Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-10-16 11:38 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1155/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maaslin3 1.0.2  (landing page)
William Nickols
Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/maaslin3
git_branch: RELEASE_3_21
git_last_commit: d86be18
git_last_commit_date: 2025-10-12 11:15:12 -0400 (Sun, 12 Oct 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  YES
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    OK    OK  YES
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for maaslin3 on nebbiolo1

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.

raw results


Summary

Package: maaslin3
Version: 1.0.2
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings maaslin3_1.0.2.tar.gz
StartedAt: 2025-10-16 00:37:19 -0400 (Thu, 16 Oct 2025)
EndedAt: 2025-10-16 00:58:59 -0400 (Thu, 16 Oct 2025)
EllapsedTime: 1299.8 seconds
RetCode: 0
Status:   OK  
CheckDir: maaslin3.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings maaslin3_1.0.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/maaslin3.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘1.0.2’
* 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 ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* 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               43.365  0.324  43.640
maaslin_plot_results_from_output   43.345  0.274  43.624
maaslin3                           20.188  0.697  20.891
maaslin_contrast_test              18.889  0.517  19.406
maaslin_write_results_lefse_format 14.173  0.162  14.337
maaslin_write_results              13.760  0.216  13.976
maaslin_fit                        13.269  0.256  13.527
* 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: OK

Installation output

maaslin3.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL maaslin3
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘maaslin3’ ...
** this is package ‘maaslin3’ version ‘1.0.2’
** 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)

Tests output

maaslin3.Rcheck/tests/testthat.Rout


R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(maaslin3)
> 
> test_check("maaslin3")
2025-10-16 00:43:27.928971 WARNING::Fitting problem for feature 50 returning NA
2025-10-16 00:43:28.014118 WARNING::Fitting problem for feature 62 returning NA
2025-10-16 00:43:28.097584 WARNING::Fitting problem for feature 74 returning NA
2025-10-16 00:43:28.126502 WARNING::Fitting problem for feature 78 returning NA
2025-10-16 00:43:28.160753 WARNING::Fitting problem for feature 84 returning NA
2025-10-16 00:43:28.235462 WARNING::Fitting problem for feature 96 returning NA
2025-10-16 00:43:28.240927 WARNING::Fitting problem for feature 97 returning NA
2025-10-16 00:43:28.25298 WARNING::Fitting problem for feature 99 returning NA
2025-10-16 00:43:28.35503 WARNING::Fitting problem for feature 114 returning NA
2025-10-16 00:43:28.360457 WARNING::Fitting problem for feature 115 returning NA
2025-10-16 00:43:28.425966 WARNING::Fitting problem for feature 123 returning NA
2025-10-16 00:43:28.467104 WARNING::Fitting problem for feature 130 returning NA
2025-10-16 00:43:28.478909 WARNING::Fitting problem for feature 132 returning NA
2025-10-16 00:43:28.518708 WARNING::Fitting problem for feature 139 returning NA
