William Nickols
| Snapshot Date: 2026-05-01 13:40 -0400 (Fri, 01 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 2026-05-02 11:35 -0400 (Sat, 02 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" | 4988 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 Patched (2026-04-24 r89963) -- "Because it was There" | 4718 |
| 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: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings maaslin3_1.4.0.tar.gz |
| StartedAt: 2026-05-02 01:48:16 -0400 (Sat, 02 May 2026) |
| EndedAt: 2026-05-02 02:04:04 -0400 (Sat, 02 May 2026) |
| EllapsedTime: 948.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maaslin3.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings maaslin3_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/maaslin3.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-02 05:48:16 UTC
* 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 loading without being on the library search path ... 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 39.615 0.577 41.076
maaslin_plot_results_from_output 38.178 0.397 38.928
maaslin_contrast_test 17.573 0.488 18.034
maaslin3 16.697 0.687 17.371
maaslin_write_results_lefse_format 14.582 0.182 14.753
maaslin_write_results 13.522 0.226 13.736
maaslin_fit 12.035 0.270 12.284
* 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: 3 NOTEs
See
‘/home/biocbuild/bbs-3.23-bioc/meat/maaslin3.Rcheck/00check.log’
for details.
maaslin3.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL maaslin3 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-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 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 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)
> library(maaslin3)
>
> test_check("maaslin3")
2026-05-02 01:54:01.97 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2026-05-02 01:54:01.99 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2026-05-02 01:54:02.00 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2026-05-02 01:54:02.05 ERROR::No fixed, group, or
ordered effects included in formula.
2026-05-02 01:54:02.06 ERROR::Effect name not found in metadata: d
2026-05-02 01:54:02.06 ERROR::No user formula provided
2026-05-02 01:54:02.09 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2026-05-02 01:54:02.10 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2026-05-02 01:54:04.58 INFO::Writing function arguments to log file
2026-05-02 01:54:04.60 INFO::Verifying options selected are valid
2026-05-02 01:54:08.85 INFO::Writing function arguments to log file
2026-05-02 01:54:08.87 INFO::Verifying options selected are valid
2026-05-02 01:54:08.88 INFO::Determining format of input files
2026-05-02 01:54:08.88 INFO::Input format is data samples as rows and metadata samples as rows
2026-05-02 01:54:08.88 INFO::Running selected normalization method: TSS
2026-05-02 01:54:08.88 INFO::Creating output feature tables folder
2026-05-02 01:54:08.88 INFO::Writing normalized data to file /tmp/RtmpwkOnSF/file1d8a572e76a2fe/features/data_norm.tsv
2026-05-02 01:54:08.89 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2026-05-02 01:54:08.89 INFO::Total samples in data: 16
2026-05-02 01:54:08.89 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2026-05-02 01:54:08.89 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2026-05-02 01:54:08.89 INFO::Total filtered features: 0
2026-05-02 01:54:08.89 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2026-05-02 01:54:08.90 INFO::Total features filtered by non-zero variance filtering: 0
2026-05-02 01:54:08.90 INFO::Filtered feature names from variance filtering:
2026-05-02 01:54:08.90 INFO::Writing filtered data to file /tmp/RtmpwkOnSF/file1d8a572e76a2fe/features/filtered_data.tsv
2026-05-02 01:54:08.90 INFO::Running selected transform method: LOG
