William Nickols
| Snapshot Date: 2026-05-05 13:40 -0400 (Tue, 05 May 2026) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: RELEASE_3_23 |
| git_last_commit: f7a411e |
| git_last_commit_date: 2026-04-28 09:04:13 -0400 (Tue, 28 Apr 2026) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-05-06 11:36 -0400 (Wed, 06 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4989 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 Patched (2026-04-24 r89963) -- "Because it was There" | 4722 |
| 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 1200/2418 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maaslin3 1.4.0 (landing page) William Nickols
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| See other builds for maaslin3 in R Universe. | ||||||||||||||
|
To the developers/maintainers of the maaslin3 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/maaslin3.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: maaslin3 |
| Version: 1.4.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings maaslin3_1.4.0.tar.gz |
| StartedAt: 2026-05-05 20:12:08 -0400 (Tue, 05 May 2026) |
| EndedAt: 2026-05-05 20:14:47 -0400 (Tue, 05 May 2026) |
| EllapsedTime: 158.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maaslin3.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings maaslin3_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/maaslin3.Rcheck’
* using R version 4.6.0 Patched (2026-04-24 r89963)
* using platform: aarch64-apple-darwin23
* R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-05-06 00:12:08 UTC
* using option ‘--no-vignettes’
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘1.4.0’
* 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 ‘maaslin3’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘lmerTest:::summary.lmerModLmerTest’ ‘survival:::summary.coxph’
See the note in ?`:::` about the use of this operator.
* 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
maaslin3.Rd: mirai
maaslin_fit.Rd: mirai
maaslin_log_arguments.Rd: mirai
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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
maaslin_plot_results 13.626 0.533 14.263
maaslin_plot_results_from_output 13.376 0.541 13.948
maaslin_contrast_test 6.824 0.685 7.525
maaslin3 6.769 0.688 7.502
maaslin_write_results 5.726 0.437 6.181
maaslin_write_results_lefse_format 5.634 0.424 6.085
maaslin_fit 4.780 0.427 5.237
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.23-bioc/meat/maaslin3.Rcheck/00check.log’
for details.
maaslin3.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL maaslin3 ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’ * installing *source* package ‘maaslin3’ ... ** this is package ‘maaslin3’ version ‘1.4.0’ ** using staged installation ** R ** 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 (maaslin3)
maaslin3.Rcheck/tests/testthat.Rout
R version 4.6.0 Patched (2026-04-24 r89963) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23
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)
> library(maaslin3)
>
> test_check("maaslin3")
2026-05-05 20:14:24.58 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2026-05-05 20:14:24.58 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2026-05-05 20:14:24.59 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2026-05-05 20:14:24.60 ERROR::No fixed, group, or
ordered effects included in formula.
2026-05-05 20:14:24.61 ERROR::Effect name not found in metadata: d
2026-05-05 20:14:24.61 ERROR::No user formula provided
2026-05-05 20:14:24.62 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2026-05-05 20:14:24.62 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2026-05-05 20:14:25.54 INFO::Writing function arguments to log file
2026-05-05 20:14:25.58 INFO::Verifying options selected are valid
2026-05-05 20:14:27.25 INFO::Writing function arguments to log file
2026-05-05 20:14:27.28 INFO::Verifying options selected are valid
2026-05-05 20:14:27.28 INFO::Determining format of input files
2026-05-05 20:14:27.28 INFO::Input format is data samples as rows and metadata samples as rows
2026-05-05 20:14:27.29 INFO::Running selected normalization method: TSS
