William Nickols
| Snapshot Date: 2026-05-22 13:40 -0400 (Fri, 22 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 Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-05-23 11:32 -0400 (Sat, 23 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" | 4995 |
| 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 | | ||||||||
| 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: 2026-05-23 01:35:30 -0400 (Sat, 23 May 2026) |
| EndedAt: 2026-05-23 01:51:24 -0400 (Sat, 23 May 2026) |
| EllapsedTime: 954.3 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: 2026-05-23 05:35:30 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 38.249 0.436 39.392
maaslin_plot_results_from_output 35.159 0.425 35.562
maaslin3 17.012 0.677 17.674
maaslin_contrast_test 17.024 0.433 17.440
maaslin_write_results_lefse_format 14.608 0.210 14.799
maaslin_fit 13.515 0.382 13.892
maaslin_write_results 13.200 0.223 13.411
* 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")
2026-05-23 01:41:15.27 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2026-05-23 01:41:15.29 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2026-05-23 01:41:15.30 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2026-05-23 01:41:15.35 ERROR::No fixed, group, or
ordered effects included in formula.
2026-05-23 01:41:15.36 ERROR::Effect name not found in metadata: d
2026-05-23 01:41:15.36 ERROR::No user formula provided
2026-05-23 01:41:15.39 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2026-05-23 01:41:15.40 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2026-05-23 01:41:18.07 INFO::Writing function arguments to log file
2026-05-23 01:41:18.09 INFO::Verifying options selected are valid
2026-05-23 01:41:22.37 INFO::Writing function arguments to log file
2026-05-23 01:41:22.40 INFO::Verifying options selected are valid
2026-05-23 01:41:22.40 INFO::Determining format of input files
2026-05-23 01:41:22.40 INFO::Input format is data samples as rows and metadata samples as rows
2026-05-23 01:41:22.40 INFO::Running selected normalization method: TSS
2026-05-23 01:41:22.40 INFO::Creating output feature tables folder
2026-05-23 01:41:22.41 INFO::Writing normalized data to file /tmp/RtmpgGJIj8/file160b211bc130c/features/data_norm.tsv
2026-05-23 01:41:22.41 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2026-05-23 01:41:22.41 INFO::Total samples in data: 16
2026-05-23 01:41:22.41 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2026-05-23 01:41:22.41 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2026-05-23 01:41:22.42 INFO::Total filtered features: 0
2026-05-23 01:41:22.42 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2026-05-23 01:41:22.42 INFO::Total features filtered by non-zero variance filtering: 0
2026-05-23 01:41:22.42 INFO::Filtered feature names from variance filtering:
2026-05-23 01:41:22.42 INFO::Writing filtered data to file /tmp/RtmpgGJIj8/file160b211bc130c/features/filtered_data.tsv
2026-05-23 01:41:22.42 INFO::Running selected transform method: LOG
2026-05-23 01:41:22.43 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpgGJIj8/file160b211bc130c/features/data_transformed.tsv
2026-05-23 01:41:22.43 INFO::Applying z-score to standardize continuous metadata
2026-05-23 01:41:22.43 INFO::Running the linear model component
2026-05-23 01:41:22.45 INFO::Fitting model to feature number 1, a
2026-05-23 01:41:22.46 INFO::Fitting model to feature number 2, b
2026-05-23 01:41:22.47 INFO::Fitting model to feature number 3, c
2026-05-23 01:41:22.47 INFO::Counting total values for each feature
2026-05-23 01:41:22.47 INFO::Running the logistic model component