2025-10-16 00:43:28.586466 WARNING::Fitting problem for feature 150 returning NA
2025-10-16 00:43:43.446772 WARNING::Fitting problem for feature 50 returning NA
2025-10-16 00:43:43.519314 WARNING::Fitting problem for feature 62 returning NA
2025-10-16 00:43:43.590058 WARNING::Fitting problem for feature 74 returning NA
2025-10-16 00:43:43.610916 WARNING::Fitting problem for feature 78 returning NA
2025-10-16 00:43:43.644146 WARNING::Fitting problem for feature 84 returning NA
2025-10-16 00:43:43.716414 WARNING::Fitting problem for feature 96 returning NA
2025-10-16 00:43:43.721483 WARNING::Fitting problem for feature 97 returning NA
2025-10-16 00:43:43.732966 WARNING::Fitting problem for feature 99 returning NA
2025-10-16 00:43:43.836597 WARNING::Fitting problem for feature 114 returning NA
2025-10-16 00:43:43.841879 WARNING::Fitting problem for feature 115 returning NA
2025-10-16 00:43:43.889215 WARNING::Fitting problem for feature 123 returning NA
2025-10-16 00:43:43.927757 WARNING::Fitting problem for feature 130 returning NA
2025-10-16 00:43:43.939284 WARNING::Fitting problem for feature 132 returning NA
2025-10-16 00:43:43.978281 WARNING::Fitting problem for feature 139 returning NA
2025-10-16 00:43:44.046813 WARNING::Fitting problem for feature 150 returning NA
2025-10-16 00:44:09.809814 WARNING::Fitting problem for feature 50 returning NA
2025-10-16 00:44:09.883671 WARNING::Fitting problem for feature 62 returning NA
2025-10-16 00:44:09.957144 WARNING::Fitting problem for feature 74 returning NA
2025-10-16 00:44:09.978433 WARNING::Fitting problem for feature 78 returning NA
2025-10-16 00:44:10.011559 WARNING::Fitting problem for feature 84 returning NA
2025-10-16 00:44:10.084174 WARNING::Fitting problem for feature 96 returning NA
2025-10-16 00:44:10.089366 WARNING::Fitting problem for feature 97 returning NA
2025-10-16 00:44:10.100766 WARNING::Fitting problem for feature 99 returning NA
2025-10-16 00:44:10.192146 WARNING::Fitting problem for feature 114 returning NA
2025-10-16 00:44:10.197455 WARNING::Fitting problem for feature 115 returning NA
2025-10-16 00:44:10.245654 WARNING::Fitting problem for feature 123 returning NA
2025-10-16 00:44:10.284667 WARNING::Fitting problem for feature 130 returning NA
2025-10-16 00:44:10.296179 WARNING::Fitting problem for feature 132 returning NA
2025-10-16 00:44:10.335327 WARNING::Fitting problem for feature 139 returning NA
2025-10-16 00:44:10.402632 WARNING::Fitting problem for feature 150 returning NA
2025-10-16 00:44:23.898532 WARNING::Fitting problem for feature 50 returning NA
2025-10-16 00:44:23.977103 WARNING::Fitting problem for feature 62 returning NA
2025-10-16 00:44:24.051228 WARNING::Fitting problem for feature 74 returning NA
2025-10-16 00:44:24.073084 WARNING::Fitting problem for feature 78 returning NA
2025-10-16 00:44:24.108542 WARNING::Fitting problem for feature 84 returning NA
2025-10-16 00:44:24.187228 WARNING::Fitting problem for feature 96 returning NA
2025-10-16 00:44:24.19282 WARNING::Fitting problem for feature 97 returning NA
2025-10-16 00:44:24.204835 WARNING::Fitting problem for feature 99 returning NA
2025-10-16 00:44:24.299279 WARNING::Fitting problem for feature 114 returning NA
2025-10-16 00:44:24.304798 WARNING::Fitting problem for feature 115 returning NA
2025-10-16 00:44:24.354586 WARNING::Fitting problem for feature 123 returning NA