2026-05-02 01:54:08.90 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpwkOnSF/file1d8a572e76a2fe/features/data_transformed.tsv
2026-05-02 01:54:08.91 INFO::Applying z-score to standardize continuous metadata
2026-05-02 01:54:08.91 INFO::Running the linear model component
2026-05-02 01:54:08.93 INFO::Fitting model to feature number 1, a
2026-05-02 01:54:08.94 INFO::Fitting model to feature number 2, b
2026-05-02 01:54:08.94 INFO::Fitting model to feature number 3, c
2026-05-02 01:54:08.95 INFO::Counting total values for each feature
2026-05-02 01:54:08.95 INFO::Running the logistic model component
2026-05-02 01:54:08.97 INFO::Fitting model to feature number 1, a
2026-05-02 01:54:08.98 INFO::Fitting model to feature number 2, b
2026-05-02 01:54:08.99 INFO::Fitting model to feature number 3, c
2026-05-02 01:54:08.99 INFO::Counting total values for each feature
2026-05-02 01:54:09.00 INFO::Re-running abundances for warn_prevalence
2026-05-02 01:54:09.00 INFO::Running selected normalization method: TSS
2026-05-02 01:54:09.00 INFO::Running selected transform method: LOG
2026-05-02 01:54:09.02 INFO::Fitting model to feature number 1, a
2026-05-02 01:54:09.03 INFO::Fitting model to feature number 2, b
2026-05-02 01:54:09.03 INFO::Fitting model to feature number 3, c
2026-05-02 01:54:09.04 INFO::Creating fits folder
2026-05-02 01:54:09.05 INFO::Writing residuals to file /tmp/RtmpwkOnSF/file1d8a572e76a2fe/fits/residuals_linear.rds
2026-05-02 01:54:09.05 INFO::Writing fitted values to file /tmp/RtmpwkOnSF/file1d8a572e76a2fe/fits/fitted_linear.rds
2026-05-02 01:54:09.05 INFO::Writing residuals to file /tmp/RtmpwkOnSF/file1d8a572e76a2fe/fits/residuals_logistic.rds
2026-05-02 01:54:09.05 INFO::Writing fitted values to file /tmp/RtmpwkOnSF/file1d8a572e76a2fe/fits/fitted_logistic.rds
2026-05-02 01:54:09.05 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpwkOnSF/file1d8a572e76a2fe/all_results.tsv
2026-05-02 01:54:09.06 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): /tmp/RtmpwkOnSF/file1d8a572e76a2fe/significant_results.tsv
2026-05-02 01:54:09.06 INFO::Creating output figures folder
2026-05-02 01:54:09.06 INFO::Writing summary plot of significant
results to file: /tmp/RtmpwkOnSF/file1d8a572e76a2fe/figures/summary_plot.pdf
2026-05-02 01:54:10.78 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpwkOnSF/file1d8a572e76a2fe/figures
2026-05-02 01:54:10.78 INFO::Plotting associations from most to least significant, grouped by metadata
2026-05-02 01:54:10.79 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-05-02 01:54:11.34 INFO::Writing summary plot of
significant results to file: /tmp/RtmpwkOnSF/file1d8a572e76a2fe/figures/summary_plot.pdf
2026-05-02 01:54:12.97 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpwkOnSF/file1d8a572e76a2fe/figures
2026-05-02 01:54:12.97 INFO::Plotting associations from most to least significant, grouped by metadata
2026-05-02 01:54:12.97 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-05-02 01:54:13.51 INFO::Running the linear model component
2026-05-02 01:54:13.52 INFO::Fitting model to feature number 1, a
2026-05-02 01:54:13.52 INFO::Fitting model to feature number 2, b
2026-05-02 01:54:13.53 INFO::Fitting model to feature number 3, c
2026-05-02 01:54:13.53 INFO::Counting total values for each feature
2026-05-02 01:54:13.54 INFO::Running the logistic model component
2026-05-02 01:54:13.55 INFO::Fitting model to feature number 1, a
2026-05-02 01:54:13.55 INFO::Fitting model to feature number 2, b
2026-05-02 01:54:13.56 INFO::Fitting model to feature number 3, c
2026-05-02 01:54:13.57 INFO::Counting total values for each feature
2026-05-02 01:54:13.57 INFO::Re-running abundances for warn_prevalence
2026-05-02 01:54:13.57 INFO::Running selected normalization method: TSS