2026-05-23 01:41:22.50 INFO::Fitting model to feature number 1, a
2026-05-23 01:41:22.51 INFO::Fitting model to feature number 2, b
2026-05-23 01:41:22.52 INFO::Fitting model to feature number 3, c
2026-05-23 01:41:22.53 INFO::Counting total values for each feature
2026-05-23 01:41:22.53 INFO::Re-running abundances for warn_prevalence
2026-05-23 01:41:22.53 INFO::Running selected normalization method: TSS
2026-05-23 01:41:22.53 INFO::Running selected transform method: LOG
2026-05-23 01:41:22.56 INFO::Fitting model to feature number 1, a
2026-05-23 01:41:22.56 INFO::Fitting model to feature number 2, b
2026-05-23 01:41:22.57 INFO::Fitting model to feature number 3, c
2026-05-23 01:41:22.58 INFO::Creating fits folder
2026-05-23 01:41:22.58 INFO::Writing residuals to file /tmp/RtmpgGJIj8/file160b211bc130c/fits/residuals_linear.rds
2026-05-23 01:41:22.59 INFO::Writing fitted values to file /tmp/RtmpgGJIj8/file160b211bc130c/fits/fitted_linear.rds
2026-05-23 01:41:22.59 INFO::Writing residuals to file /tmp/RtmpgGJIj8/file160b211bc130c/fits/residuals_logistic.rds
2026-05-23 01:41:22.59 INFO::Writing fitted values to file /tmp/RtmpgGJIj8/file160b211bc130c/fits/fitted_logistic.rds
2026-05-23 01:41:22.59 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpgGJIj8/file160b211bc130c/all_results.tsv
2026-05-23 01:41:22.59 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/RtmpgGJIj8/file160b211bc130c/significant_results.tsv
2026-05-23 01:41:22.60 INFO::Creating output figures folder
2026-05-23 01:41:22.60 INFO::Writing summary plot of significant
results to file: /tmp/RtmpgGJIj8/file160b211bc130c/figures/summary_plot.pdf
2026-05-23 01:41:24.21 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpgGJIj8/file160b211bc130c/figures
2026-05-23 01:41:24.21 INFO::Plotting associations from most to least significant, grouped by metadata
2026-05-23 01:41:24.22 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-05-23 01:41:24.75 INFO::Writing summary plot of
significant results to file: /tmp/RtmpgGJIj8/file160b211bc130c/figures/summary_plot.pdf
2026-05-23 01:41:26.30 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpgGJIj8/file160b211bc130c/figures
2026-05-23 01:41:26.30 INFO::Plotting associations from most to least significant, grouped by metadata
2026-05-23 01:41:26.31 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-05-23 01:41:26.84 INFO::Running the linear model component
2026-05-23 01:41:26.85 INFO::Fitting model to feature number 1, a
2026-05-23 01:41:26.85 INFO::Fitting model to feature number 2, b
2026-05-23 01:41:26.86 INFO::Fitting model to feature number 3, c
2026-05-23 01:41:26.86 INFO::Counting total values for each feature
2026-05-23 01:41:26.86 INFO::Running the logistic model component
2026-05-23 01:41:26.87 INFO::Fitting model to feature number 1, a
2026-05-23 01:41:26.88 INFO::Fitting model to feature number 2, b
2026-05-23 01:41:26.89 INFO::Fitting model to feature number 3, c
2026-05-23 01:41:26.90 INFO::Counting total values for each feature
2026-05-23 01:41:26.90 INFO::Re-running abundances for warn_prevalence
2026-05-23 01:41:26.90 INFO::Running selected normalization method: TSS
2026-05-23 01:41:26.90 INFO::Running selected transform method: LOG
2026-05-23 01:41:26.92 INFO::Fitting model to feature number 1, a
2026-05-23 01:41:26.93 INFO::Fitting model to feature number 2, b
2026-05-23 01:41:26.93 INFO::Fitting model to feature number 3, c
2026-05-23 01:41:26.94 INFO::Creating output folder
2026-05-23 01:41:26.94 INFO::Creating output figures folder
2026-05-23 01:41:26.95 INFO::Writing summary plot of significant
results to file: /tmp/RtmpgGJIj8/file160b236f9bef9/figures/summary_plot.pdf