2025-10-16 00:44:24.395962 WARNING::Fitting problem for feature 130 returning NA
2025-10-16 00:44:24.408595 WARNING::Fitting problem for feature 132 returning NA
2025-10-16 00:44:24.450926 WARNING::Fitting problem for feature 139 returning NA
2025-10-16 00:44:24.522529 WARNING::Fitting problem for feature 150 returning NA
2025-10-16 00:44:24.773354 WARNING::Deleting existing residuals file: /tmp/RtmpXly8xD/file1b21ef2f434d40/fits/residuals_linear.rds
2025-10-16 00:44:24.835275 WARNING::Deleting existing fitted file: /tmp/RtmpXly8xD/file1b21ef2f434d40/fits/fitted_linear.rds
2025-10-16 00:44:24.899169 WARNING::Deleting existing residuals file: /tmp/RtmpXly8xD/file1b21ef2f434d40/fits/residuals_logistic.rds
2025-10-16 00:44:25.201896 WARNING::Deleting existing fitted file: /tmp/RtmpXly8xD/file1b21ef2f434d40/fits/fitted_logistic.rds
2025-10-16 00:44:47.047393 WARNING::Fitting problem for feature 50 returning NA
2025-10-16 00:44:47.124804 WARNING::Fitting problem for feature 62 returning NA
2025-10-16 00:44:47.222709 WARNING::Fitting problem for feature 74 returning NA
2025-10-16 00:44:47.244831 WARNING::Fitting problem for feature 78 returning NA
2025-10-16 00:44:47.279281 WARNING::Fitting problem for feature 84 returning NA
2025-10-16 00:44:47.355289 WARNING::Fitting problem for feature 96 returning NA
2025-10-16 00:44:47.360848 WARNING::Fitting problem for feature 97 returning NA
2025-10-16 00:44:47.372779 WARNING::Fitting problem for feature 99 returning NA
2025-10-16 00:44:47.468866 WARNING::Fitting problem for feature 114 returning NA
2025-10-16 00:44:47.474697 WARNING::Fitting problem for feature 115 returning NA
2025-10-16 00:44:47.52769 WARNING::Fitting problem for feature 123 returning NA
2025-10-16 00:44:47.571237 WARNING::Fitting problem for feature 130 returning NA
2025-10-16 00:44:47.584002 WARNING::Fitting problem for feature 132 returning NA
2025-10-16 00:44:47.624853 WARNING::Fitting problem for feature 139 returning NA
2025-10-16 00:44:47.692801 WARNING::Fitting problem for feature 150 returning NA
2025-10-16 00:44:59.658001 WARNING::Fitting problem for feature 50 returning NA
2025-10-16 00:44:59.733392 WARNING::Fitting problem for feature 62 returning NA
2025-10-16 00:44:59.807222 WARNING::Fitting problem for feature 74 returning NA
2025-10-16 00:44:59.828955 WARNING::Fitting problem for feature 78 returning NA
2025-10-16 00:44:59.863396 WARNING::Fitting problem for feature 84 returning NA
2025-10-16 00:44:59.938242 WARNING::Fitting problem for feature 96 returning NA
2025-10-16 00:44:59.943776 WARNING::Fitting problem for feature 97 returning NA
2025-10-16 00:44:59.956006 WARNING::Fitting problem for feature 99 returning NA
2025-10-16 00:45:00.05282 WARNING::Fitting problem for feature 114 returning NA
2025-10-16 00:45:00.058297 WARNING::Fitting problem for feature 115 returning NA
2025-10-16 00:45:00.109123 WARNING::Fitting problem for feature 123 returning NA
2025-10-16 00:45:00.149206 WARNING::Fitting problem for feature 130 returning NA
2025-10-16 00:45:00.161404 WARNING::Fitting problem for feature 132 returning NA
2025-10-16 00:45:00.203733 WARNING::Fitting problem for feature 139 returning NA
2025-10-16 00:45:00.273145 WARNING::Fitting problem for feature 150 returning NA