2026-05-05 20:14:27.29 INFO::Creating output feature tables folder
2026-05-05 20:14:27.29 INFO::Writing normalized data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpqBjAx0/file1097e15581f68/features/data_norm.tsv
2026-05-05 20:14:27.29 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2026-05-05 20:14:27.29 INFO::Total samples in data: 16
2026-05-05 20:14:27.29 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2026-05-05 20:14:27.30 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2026-05-05 20:14:27.30 INFO::Total filtered features: 0
2026-05-05 20:14:27.30 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2026-05-05 20:14:27.30 INFO::Total features filtered by non-zero variance filtering: 0
2026-05-05 20:14:27.30 INFO::Filtered feature names from variance filtering:
2026-05-05 20:14:27.30 INFO::Writing filtered data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpqBjAx0/file1097e15581f68/features/filtered_data.tsv
2026-05-05 20:14:27.31 INFO::Running selected transform method: LOG
2026-05-05 20:14:27.31 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpqBjAx0/file1097e15581f68/features/data_transformed.tsv
2026-05-05 20:14:27.31 INFO::Applying z-score to standardize continuous metadata
2026-05-05 20:14:27.31 INFO::Running the linear model component
2026-05-05 20:14:27.33 INFO::Fitting model to feature number 1, a
2026-05-05 20:14:27.33 INFO::Fitting model to feature number 2, b
2026-05-05 20:14:27.34 INFO::Fitting model to feature number 3, c
2026-05-05 20:14:27.34 INFO::Counting total values for each feature
2026-05-05 20:14:27.34 INFO::Running the logistic model component
2026-05-05 20:14:27.37 INFO::Fitting model to feature number 1, a
2026-05-05 20:14:27.37 INFO::Fitting model to feature number 2, b
2026-05-05 20:14:27.37 INFO::Fitting model to feature number 3, c
2026-05-05 20:14:27.38 INFO::Counting total values for each feature
2026-05-05 20:14:27.38 INFO::Re-running abundances for warn_prevalence
2026-05-05 20:14:27.38 INFO::Running selected normalization method: TSS
2026-05-05 20:14:27.38 INFO::Running selected transform method: LOG
2026-05-05 20:14:27.41 INFO::Fitting model to feature number 1, a
2026-05-05 20:14:27.41 INFO::Fitting model to feature number 2, b
2026-05-05 20:14:27.42 INFO::Fitting model to feature number 3, c
2026-05-05 20:14:27.42 INFO::Creating fits folder
2026-05-05 20:14:27.42 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpqBjAx0/file1097e15581f68/fits/residuals_linear.rds
2026-05-05 20:14:27.42 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpqBjAx0/file1097e15581f68/fits/fitted_linear.rds
2026-05-05 20:14:27.43 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpqBjAx0/file1097e15581f68/fits/residuals_logistic.rds
2026-05-05 20:14:27.43 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpqBjAx0/file1097e15581f68/fits/fitted_logistic.rds
2026-05-05 20:14:27.43 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpqBjAx0/file1097e15581f68/all_results.tsv
2026-05-05 20:14:27.43 INFO::Writing the significant results without errors (those which have joint q-values less than or equal to the threshold of 0.100000 ) to file (ordered by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpqBjAx0/file1097e15581f68/significant_results.tsv
2026-05-05 20:14:27.43 INFO::Creating output figures folder
2026-05-05 20:14:27.44 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpqBjAx0/file1097e15581f68/figures/summary_plot.pdf
2026-05-05 20:14:28.05 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpqBjAx0/file1097e15581f68/figures
2026-05-05 20:14:28.05 INFO::Plotting associations from most to least significant, grouped by metadata
2026-05-05 20:14:28.05 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-05-05 20:14:28.24 INFO::Writing summary plot of
significant results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpqBjAx0/file1097e15581f68/figures/summary_plot.pdf
2026-05-05 20:14:28.79 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpqBjAx0/file1097e15581f68/figures
2026-05-05 20:14:28.79 INFO::Plotting associations from most to least significant, grouped by metadata