2026-05-23 01:41:28.52 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpgGJIj8/file160b236f9bef9/figures
2026-05-23 01:41:28.52 INFO::Plotting associations from most to least significant, grouped by metadata
2026-05-23 01:41:28.52 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-05-23 01:41:29.06 INFO::Applying z-score to standardize continuous metadata
2026-05-23 01:41:29.06 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2026-05-23 01:41:29.07 INFO::Bypass z-score application to metadata
2026-05-23 01:41:29.07 INFO::Bypass z-score application to metadata
2026-05-23 01:41:29.11 INFO::Determining format of input files
2026-05-23 01:41:29.11 INFO::Input format is data samples as rows and metadata samples as rows
2026-05-23 01:41:29.11 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2026-05-23 01:41:29.12 INFO::Determining format of input files
2026-05-23 01:41:29.12 INFO::Input format is data samples as columns and metadata samples as rows
2026-05-23 01:41:29.13 INFO::Input format is feature_specific_covariate samples as columns
2026-05-23 01:41:29.13 INFO::Determining format of input files
2026-05-23 01:41:29.13 INFO::Input format is data samples as rows and metadata samples as rows
2026-05-23 01:41:29.14 INFO::Input format is feature_specific_covariate samples as columns
2026-05-23 01:41:29.14 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2026-05-23 01:41:29.14 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2026-05-23 01:41:29.15 INFO::Running selected transform method: LOG
2026-05-23 01:41:29.15 INFO::Creating output feature tables folder
2026-05-23 01:41:29.15 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpgGJIj8/file160b242c4b00c/features/data_transformed.tsv
2026-05-23 01:41:29.16 INFO::Running selected transform method: LOG
2026-05-23 01:41:29.16 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpgGJIj8/file160b242c4b00c/features/data_transformed.tsv
2026-05-23 01:41:29.16 INFO::Running selected transform method: PLOG
2026-05-23 01:41:29.16 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpgGJIj8/file160b242c4b00c/features/data_transformed.tsv
2026-05-23 01:41:29.17 INFO::Running selected transform method: NONE
2026-05-23 01:41:29.17 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpgGJIj8/file160b242c4b00c/features/data_transformed.tsv
2026-05-23 01:41:29.18 INFO::Running the linear model component
2026-05-23 01:41:29.19 INFO::Fitting model to feature number 1, a
2026-05-23 01:41:29.19 INFO::Fitting model to feature number 2, b
2026-05-23 01:41:29.20 INFO::Fitting model to feature number 3, c
2026-05-23 01:41:29.20 INFO::Counting total values for each feature
2026-05-23 01:41:29.20 INFO::Running the logistic model component
2026-05-23 01:41:29.21 INFO::Fitting model to feature number 1, a
2026-05-23 01:41:29.22 INFO::Fitting model to feature number 2, b
2026-05-23 01:41:29.23 INFO::Fitting model to feature number 3, c
2026-05-23 01:41:29.23 INFO::Counting total values for each feature
2026-05-23 01:41:29.24 INFO::Re-running abundances for warn_prevalence
2026-05-23 01:41:29.24 INFO::Running selected normalization method: TSS
2026-05-23 01:41:29.24 INFO::Running selected transform method: LOG
2026-05-23 01:41:29.25 INFO::Fitting model to feature number 1, a
2026-05-23 01:41:29.25 INFO::Fitting model to feature number 2, b
2026-05-23 01:41:29.26 INFO::Fitting model to feature number 3, c
2026-05-23 01:41:29.27 INFO::Creating output folder
2026-05-23 01:41:29.27 INFO::Creating fits folder
2026-05-23 01:41:29.27 INFO::Writing residuals to file /tmp/RtmpgGJIj8/file160b21965d57a/fits/residuals_linear.rds