2025-10-16 00:45:00.48747 WARNING::Deleting existing residuals file: /tmp/RtmpXly8xD/file1b21ef2f434d40/fits/residuals_linear.rds
2025-10-16 00:45:00.547933 WARNING::Deleting existing fitted file: /tmp/RtmpXly8xD/file1b21ef2f434d40/fits/fitted_linear.rds
2025-10-16 00:45:00.610199 WARNING::Deleting existing residuals file: /tmp/RtmpXly8xD/file1b21ef2f434d40/fits/residuals_logistic.rds
2025-10-16 00:45:00.909578 WARNING::Deleting existing fitted file: /tmp/RtmpXly8xD/file1b21ef2f434d40/fits/fitted_logistic.rds
2025-10-16 00:45:22.199674 WARNING::Fitting problem for feature 50 returning NA
2025-10-16 00:45:22.278542 WARNING::Fitting problem for feature 62 returning NA
2025-10-16 00:45:22.356085 WARNING::Fitting problem for feature 74 returning NA
2025-10-16 00:45:22.378966 WARNING::Fitting problem for feature 78 returning NA
2025-10-16 00:45:22.413531 WARNING::Fitting problem for feature 84 returning NA
2025-10-16 00:45:22.491283 WARNING::Fitting problem for feature 96 returning NA
2025-10-16 00:45:22.497177 WARNING::Fitting problem for feature 97 returning NA
2025-10-16 00:45:22.509892 WARNING::Fitting problem for feature 99 returning NA
2025-10-16 00:45:22.608751 WARNING::Fitting problem for feature 114 returning NA
2025-10-16 00:45:22.614597 WARNING::Fitting problem for feature 115 returning NA
2025-10-16 00:45:22.66633 WARNING::Fitting problem for feature 123 returning NA
2025-10-16 00:45:22.707252 WARNING::Fitting problem for feature 130 returning NA
2025-10-16 00:45:22.719852 WARNING::Fitting problem for feature 132 returning NA
2025-10-16 00:45:22.761224 WARNING::Fitting problem for feature 139 returning NA
2025-10-16 00:45:22.830833 WARNING::Fitting problem for feature 150 returning NA
2025-10-16 00:45:34.699212 WARNING::Fitting problem for feature 50 returning NA
2025-10-16 00:45:34.773088 WARNING::Fitting problem for feature 62 returning NA
2025-10-16 00:45:34.844772 WARNING::Fitting problem for feature 74 returning NA
2025-10-16 00:45:34.866201 WARNING::Fitting problem for feature 78 returning NA
2025-10-16 00:45:34.900453 WARNING::Fitting problem for feature 84 returning NA
2025-10-16 00:45:34.976869 WARNING::Fitting problem for feature 96 returning NA
2025-10-16 00:45:34.982372 WARNING::Fitting problem for feature 97 returning NA
2025-10-16 00:45:34.994449 WARNING::Fitting problem for feature 99 returning NA
2025-10-16 00:45:35.090441 WARNING::Fitting problem for feature 114 returning NA
2025-10-16 00:45:35.095886 WARNING::Fitting problem for feature 115 returning NA
2025-10-16 00:45:35.144898 WARNING::Fitting problem for feature 123 returning NA
2025-10-16 00:45:35.183872 WARNING::Fitting problem for feature 130 returning NA
2025-10-16 00:45:35.195287 WARNING::Fitting problem for feature 132 returning NA
2025-10-16 00:45:35.234831 WARNING::Fitting problem for feature 139 returning NA
2025-10-16 00:45:35.305102 WARNING::Fitting problem for feature 150 returning NA
2025-10-16 00:45:35.505888 WARNING::Deleting existing residuals file: /tmp/RtmpXly8xD/file1b21ef2f434d40/fits/residuals_linear.rds
2025-10-16 00:45:35.567317 WARNING::Deleting existing fitted file: /tmp/RtmpXly8xD/file1b21ef2f434d40/fits/fitted_linear.rds
2025-10-16 00:45:35.630955 WARNING::Deleting existing residuals file: /tmp/RtmpXly8xD/file1b21ef2f434d40/fits/residuals_logistic.rds
2025-10-16 00:45:35.933055 WARNING::Deleting existing fitted file: /tmp/RtmpXly8xD/file1b21ef2f434d40/fits/fitted_logistic.rds