2026-05-05 20:14:28.80 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-05-05 20:14:28.98 INFO::Running the linear model component
2026-05-05 20:14:28.99 INFO::Fitting model to feature number 1, a
2026-05-05 20:14:28.99 INFO::Fitting model to feature number 2, b
2026-05-05 20:14:29.00 INFO::Fitting model to feature number 3, c
2026-05-05 20:14:29.00 INFO::Counting total values for each feature
2026-05-05 20:14:29.00 INFO::Running the logistic model component
2026-05-05 20:14:29.01 INFO::Fitting model to feature number 1, a
2026-05-05 20:14:29.01 INFO::Fitting model to feature number 2, b
2026-05-05 20:14:29.01 INFO::Fitting model to feature number 3, c
2026-05-05 20:14:29.01 INFO::Counting total values for each feature
2026-05-05 20:14:29.01 INFO::Re-running abundances for warn_prevalence
2026-05-05 20:14:29.02 INFO::Running selected normalization method: TSS
2026-05-05 20:14:29.02 INFO::Running selected transform method: LOG
2026-05-05 20:14:29.02 INFO::Fitting model to feature number 1, a
2026-05-05 20:14:29.03 INFO::Fitting model to feature number 2, b
2026-05-05 20:14:29.03 INFO::Fitting model to feature number 3, c
2026-05-05 20:14:29.03 INFO::Creating output folder
2026-05-05 20:14:29.04 INFO::Creating output figures folder
2026-05-05 20:14:29.04 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpqBjAx0/file1097e50453785/figures/summary_plot.pdf
2026-05-05 20:14:29.59 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpqBjAx0/file1097e50453785/figures
2026-05-05 20:14:29.59 INFO::Plotting associations from most to least significant, grouped by metadata
2026-05-05 20:14:29.59 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-05-05 20:14:29.79 INFO::Applying z-score to standardize continuous metadata
2026-05-05 20:14:29.79 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2026-05-05 20:14:29.79 INFO::Bypass z-score application to metadata
2026-05-05 20:14:29.79 INFO::Bypass z-score application to metadata
2026-05-05 20:14:29.81 INFO::Determining format of input files
2026-05-05 20:14:29.81 INFO::Input format is data samples as rows and metadata samples as rows
2026-05-05 20:14:29.81 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2026-05-05 20:14:29.81 INFO::Determining format of input files
2026-05-05 20:14:29.82 INFO::Input format is data samples as columns and metadata samples as rows
2026-05-05 20:14:29.82 INFO::Input format is feature_specific_covariate samples as columns
2026-05-05 20:14:29.82 INFO::Determining format of input files
2026-05-05 20:14:29.82 INFO::Input format is data samples as rows and metadata samples as rows
2026-05-05 20:14:29.82 INFO::Input format is feature_specific_covariate samples as columns
2026-05-05 20:14:29.82 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2026-05-05 20:14:29.82 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2026-05-05 20:14:29.83 INFO::Running selected transform method: LOG
2026-05-05 20:14:29.83 INFO::Creating output feature tables folder
2026-05-05 20:14:29.83 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpqBjAx0/file1097e5d0f379c/features/data_transformed.tsv
2026-05-05 20:14:29.83 INFO::Running selected transform method: LOG
2026-05-05 20:14:29.83 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpqBjAx0/file1097e5d0f379c/features/data_transformed.tsv
2026-05-05 20:14:29.84 INFO::Running selected transform method: PLOG
2026-05-05 20:14:29.84 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpqBjAx0/file1097e5d0f379c/features/data_transformed.tsv
2026-05-05 20:14:29.84 INFO::Running selected transform method: NONE
2026-05-05 20:14:29.84 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpqBjAx0/file1097e5d0f379c/features/data_transformed.tsv
2026-05-05 20:14:29.85 INFO::Running the linear model component
2026-05-05 20:14:29.85 INFO::Fitting model to feature number 1, a
2026-05-05 20:14:29.86 INFO::Fitting model to feature number 2, b
2026-05-05 20:14:29.86 INFO::Fitting model to feature number 3, c
2026-05-05 20:14:29.86 INFO::Counting total values for each feature
2026-05-05 20:14:29.86 INFO::Running the logistic model component
2026-05-05 20:14:29.87 INFO::Fitting model to feature number 1, a