2026-05-23 01:41:29.27 INFO::Writing fitted values to file /tmp/RtmpgGJIj8/file160b21965d57a/fits/fitted_linear.rds
2026-05-23 01:41:29.27 INFO::Writing residuals to file /tmp/RtmpgGJIj8/file160b21965d57a/fits/residuals_logistic.rds
2026-05-23 01:41:29.27 INFO::Writing fitted values to file /tmp/RtmpgGJIj8/file160b21965d57a/fits/fitted_logistic.rds
2026-05-23 01:41:29.28 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpgGJIj8/file160b21965d57a/all_results.tsv
2026-05-23 01:41:29.28 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/RtmpgGJIj8/file160b21965d57a/significant_results.tsv
2026-05-23 01:41:29.92 INFO::Running the linear model component
2026-05-23 01:41:29.93 INFO::Fitting model to feature number 1, a
2026-05-23 01:41:29.93 INFO::Fitting model to feature number 2, b
2026-05-23 01:41:29.94 INFO::Fitting model to feature number 3, c
2026-05-23 01:41:29.94 INFO::Counting total values for each feature
2026-05-23 01:41:29.95 INFO::Running the logistic model component
2026-05-23 01:41:29.96 INFO::Fitting model to feature number 1, a
2026-05-23 01:41:29.96 INFO::Fitting model to feature number 2, b
2026-05-23 01:41:29.96 INFO::Fitting model to feature number 3, c
2026-05-23 01:41:29.97 INFO::Counting total values for each feature
2026-05-23 01:41:29.97 INFO::Re-running abundances for warn_prevalence
2026-05-23 01:41:29.98 INFO::Running selected normalization method: TSS
2026-05-23 01:41:29.98 INFO::Running selected transform method: LOG
2026-05-23 01:41:29.99 INFO::Fitting model to feature number 1, a
2026-05-23 01:41:29.99 INFO::Fitting model to feature number 2, b
2026-05-23 01:41:30.00 INFO::Fitting model to feature number 3, c
2026-05-23 01:41:30.86 INFO::Started 2 mirai daemons via `cores` argument
2026-05-23 01:41:30.86 INFO::Running the linear model component
2026-05-23 01:41:32.23 INFO::Counting total values for each feature
2026-05-23 01:41:32.23 INFO::Running the logistic model component
2026-05-23 01:41:32.32 INFO::Counting total values for each feature
2026-05-23 01:41:32.32 INFO::Re-running abundances for warn_prevalence
2026-05-23 01:41:32.32 INFO::Running selected normalization method: TSS
2026-05-23 01:41:32.32 INFO::Running selected transform method: LOG
2026-05-23 01:41:34.31 INFO::Running the linear model component
2026-05-23 01:41:35.70 INFO::Counting total values for each feature
2026-05-23 01:41:35.71 INFO::Running the logistic model component
2026-05-23 01:41:35.80 INFO::Counting total values for each feature
2026-05-23 01:41:35.81 INFO::Re-running abundances for warn_prevalence
2026-05-23 01:41:35.81 INFO::Running selected normalization method: TSS
2026-05-23 01:41:35.81 INFO::Running selected transform method: LOG
2026-05-23 01:41:38.33 INFO::Running the linear model component
2026-05-23 01:41:39.79 INFO::Counting total values for each feature
2026-05-23 01:41:39.79 INFO::Running the logistic model component
2026-05-23 01:41:39.87 INFO::Counting total values for each feature
2026-05-23 01:41:39.88 INFO::Re-running abundances for warn_prevalence
2026-05-23 01:41:39.88 INFO::Running selected normalization method: TSS
2026-05-23 01:41:39.88 INFO::Running selected transform method: LOG
2026-05-23 01:41:41.86 INFO::Writing function arguments to log file
2026-05-23 01:41:41.91 INFO::Verifying options selected are valid
2026-05-23 01:41:41.91 INFO::Determining format of input files
2026-05-23 01:41:41.91 INFO::Input format is data samples as rows and metadata samples as rows
2026-05-23 01:41:41.92 INFO::Running selected normalization method: TSS
2026-05-23 01:41:41.92 INFO::Creating output feature tables folder
2026-05-23 01:41:41.92 INFO::Writing normalized data to file /tmp/RtmpgGJIj8/maaslin3_parallel_test_160b272b99058/features/data_norm.tsv