2025-10-16 00:45:58.292433 WARNING::Fitting problem for feature 50 returning NA
2025-10-16 00:45:58.370115 WARNING::Fitting problem for feature 62 returning NA
2025-10-16 00:45:58.44529 WARNING::Fitting problem for feature 74 returning NA
2025-10-16 00:45:58.467252 WARNING::Fitting problem for feature 78 returning NA
2025-10-16 00:45:58.502973 WARNING::Fitting problem for feature 84 returning NA
2025-10-16 00:45:58.580893 WARNING::Fitting problem for feature 96 returning NA
2025-10-16 00:45:58.586522 WARNING::Fitting problem for feature 97 returning NA
2025-10-16 00:45:58.59846 WARNING::Fitting problem for feature 99 returning NA
2025-10-16 00:45:58.69497 WARNING::Fitting problem for feature 114 returning NA
2025-10-16 00:45:58.700552 WARNING::Fitting problem for feature 115 returning NA
2025-10-16 00:45:58.749681 WARNING::Fitting problem for feature 123 returning NA
2025-10-16 00:45:58.789207 WARNING::Fitting problem for feature 130 returning NA
2025-10-16 00:45:58.80104 WARNING::Fitting problem for feature 132 returning NA
2025-10-16 00:45:58.840762 WARNING::Fitting problem for feature 139 returning NA
2025-10-16 00:45:58.908344 WARNING::Fitting problem for feature 150 returning NA
2025-10-16 00:46:09.716013 WARNING::Fitting problem for feature 50 returning NA
2025-10-16 00:46:09.792307 WARNING::Fitting problem for feature 62 returning NA
2025-10-16 00:46:09.867885 WARNING::Fitting problem for feature 74 returning NA
2025-10-16 00:46:09.889211 WARNING::Fitting problem for feature 78 returning NA
2025-10-16 00:46:09.924502 WARNING::Fitting problem for feature 84 returning NA
2025-10-16 00:46:10.030828 WARNING::Fitting problem for feature 96 returning NA
2025-10-16 00:46:10.036726 WARNING::Fitting problem for feature 97 returning NA
2025-10-16 00:46:10.050222 WARNING::Fitting problem for feature 99 returning NA
2025-10-16 00:46:10.15046 WARNING::Fitting problem for feature 114 returning NA
2025-10-16 00:46:10.155997 WARNING::Fitting problem for feature 115 returning NA
2025-10-16 00:46:10.204351 WARNING::Fitting problem for feature 123 returning NA
2025-10-16 00:46:10.244653 WARNING::Fitting problem for feature 130 returning NA
2025-10-16 00:46:10.256461 WARNING::Fitting problem for feature 132 returning NA
2025-10-16 00:46:10.297306 WARNING::Fitting problem for feature 139 returning NA
2025-10-16 00:46:10.367104 WARNING::Fitting problem for feature 150 returning NA
2025-10-16 00:46:35.457211 WARNING::Fitting problem for feature 124 returning NA
2025-10-16 00:46:44.388302 WARNING::Fitting problem for feature 124 returning NA
2025-10-16 00:47:09.639057 WARNING::Fitting problem for feature 124 returning NA
2025-10-16 00:47:19.745395 WARNING::Fitting problem for feature 124 returning NA
2025-10-16 00:47:20.385418 WARNING::Deleting existing residuals file: /tmp/RtmpXly8xD/file1b21ef96c2231/fits/residuals_linear.rds
2025-10-16 00:47:20.447539 WARNING::Deleting existing fitted file: /tmp/RtmpXly8xD/file1b21ef96c2231/fits/fitted_linear.rds
2025-10-16 00:47:20.486083 WARNING::Deleting existing residuals file: /tmp/RtmpXly8xD/file1b21ef96c2231/fits/residuals_logistic.rds
2025-10-16 00:47:20.554762 WARNING::Deleting existing fitted file: /tmp/RtmpXly8xD/file1b21ef96c2231/fits/fitted_logistic.rds