2026-05-02 01:54:13.57 INFO::Running selected transform method: LOG
2026-05-02 01:54:13.58 INFO::Fitting model to feature number 1, a
2026-05-02 01:54:13.59 INFO::Fitting model to feature number 2, b
2026-05-02 01:54:13.59 INFO::Fitting model to feature number 3, c
2026-05-02 01:54:13.61 INFO::Creating output folder
2026-05-02 01:54:13.61 INFO::Creating output figures folder
2026-05-02 01:54:13.61 INFO::Writing summary plot of significant
results to file: /tmp/RtmpwkOnSF/file1d8a577765f51e/figures/summary_plot.pdf
2026-05-02 01:54:15.21 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpwkOnSF/file1d8a577765f51e/figures
2026-05-02 01:54:15.21 INFO::Plotting associations from most to least significant, grouped by metadata
2026-05-02 01:54:15.21 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-05-02 01:54:15.75 INFO::Applying z-score to standardize continuous metadata
2026-05-02 01:54:15.75 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2026-05-02 01:54:15.75 INFO::Bypass z-score application to metadata
2026-05-02 01:54:15.75 INFO::Bypass z-score application to metadata
2026-05-02 01:54:15.80 INFO::Determining format of input files
2026-05-02 01:54:15.80 INFO::Input format is data samples as rows and metadata samples as rows
2026-05-02 01:54:15.80 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2026-05-02 01:54:15.81 INFO::Determining format of input files
2026-05-02 01:54:15.81 INFO::Input format is data samples as columns and metadata samples as rows
2026-05-02 01:54:15.81 INFO::Input format is feature_specific_covariate samples as columns
2026-05-02 01:54:15.82 INFO::Determining format of input files
2026-05-02 01:54:15.82 INFO::Input format is data samples as rows and metadata samples as rows
2026-05-02 01:54:15.82 INFO::Input format is feature_specific_covariate samples as columns
2026-05-02 01:54:15.83 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2026-05-02 01:54:15.83 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2026-05-02 01:54:15.84 INFO::Running selected transform method: LOG
2026-05-02 01:54:15.84 INFO::Creating output feature tables folder
2026-05-02 01:54:15.84 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpwkOnSF/file1d8a57a3491be/features/data_transformed.tsv
2026-05-02 01:54:15.85 INFO::Running selected transform method: LOG
2026-05-02 01:54:15.85 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpwkOnSF/file1d8a57a3491be/features/data_transformed.tsv
2026-05-02 01:54:15.85 INFO::Running selected transform method: PLOG
2026-05-02 01:54:15.85 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpwkOnSF/file1d8a57a3491be/features/data_transformed.tsv
2026-05-02 01:54:15.86 INFO::Running selected transform method: NONE
2026-05-02 01:54:15.86 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpwkOnSF/file1d8a57a3491be/features/data_transformed.tsv
2026-05-02 01:54:15.87 INFO::Running the linear model component
2026-05-02 01:54:15.88 INFO::Fitting model to feature number 1, a
2026-05-02 01:54:15.88 INFO::Fitting model to feature number 2, b
2026-05-02 01:54:15.89 INFO::Fitting model to feature number 3, c
2026-05-02 01:54:15.89 INFO::Counting total values for each feature
2026-05-02 01:54:15.89 INFO::Running the logistic model component
2026-05-02 01:54:15.90 INFO::Fitting model to feature number 1, a
2026-05-02 01:54:15.91 INFO::Fitting model to feature number 2, b
2026-05-02 01:54:15.92 INFO::Fitting model to feature number 3, c
2026-05-02 01:54:15.92 INFO::Counting total values for each feature
2026-05-02 01:54:15.93 INFO::Re-running abundances for warn_prevalence
2026-05-02 01:54:15.93 INFO::Running selected normalization method: TSS
2026-05-02 01:54:15.93 INFO::Running selected transform method: LOG
2026-05-02 01:54:15.94 INFO::Fitting model to feature number 1, a