2026-05-05 20:14:29.87 INFO::Fitting model to feature number 2, b
2026-05-05 20:14:29.87 INFO::Fitting model to feature number 3, c
2026-05-05 20:14:29.88 INFO::Counting total values for each feature
2026-05-05 20:14:29.88 INFO::Re-running abundances for warn_prevalence
2026-05-05 20:14:29.88 INFO::Running selected normalization method: TSS
2026-05-05 20:14:29.88 INFO::Running selected transform method: LOG
2026-05-05 20:14:29.89 INFO::Fitting model to feature number 1, a
2026-05-05 20:14:29.89 INFO::Fitting model to feature number 2, b
2026-05-05 20:14:29.89 INFO::Fitting model to feature number 3, c
2026-05-05 20:14:29.90 INFO::Creating output folder
2026-05-05 20:14:29.90 INFO::Creating fits folder
2026-05-05 20:14:29.90 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpqBjAx0/file1097e120c127f/fits/residuals_linear.rds
2026-05-05 20:14:29.90 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpqBjAx0/file1097e120c127f/fits/fitted_linear.rds
2026-05-05 20:14:29.90 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpqBjAx0/file1097e120c127f/fits/residuals_logistic.rds
2026-05-05 20:14:29.90 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpqBjAx0/file1097e120c127f/fits/fitted_logistic.rds
2026-05-05 20:14:29.90 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpqBjAx0/file1097e120c127f/all_results.tsv
2026-05-05 20:14:29.91 INFO::Writing the significant results without errors (those which have joint q-values less than or equal to the threshold of 0.100000 ) to file (ordered by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpqBjAx0/file1097e120c127f/significant_results.tsv
2026-05-05 20:14:30.48 INFO::Running the linear model component
2026-05-05 20:14:30.49 INFO::Fitting model to feature number 1, a
2026-05-05 20:14:30.49 INFO::Fitting model to feature number 2, b
2026-05-05 20:14:30.49 INFO::Fitting model to feature number 3, c
2026-05-05 20:14:30.49 INFO::Counting total values for each feature
2026-05-05 20:14:30.49 INFO::Running the logistic model component
2026-05-05 20:14:30.50 INFO::Fitting model to feature number 1, a
2026-05-05 20:14:30.50 INFO::Fitting model to feature number 2, b
2026-05-05 20:14:30.50 INFO::Fitting model to feature number 3, c
2026-05-05 20:14:30.51 INFO::Counting total values for each feature
2026-05-05 20:14:30.51 INFO::Re-running abundances for warn_prevalence
2026-05-05 20:14:30.51 INFO::Running selected normalization method: TSS
2026-05-05 20:14:30.51 INFO::Running selected transform method: LOG
2026-05-05 20:14:30.52 INFO::Fitting model to feature number 1, a
2026-05-05 20:14:30.52 INFO::Fitting model to feature number 2, b
2026-05-05 20:14:30.52 INFO::Fitting model to feature number 3, c
2026-05-05 20:14:31.35 INFO::Started 2 mirai daemons via `cores` argument
2026-05-05 20:14:31.35 INFO::Running the linear model component
2026-05-05 20:14:31.91 INFO::Counting total values for each feature
2026-05-05 20:14:31.91 INFO::Running the logistic model component
2026-05-05 20:14:31.94 INFO::Counting total values for each feature
2026-05-05 20:14:31.95 INFO::Re-running abundances for warn_prevalence
2026-05-05 20:14:31.95 INFO::Running selected normalization method: TSS
2026-05-05 20:14:31.95 INFO::Running selected transform method: LOG
2026-05-05 20:14:33.52 INFO::Running the linear model component
2026-05-05 20:14:34.10 INFO::Counting total values for each feature
2026-05-05 20:14:34.10 INFO::Running the logistic model component
2026-05-05 20:14:34.13 INFO::Counting total values for each feature
2026-05-05 20:14:34.13 INFO::Re-running abundances for warn_prevalence
2026-05-05 20:14:34.14 INFO::Running selected normalization method: TSS
2026-05-05 20:14:34.14 INFO::Running selected transform method: LOG
2026-05-05 20:14:36.21 INFO::Running the linear model component
2026-05-05 20:14:36.78 INFO::Counting total values for each feature
2026-05-05 20:14:36.78 INFO::Running the logistic model component
2026-05-05 20:14:36.81 INFO::Counting total values for each feature
2026-05-05 20:14:36.82 INFO::Re-running abundances for warn_prevalence
2026-05-05 20:14:36.82 INFO::Running selected normalization method: TSS
2026-05-05 20:14:36.82 INFO::Running selected transform method: LOG