2026-05-23 01:41:41.92 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2026-05-23 01:41:41.93 INFO::Total samples in data: 30
2026-05-23 01:41:41.93 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2026-05-23 01:41:41.93 INFO::Max samples allowed with min abundance for a feature not to be filtered: 30.300000
2026-05-23 01:41:41.93 INFO::Total filtered features: 0
2026-05-23 01:41:41.93 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2026-05-23 01:41:41.94 INFO::Total features filtered by non-zero variance filtering: 0
2026-05-23 01:41:41.94 INFO::Filtered feature names from variance filtering:
2026-05-23 01:41:41.94 INFO::Writing filtered data to file /tmp/RtmpgGJIj8/maaslin3_parallel_test_160b272b99058/features/filtered_data.tsv
2026-05-23 01:41:41.94 INFO::Running selected transform method: LOG
2026-05-23 01:41:41.94 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpgGJIj8/maaslin3_parallel_test_160b272b99058/features/data_transformed.tsv
2026-05-23 01:41:41.94 INFO::Applying z-score to standardize continuous metadata
2026-05-23 01:41:41.95 INFO::Running the linear model component
2026-05-23 01:41:43.38 INFO::Counting total values for each feature
2026-05-23 01:41:43.39 INFO::Running the logistic model component
2026-05-23 01:41:43.50 INFO::Counting total values for each feature
2026-05-23 01:41:43.51 INFO::Creating fits folder
2026-05-23 01:41:43.51 INFO::Writing residuals to file /tmp/RtmpgGJIj8/maaslin3_parallel_test_160b272b99058/fits/residuals_linear.rds
2026-05-23 01:41:43.51 INFO::Writing fitted values to file /tmp/RtmpgGJIj8/maaslin3_parallel_test_160b272b99058/fits/fitted_linear.rds
2026-05-23 01:41:43.51 INFO::Writing residuals to file /tmp/RtmpgGJIj8/maaslin3_parallel_test_160b272b99058/fits/residuals_logistic.rds
2026-05-23 01:41:43.51 INFO::Writing fitted values to file /tmp/RtmpgGJIj8/maaslin3_parallel_test_160b272b99058/fits/fitted_logistic.rds
2026-05-23 01:41:43.51 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpgGJIj8/maaslin3_parallel_test_160b272b99058/all_results.tsv
2026-05-23 01:41:43.52 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/RtmpgGJIj8/maaslin3_parallel_test_160b272b99058/significant_results.tsv
2026-05-23 01:41:44.24 INFO::Running the linear model component
2026-05-23 01:41:44.26 INFO::Fitting model to feature number 1, a
2026-05-23 01:41:44.26 INFO::Fitting model to feature number 2, b
2026-05-23 01:41:44.27 INFO::Fitting model to feature number 3, c
2026-05-23 01:41:44.27 INFO::Counting total values for each feature
2026-05-23 01:41:44.28 INFO::Running the logistic model component
2026-05-23 01:41:44.29 INFO::Fitting model to feature number 1, a
2026-05-23 01:41:44.29 INFO::Fitting model to feature number 2, b
2026-05-23 01:41:44.30 INFO::Fitting model to feature number 3, c
2026-05-23 01:41:44.31 INFO::Counting total values for each feature
2026-05-23 01:41:44.31 INFO::Re-running abundances for warn_prevalence
2026-05-23 01:41:44.31 INFO::Running selected normalization method: TSS
2026-05-23 01:41:44.31 INFO::Running selected transform method: LOG
2026-05-23 01:41:44.32 INFO::Fitting model to feature number 1, a
2026-05-23 01:41:44.33 INFO::Fitting model to feature number 2, b
2026-05-23 01:41:44.33 INFO::Fitting model to feature number 3, c
2026-05-23 01:41:45.05 INFO::Started 2 mirai daemons via `cores` argument
2026-05-23 01:41:45.05 INFO::Running the linear model component
2026-05-23 01:41:46.45 INFO::Counting total values for each feature
2026-05-23 01:41:46.46 INFO::Running the logistic model component
2026-05-23 01:41:46.55 INFO::Counting total values for each feature