2026-05-02 01:54:15.94 INFO::Fitting model to feature number 2, b
2026-05-02 01:54:15.95 INFO::Fitting model to feature number 3, c
2026-05-02 01:54:15.96 INFO::Creating output folder
2026-05-02 01:54:15.96 INFO::Creating fits folder
2026-05-02 01:54:15.96 INFO::Writing residuals to file /tmp/RtmpwkOnSF/file1d8a576e4c4638/fits/residuals_linear.rds
2026-05-02 01:54:15.96 INFO::Writing fitted values to file /tmp/RtmpwkOnSF/file1d8a576e4c4638/fits/fitted_linear.rds
2026-05-02 01:54:15.97 INFO::Writing residuals to file /tmp/RtmpwkOnSF/file1d8a576e4c4638/fits/residuals_logistic.rds
2026-05-02 01:54:15.97 INFO::Writing fitted values to file /tmp/RtmpwkOnSF/file1d8a576e4c4638/fits/fitted_logistic.rds
2026-05-02 01:54:15.97 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpwkOnSF/file1d8a576e4c4638/all_results.tsv
2026-05-02 01:54:15.97 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): /tmp/RtmpwkOnSF/file1d8a576e4c4638/significant_results.tsv
2026-05-02 01:54:16.61 INFO::Running the linear model component
2026-05-02 01:54:16.62 INFO::Fitting model to feature number 1, a
2026-05-02 01:54:16.63 INFO::Fitting model to feature number 2, b
2026-05-02 01:54:16.63 INFO::Fitting model to feature number 3, c
2026-05-02 01:54:16.64 INFO::Counting total values for each feature
2026-05-02 01:54:16.64 INFO::Running the logistic model component
2026-05-02 01:54:16.65 INFO::Fitting model to feature number 1, a
2026-05-02 01:54:16.65 INFO::Fitting model to feature number 2, b
2026-05-02 01:54:16.67 INFO::Fitting model to feature number 3, c
2026-05-02 01:54:16.68 INFO::Counting total values for each feature
2026-05-02 01:54:16.68 INFO::Re-running abundances for warn_prevalence
2026-05-02 01:54:16.68 INFO::Running selected normalization method: TSS
2026-05-02 01:54:16.68 INFO::Running selected transform method: LOG
2026-05-02 01:54:16.70 INFO::Fitting model to feature number 1, a
2026-05-02 01:54:16.70 INFO::Fitting model to feature number 2, b
2026-05-02 01:54:16.70 INFO::Fitting model to feature number 3, c
2026-05-02 01:54:17.68 INFO::Started 2 mirai daemons via `cores` argument
2026-05-02 01:54:17.68 INFO::Running the linear model component
2026-05-02 01:54:19.19 INFO::Counting total values for each feature
2026-05-02 01:54:19.19 INFO::Running the logistic model component
2026-05-02 01:54:19.28 INFO::Counting total values for each feature
2026-05-02 01:54:19.28 INFO::Re-running abundances for warn_prevalence
2026-05-02 01:54:19.28 INFO::Running selected normalization method: TSS
2026-05-02 01:54:19.28 INFO::Running selected transform method: LOG
2026-05-02 01:54:20.99 INFO::Running the linear model component
2026-05-02 01:54:22.48 INFO::Counting total values for each feature
2026-05-02 01:54:22.48 INFO::Running the logistic model component
2026-05-02 01:54:22.57 INFO::Counting total values for each feature
2026-05-02 01:54:22.57 INFO::Re-running abundances for warn_prevalence
2026-05-02 01:54:22.58 INFO::Running selected normalization method: TSS
2026-05-02 01:54:22.58 INFO::Running selected transform method: LOG
2026-05-02 01:54:24.80 INFO::Running the linear model component
2026-05-02 01:54:26.29 INFO::Counting total values for each feature
2026-05-02 01:54:26.30 INFO::Running the logistic model component
2026-05-02 01:54:26.40 INFO::Counting total values for each feature
2026-05-02 01:54:26.40 INFO::Re-running abundances for warn_prevalence
2026-05-02 01:54:26.40 INFO::Running selected normalization method: TSS
2026-05-02 01:54:26.41 INFO::Running selected transform method: LOG
2026-05-02 01:54:28.13 INFO::Writing function arguments to log file
2026-05-02 01:54:28.18 INFO::Verifying options selected are valid
2026-05-02 01:54:28.18 INFO::Determining format of input files
