenness | 0.027 | 0.004 | 0.031 | |
| find_optima | 0 | 0 | 0 | |
| gktau | 0.017 | 0.002 | 0.019 | |
| group_age | 0.029 | 0.003 | 0.033 | |
| group_bmi | 0.001 | 0.000 | 0.001 | |
| heat | 0.067 | 0.003 | 0.071 | |
| hotplot | 0.178 | 0.007 | 0.186 | |
| inequality | 0.137 | 0.009 | 0.146 | |
| intermediate_stability | 0.428 | 0.005 | 0.432 | |
| is_compositional | 0.052 | 0.003 | 0.055 | |
| log_modulo_skewness | 0.094 | 0.005 | 0.101 | |
| low_abundance | 0.015 | 0.003 | 0.018 | |
| map_levels | 0.043 | 0.003 | 0.045 | |
| merge_taxa2 | 0.024 | 0.002 | 0.026 | |
| meta | 0.008 | 0.002 | 0.011 | |
| microbiome-package | 0.011 | 0.001 | 0.013 | |
| multimodality | 0.000 | 0.001 | 0.000 | |
| neat | 0.072 | 0.004 | 0.076 | |
| neatsort | 0.179 | 0.007 | 0.186 | |
| overlap | 18.207 | 2.290 | 20.557 | |
| plot_atlas | 0.074 | 0.003 | 0.078 | |
| plot_composition | 0.197 | 0.006 | 0.203 | |
| plot_core | 0.065 | 0.006 | 0.072 | |
| plot_density | 0.046 | 0.003 | 0.049 | |
| plot_frequencies | 0.031 | 0.003 | 0.034 | |
| plot_landscape | 1.019 | 0.026 | 1.047 | |
| plot_regression | 0.152 | 0.005 | 0.157 | |
| plot_taxa_prevalence | 0.564 | 0.050 | 0.615 | |
| plot_tipping | 0.119 | 0.006 | 0.125 | |
| potential_analysis | 0.035 | 0.003 | 0.039 | |
| potential_univariate | 0.000 | 0.000 | 0.001 | |
| prevalence | 0.016 | 0.003 | 0.019 | |
| psmelt2 | 0.078 | 0.004 | 0.082 | |
| quiet | 0.001 | 0.000 | 0.000 | |
| rare | 0.020 | 0.003 | 0.023 | |
| rare_abundance | 0.032 | 0.002 | 0.035 | |
| rare_members | 0.010 | 0.005 | 0.029 | |
| rarity | 0.067 | 0.004 | 0.073 | |
| read_biom2phyloseq | 0.001 | 0.000 | 0.001 | |
| read_csv2phyloseq | 0.000 | 0.000 | 0.001 | |
| read_mothur2phyloseq | 0.001 | 0.001 | 0.001 | |
| read_phyloseq | 0 | 0 | 0 | |
| readcount | 0.009 | 0.003 | 0.011 | |
| remove_samples | 0.016 | 0.003 | 0.018 | |
| remove_taxa | 0.018 | 0.003 | 0.020 | |
| richness | 0.012 | 0.003 | 0.014 | |
| spreadplot | 0.066 | 0.004 | 0.071 | |
| summarize_phyloseq | 0.015 | 0.003 | 0.019 | |
| taxa | 0.008 | 0.002 | 0.011 | |
| time_normalize | 0.034 | 0.002 | 0.036 | |
| time_sort | 0.147 | 0.008 | 0.155 | |
| timesplit | 0.097 | 0.004 | 0.101 | |
| top | 0.009 | 0.003 | 0.012 | |
| top_taxa | 0.008 | 0.002 | 0.010 | |
| transform | 0.316 | 0.016 | 0.331 | |
| ztransform | 0 | 0 | 0 | |