2026-05-23 01:41:46.55 INFO::Re-running abundances for warn_prevalence
2026-05-23 01:41:46.56 INFO::Running selected normalization method: TSS
2026-05-23 01:41:46.56 INFO::Running selected transform method: LOG
2026-05-23 01:41:46.84 INFO::Running the linear model component
2026-05-23 01:41:46.86 INFO::Fitting model to feature number 1, a
2026-05-23 01:41:46.86 INFO::Fitting model to feature number 2, b
2026-05-23 01:41:46.87 INFO::Counting total values for each feature
2026-05-23 01:41:46.87 INFO::Running the logistic model component
2026-05-23 01:41:46.88 INFO::Fitting model to feature number 1, a
2026-05-23 01:41:46.89 INFO::Fitting model to feature number 2, b
2026-05-23 01:41:46.89 INFO::Counting total values for each feature
2026-05-23 01:41:46.90 INFO::Re-running abundances for warn_prevalence
2026-05-23 01:41:46.90 INFO::Running selected normalization method: TSS
2026-05-23 01:41:46.90 INFO::Running selected transform method: LOG
2026-05-23 01:41:46.91 INFO::Fitting model to feature number 1, a
2026-05-23 01:41:46.92 INFO::Fitting model to feature number 2, b
2026-05-23 01:41:46.93 INFO::Creating output folder
2026-05-23 01:41:46.93 INFO::Creating output figures folder
2026-05-23 01:41:46.93 INFO::Writing summary plot of significant
results to file: /tmp/RtmpgGJIj8/file160b214eae970/figures/summary_plot.pdf
2026-05-23 01:41:49.07 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpgGJIj8/file160b214eae970/figures
2026-05-23 01:41:49.08 INFO::Plotting associations from most to least significant, grouped by metadata
2026-05-23 01:41:49.08 INFO::Creating scatter plot for continuous
data (linear), var1 vs b
2026-05-23 01:41:49.63 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-05-23 01:41:51.60 INFO::Running the linear model component
2026-05-23 01:41:51.61 INFO::Fitting model to feature number 1, a
2026-05-23 01:41:51.68 INFO::Fitting model to feature number 2, b
2026-05-23 01:41:51.75 INFO::Counting total values for each feature
2026-05-23 01:41:51.75 INFO::Running the logistic model component
2026-05-23 01:41:51.76 INFO::Fitting model to feature number 1, a
2026-05-23 01:41:51.84 INFO::Fitting model to feature number 2, b
2026-05-23 01:41:51.93 INFO::Counting total values for each feature
2026-05-23 01:41:51.94 INFO::Re-running abundances for warn_prevalence
2026-05-23 01:41:51.94 INFO::Running selected normalization method: TSS
2026-05-23 01:41:51.94 INFO::Running selected transform method: LOG
2026-05-23 01:41:51.95 INFO::Fitting model to feature number 1, a
2026-05-23 01:41:52.01 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
158.315 2.837 177.921
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 17.012 | 0.677 | 17.674 | |
| maaslin_check_arguments | 0.119 | 0.004 | 0.124 | |
| maaslin_check_formula | 0.139 | 0.006 | 0.146 | |
| maaslin_compute_formula | 0.161 | 0.004 | 0.165 | |
| maaslin_contrast_test | 17.024 | 0.433 | 17.440 | |
| maaslin_filter | 0.452 | 0.018 | 0.471 | |
| maaslin_fit | 13.515 | 0.382 | 13.892 | |
| maaslin_log_arguments | 0.140 | 0.011 | 0.152 | |
| maaslin_normalize | 0.275 | 0.016 | 0.290 | |
| maaslin_plot_results | 38.249 | 0.436 | 39.392 | |
| maaslin_plot_results_from_output | 35.159 | 0.425 | 35.562 | |
| maaslin_process_metadata | 0.455 | 0.035 | 0.491 | |
| maaslin_read_data | 0.151 | 0.007 | 0.158 | |
| maaslin_reorder_data | 0.151 | 0.007 | 0.158 | |
| maaslin_transform | 0.569 | 0.020 | 0.589 | |
| maaslin_write_results | 13.200 | 0.223 | 13.411 | |
| maaslin_write_results_lefse_format | 14.608 | 0.210 | 14.799 | |
| preprocess_dna_mtx | 0.002 | 0.002 | 0.004 | |
| preprocess_taxa_mtx | 0.003 | 0.001 | 0.005 | |