2026-05-02 01:54:28.19 INFO::Input format is data samples as rows and metadata samples as rows
2026-05-02 01:54:28.19 INFO::Running selected normalization method: TSS
2026-05-02 01:54:28.20 INFO::Creating output feature tables folder
2026-05-02 01:54:28.20 INFO::Writing normalized data to file /tmp/RtmpwkOnSF/maaslin3_parallel_test_1d8a572e82b9cd/features/data_norm.tsv
2026-05-02 01:54:28.20 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2026-05-02 01:54:28.20 INFO::Total samples in data: 30
2026-05-02 01:54:28.21 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2026-05-02 01:54:28.21 INFO::Max samples allowed with min abundance for a feature not to be filtered: 30.300000
2026-05-02 01:54:28.21 INFO::Total filtered features: 0
2026-05-02 01:54:28.21 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2026-05-02 01:54:28.22 INFO::Total features filtered by non-zero variance filtering: 0
2026-05-02 01:54:28.22 INFO::Filtered feature names from variance filtering:
2026-05-02 01:54:28.22 INFO::Writing filtered data to file /tmp/RtmpwkOnSF/maaslin3_parallel_test_1d8a572e82b9cd/features/filtered_data.tsv
2026-05-02 01:54:28.22 INFO::Running selected transform method: LOG
2026-05-02 01:54:28.22 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpwkOnSF/maaslin3_parallel_test_1d8a572e82b9cd/features/data_transformed.tsv
2026-05-02 01:54:28.23 INFO::Applying z-score to standardize continuous metadata
2026-05-02 01:54:28.23 INFO::Running the linear model component
2026-05-02 01:54:29.55 INFO::Counting total values for each feature
2026-05-02 01:54:29.55 INFO::Running the logistic model component
2026-05-02 01:54:29.66 INFO::Counting total values for each feature
2026-05-02 01:54:29.66 INFO::Creating fits folder
2026-05-02 01:54:29.67 INFO::Writing residuals to file /tmp/RtmpwkOnSF/maaslin3_parallel_test_1d8a572e82b9cd/fits/residuals_linear.rds
2026-05-02 01:54:29.67 INFO::Writing fitted values to file /tmp/RtmpwkOnSF/maaslin3_parallel_test_1d8a572e82b9cd/fits/fitted_linear.rds
2026-05-02 01:54:29.67 INFO::Writing residuals to file /tmp/RtmpwkOnSF/maaslin3_parallel_test_1d8a572e82b9cd/fits/residuals_logistic.rds
2026-05-02 01:54:29.67 INFO::Writing fitted values to file /tmp/RtmpwkOnSF/maaslin3_parallel_test_1d8a572e82b9cd/fits/fitted_logistic.rds
2026-05-02 01:54:29.67 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpwkOnSF/maaslin3_parallel_test_1d8a572e82b9cd/all_results.tsv
2026-05-02 01:54:29.68 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): /tmp/RtmpwkOnSF/maaslin3_parallel_test_1d8a572e82b9cd/significant_results.tsv
2026-05-02 01:54:30.40 INFO::Running the linear model component
2026-05-02 01:54:30.42 INFO::Fitting model to feature number 1, a
2026-05-02 01:54:30.42 INFO::Fitting model to feature number 2, b
2026-05-02 01:54:30.43 INFO::Fitting model to feature number 3, c
2026-05-02 01:54:30.44 INFO::Counting total values for each feature
2026-05-02 01:54:30.44 INFO::Running the logistic model component
2026-05-02 01:54:30.45 INFO::Fitting model to feature number 1, a
2026-05-02 01:54:30.46 INFO::Fitting model to feature number 2, b
2026-05-02 01:54:30.46 INFO::Fitting model to feature number 3, c
2026-05-02 01:54:30.47 INFO::Counting total values for each feature
2026-05-02 01:54:30.47 INFO::Re-running abundances for warn_prevalence
2026-05-02 01:54:30.47 INFO::Running selected normalization method: TSS
2026-05-02 01:54:30.48 INFO::Running selected transform method: LOG
2026-05-02 01:54:30.49 INFO::Fitting model to feature number 1, a
2026-05-02 01:54:30.49 INFO::Fitting model to feature number 2, b
2026-05-02 01:54:30.50 INFO::Fitting model to feature number 3, c
2026-05-02 01:54:30.94 INFO::Started 2 mirai daemons via `cores` argument
2026-05-02 01:54:30.96 INFO::Running the linear model component
2026-05-02 01:54:32.41 INFO::Counting total values for each feature