2026-05-05 20:14:38.38 INFO::Writing function arguments to log file
2026-05-05 20:14:38.40 INFO::Verifying options selected are valid
2026-05-05 20:14:38.40 INFO::Determining format of input files
2026-05-05 20:14:38.41 INFO::Input format is data samples as rows and metadata samples as rows
2026-05-05 20:14:38.41 INFO::Running selected normalization method: TSS
2026-05-05 20:14:38.42 INFO::Creating output feature tables folder
2026-05-05 20:14:38.42 INFO::Writing normalized data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpqBjAx0/maaslin3_parallel_test_1097e49ffe22b/features/data_norm.tsv
2026-05-05 20:14:38.42 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2026-05-05 20:14:38.42 INFO::Total samples in data: 30
2026-05-05 20:14:38.42 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2026-05-05 20:14:38.43 INFO::Max samples allowed with min abundance for a feature not to be filtered: 30.300000
2026-05-05 20:14:38.43 INFO::Total filtered features: 0
2026-05-05 20:14:38.43 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2026-05-05 20:14:38.43 INFO::Total features filtered by non-zero variance filtering: 0
2026-05-05 20:14:38.43 INFO::Filtered feature names from variance filtering:
2026-05-05 20:14:38.43 INFO::Writing filtered data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpqBjAx0/maaslin3_parallel_test_1097e49ffe22b/features/filtered_data.tsv
2026-05-05 20:14:38.44 INFO::Running selected transform method: LOG
2026-05-05 20:14:38.44 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpqBjAx0/maaslin3_parallel_test_1097e49ffe22b/features/data_transformed.tsv
2026-05-05 20:14:38.44 INFO::Applying z-score to standardize continuous metadata
2026-05-05 20:14:38.44 INFO::Running the linear model component
2026-05-05 20:14:39.02 INFO::Counting total values for each feature
2026-05-05 20:14:39.02 INFO::Running the logistic model component
2026-05-05 20:14:39.08 INFO::Counting total values for each feature
2026-05-05 20:14:39.09 INFO::Creating fits folder
2026-05-05 20:14:39.09 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpqBjAx0/maaslin3_parallel_test_1097e49ffe22b/fits/residuals_linear.rds
2026-05-05 20:14:39.09 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpqBjAx0/maaslin3_parallel_test_1097e49ffe22b/fits/fitted_linear.rds
2026-05-05 20:14:39.09 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpqBjAx0/maaslin3_parallel_test_1097e49ffe22b/fits/residuals_logistic.rds
2026-05-05 20:14:39.09 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpqBjAx0/maaslin3_parallel_test_1097e49ffe22b/fits/fitted_logistic.rds
2026-05-05 20:14:39.10 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpqBjAx0/maaslin3_parallel_test_1097e49ffe22b/all_results.tsv
2026-05-05 20:14:39.10 INFO::Writing the significant results without errors (those which have joint q-values less than or equal to the threshold of 0.100000 ) to file (ordered by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpqBjAx0/maaslin3_parallel_test_1097e49ffe22b/significant_results.tsv
2026-05-05 20:14:39.83 INFO::Running the linear model component
2026-05-05 20:14:39.84 INFO::Fitting model to feature number 1, a
2026-05-05 20:14:39.84 INFO::Fitting model to feature number 2, b
2026-05-05 20:14:39.84 INFO::Fitting model to feature number 3, c
2026-05-05 20:14:39.84 INFO::Counting total values for each feature
2026-05-05 20:14:39.84 INFO::Running the logistic model component
2026-05-05 20:14:39.85 INFO::Fitting model to feature number 1, a
2026-05-05 20:14:39.85 INFO::Fitting model to feature number 2, b
2026-05-05 20:14:39.85 INFO::Fitting model to feature number 3, c
2026-05-05 20:14:39.86 INFO::Counting total values for each feature
2026-05-05 20:14:39.86 INFO::Re-running abundances for warn_prevalence
2026-05-05 20:14:39.86 INFO::Running selected normalization method: TSS
2026-05-05 20:14:39.86 INFO::Running selected transform method: LOG
2026-05-05 20:14:39.87 INFO::Fitting model to feature number 1, a
2026-05-05 20:14:39.87 INFO::Fitting model to feature number 2, b
2026-05-05 20:14:39.87 INFO::Fitting model to feature number 3, c