2026-05-02 01:54:32.42 INFO::Running the logistic model component
2026-05-02 01:54:32.52 INFO::Counting total values for each feature
2026-05-02 01:54:32.52 INFO::Re-running abundances for warn_prevalence
2026-05-02 01:54:32.52 INFO::Running selected normalization method: TSS
2026-05-02 01:54:32.52 INFO::Running selected transform method: LOG
2026-05-02 01:54:32.81 INFO::Running the linear model component
2026-05-02 01:54:32.83 INFO::Fitting model to feature number 1, a
2026-05-02 01:54:32.83 INFO::Fitting model to feature number 2, b
2026-05-02 01:54:32.84 INFO::Counting total values for each feature
2026-05-02 01:54:32.84 INFO::Running the logistic model component
2026-05-02 01:54:32.85 INFO::Fitting model to feature number 1, a
2026-05-02 01:54:32.86 INFO::Fitting model to feature number 2, b
2026-05-02 01:54:32.87 INFO::Counting total values for each feature
2026-05-02 01:54:32.87 INFO::Re-running abundances for warn_prevalence
2026-05-02 01:54:32.87 INFO::Running selected normalization method: TSS
2026-05-02 01:54:32.87 INFO::Running selected transform method: LOG
2026-05-02 01:54:32.89 INFO::Fitting model to feature number 1, a
2026-05-02 01:54:32.89 INFO::Fitting model to feature number 2, b
2026-05-02 01:54:32.90 INFO::Creating output folder
2026-05-02 01:54:32.90 INFO::Creating output figures folder
2026-05-02 01:54:32.91 INFO::Writing summary plot of significant
results to file: /tmp/RtmpwkOnSF/file1d8a5742faeba8/figures/summary_plot.pdf
2026-05-02 01:54:35.26 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpwkOnSF/file1d8a5742faeba8/figures
2026-05-02 01:54:35.26 INFO::Plotting associations from most to least significant, grouped by metadata
2026-05-02 01:54:35.27 INFO::Creating scatter plot for continuous
data (linear), var1 vs b
2026-05-02 01:54:35.84 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-05-02 01:54:37.76 INFO::Running the linear model component
2026-05-02 01:54:37.77 INFO::Fitting model to feature number 1, a
2026-05-02 01:54:37.87 INFO::Fitting model to feature number 2, b
2026-05-02 01:54:37.94 INFO::Counting total values for each feature
2026-05-02 01:54:37.94 INFO::Running the logistic model component
2026-05-02 01:54:37.95 INFO::Fitting model to feature number 1, a
2026-05-02 01:54:38.03 INFO::Fitting model to feature number 2, b
2026-05-02 01:54:38.11 INFO::Counting total values for each feature
2026-05-02 01:54:38.12 INFO::Re-running abundances for warn_prevalence
2026-05-02 01:54:38.12 INFO::Running selected normalization method: TSS
2026-05-02 01:54:38.12 INFO::Running selected transform method: LOG
2026-05-02 01:54:38.13 INFO::Fitting model to feature number 1, a
2026-05-02 01:54:38.19 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
155.469 3.159 173.586
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 16.697 | 0.687 | 17.371 | |
| maaslin_check_arguments | 0.122 | 0.000 | 0.122 | |
| maaslin_check_formula | 0.136 | 0.010 | 0.146 | |
| maaslin_compute_formula | 0.156 | 0.010 | 0.166 | |
| maaslin_contrast_test | 17.573 | 0.488 | 18.034 | |
| maaslin_filter | 0.453 | 0.019 | 0.472 | |
| maaslin_fit | 12.035 | 0.270 | 12.284 | |
| maaslin_log_arguments | 0.140 | 0.004 | 0.142 | |
| maaslin_normalize | 0.266 | 0.016 | 0.283 | |
| maaslin_plot_results | 39.615 | 0.577 | 41.076 | |
| maaslin_plot_results_from_output | 38.178 | 0.397 | 38.928 | |
| maaslin_process_metadata | 0.469 | 0.030 | 0.499 | |
| maaslin_read_data | 0.153 | 0.005 | 0.158 | |
| maaslin_reorder_data | 0.153 | 0.003 | 0.157 | |
| maaslin_transform | 0.596 | 0.016 | 0.612 | |
| maaslin_write_results | 13.522 | 0.226 | 13.736 | |
| maaslin_write_results_lefse_format | 14.582 | 0.182 | 14.753 | |
| preprocess_dna_mtx | 0.004 | 0.000 | 0.004 | |
| preprocess_taxa_mtx | 0.002 | 0.002 | 0.004 | |