2026-05-05 20:14:40.17 INFO::Started 2 mirai daemons via `cores` argument
2026-05-05 20:14:40.17 INFO::Running the linear model component
2026-05-05 20:14:40.72 INFO::Counting total values for each feature
2026-05-05 20:14:40.72 INFO::Running the logistic model component
2026-05-05 20:14:40.75 INFO::Counting total values for each feature
2026-05-05 20:14:40.76 INFO::Re-running abundances for warn_prevalence
2026-05-05 20:14:40.76 INFO::Running selected normalization method: TSS
2026-05-05 20:14:40.76 INFO::Running selected transform method: LOG
2026-05-05 20:14:41.00 INFO::Running the linear model component
2026-05-05 20:14:41.00 INFO::Fitting model to feature number 1, a
2026-05-05 20:14:41.00 INFO::Fitting model to feature number 2, b
2026-05-05 20:14:41.01 INFO::Counting total values for each feature
2026-05-05 20:14:41.01 INFO::Running the logistic model component
2026-05-05 20:14:41.01 INFO::Fitting model to feature number 1, a
2026-05-05 20:14:41.02 INFO::Fitting model to feature number 2, b
2026-05-05 20:14:41.02 INFO::Counting total values for each feature
2026-05-05 20:14:41.02 INFO::Re-running abundances for warn_prevalence
2026-05-05 20:14:41.02 INFO::Running selected normalization method: TSS
2026-05-05 20:14:41.02 INFO::Running selected transform method: LOG
2026-05-05 20:14:41.03 INFO::Fitting model to feature number 1, a
2026-05-05 20:14:41.03 INFO::Fitting model to feature number 2, b
2026-05-05 20:14:41.03 INFO::Creating output folder
2026-05-05 20:14:41.04 INFO::Creating output figures folder
2026-05-05 20:14:41.04 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpqBjAx0/file1097eefb11d9/figures/summary_plot.pdf
2026-05-05 20:14:41.85 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpqBjAx0/file1097eefb11d9/figures
2026-05-05 20:14:41.86 INFO::Plotting associations from most to least significant, grouped by metadata
2026-05-05 20:14:41.86 INFO::Creating scatter plot for continuous
data (linear), var1 vs b
2026-05-05 20:14:42.06 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-05-05 20:14:42.83 INFO::Running the linear model component
2026-05-05 20:14:42.83 INFO::Fitting model to feature number 1, a
2026-05-05 20:14:42.86 INFO::Fitting model to feature number 2, b
2026-05-05 20:14:42.88 INFO::Counting total values for each feature
2026-05-05 20:14:42.88 INFO::Running the logistic model component
2026-05-05 20:14:42.88 INFO::Fitting model to feature number 1, a
2026-05-05 20:14:42.92 INFO::Fitting model to feature number 2, b
2026-05-05 20:14:42.95 INFO::Counting total values for each feature
2026-05-05 20:14:42.95 INFO::Re-running abundances for warn_prevalence
2026-05-05 20:14:42.95 INFO::Running selected normalization method: TSS
2026-05-05 20:14:42.95 INFO::Running selected transform method: LOG
2026-05-05 20:14:42.96 INFO::Fitting model to feature number 1, a
2026-05-05 20:14:42.98 INFO::Fitting model to feature number 2, b
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 190 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_no_dplyr_in_tests.R:4:1'
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 190 ]
>
>
> proc.time()
user system elapsed
58.460 1.586 70.548
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 6.769 | 0.688 | 7.502 | |
| maaslin_check_arguments | 0.053 | 0.002 | 0.054 | |
| maaslin_check_formula | 0.063 | 0.019 | 0.082 | |
| maaslin_compute_formula | 0.065 | 0.023 | 0.088 | |
| maaslin_contrast_test | 6.824 | 0.685 | 7.525 | |
| maaslin_filter | 0.239 | 0.037 | 0.277 | |
| maaslin_fit | 4.780 | 0.427 | 5.237 | |
| maaslin_log_arguments | 0.064 | 0.016 | 0.081 | |
| maaslin_normalize | 0.136 | 0.023 | 0.161 | |
| maaslin_plot_results | 13.626 | 0.533 | 14.263 | |
| maaslin_plot_results_from_output | 13.376 | 0.541 | 13.948 | |
| maaslin_process_metadata | 0.246 | 0.056 | 0.303 | |
| maaslin_read_data | 0.064 | 0.018 | 0.082 | |
| maaslin_reorder_data | 0.066 | 0.019 | 0.085 | |
| maaslin_transform | 0.301 | 0.042 | 0.345 | |
| maaslin_write_results | 5.726 | 0.437 | 6.181 | |
| maaslin_write_results_lefse_format | 5.634 | 0.424 | 6.085 | |
| preprocess_dna_mtx | 0.001 | 0.000 | 0.002 | |
| preprocess_taxa_mtx | 0.001 | 0.000 | 0.001 | |