2025-10-16 00:47:43.410675 WARNING::Fitting problem for feature 124 returning NA
2025-10-16 00:47:48.551482 WARNING::Fitting problem for feature 124 returning NA
2025-10-16 00:47:48.853454 WARNING::Deleting existing residuals file: /tmp/RtmpXly8xD/file1b21ef96c2231/fits/residuals_linear.rds
2025-10-16 00:47:48.914668 WARNING::Deleting existing fitted file: /tmp/RtmpXly8xD/file1b21ef96c2231/fits/fitted_linear.rds
2025-10-16 00:47:48.953101 WARNING::Deleting existing residuals file: /tmp/RtmpXly8xD/file1b21ef96c2231/fits/residuals_logistic.rds
2025-10-16 00:47:49.021828 WARNING::Deleting existing fitted file: /tmp/RtmpXly8xD/file1b21ef96c2231/fits/fitted_logistic.rds
2025-10-16 00:48:07.750064 WARNING::Fitting problem for feature 124 returning NA
2025-10-16 00:48:14.401747 WARNING::Fitting problem for feature 124 returning NA
2025-10-16 00:48:14.754454 WARNING::Deleting existing residuals file: /tmp/RtmpXly8xD/file1b21ef96c2231/fits/residuals_linear.rds
2025-10-16 00:48:14.816572 WARNING::Deleting existing fitted file: /tmp/RtmpXly8xD/file1b21ef96c2231/fits/fitted_linear.rds
2025-10-16 00:48:14.855939 WARNING::Deleting existing residuals file: /tmp/RtmpXly8xD/file1b21ef96c2231/fits/residuals_logistic.rds
2025-10-16 00:48:14.927253 WARNING::Deleting existing fitted file: /tmp/RtmpXly8xD/file1b21ef96c2231/fits/fitted_logistic.rds
2025-10-16 00:48:33.112132 WARNING::Fitting problem for feature 50 returning NA
2025-10-16 00:48:33.188617 WARNING::Fitting problem for feature 62 returning NA
2025-10-16 00:48:33.261088 WARNING::Fitting problem for feature 74 returning NA
2025-10-16 00:48:33.282268 WARNING::Fitting problem for feature 78 returning NA
2025-10-16 00:48:33.316085 WARNING::Fitting problem for feature 84 returning NA
2025-10-16 00:48:33.391202 WARNING::Fitting problem for feature 96 returning NA
2025-10-16 00:48:33.396629 WARNING::Fitting problem for feature 97 returning NA
2025-10-16 00:48:33.408442 WARNING::Fitting problem for feature 99 returning NA
2025-10-16 00:48:33.501194 WARNING::Fitting problem for feature 114 returning NA
2025-10-16 00:48:33.506523 WARNING::Fitting problem for feature 115 returning NA
2025-10-16 00:48:33.556701 WARNING::Fitting problem for feature 123 returning NA
2025-10-16 00:48:33.597066 WARNING::Fitting problem for feature 130 returning NA
2025-10-16 00:48:33.608799 WARNING::Fitting problem for feature 132 returning NA
2025-10-16 00:48:33.650341 WARNING::Fitting problem for feature 139 returning NA
2025-10-16 00:48:33.719317 WARNING::Fitting problem for feature 150 returning NA
2025-10-16 00:48:45.809977 WARNING::Fitting problem for feature 50 returning NA
2025-10-16 00:48:45.884612 WARNING::Fitting problem for feature 62 returning NA
2025-10-16 00:48:45.957936 WARNING::Fitting problem for feature 74 returning NA
2025-10-16 00:48:45.979483 WARNING::Fitting problem for feature 78 returning NA
2025-10-16 00:48:46.013835 WARNING::Fitting problem for feature 84 returning NA
2025-10-16 00:48:46.088512 WARNING::Fitting problem for feature 96 returning NA
2025-10-16 00:48:46.093849 WARNING::Fitting problem for feature 97 returning NA
2025-10-16 00:48:46.106204 WARNING::Fitting problem for feature 99 returning NA
2025-10-16 00:48:46.19997 WARNING::Fitting problem for feature 114 returning NA
2025-10-16 00:48:46.205439 WARNING::Fitting problem for feature 115 returning NA
2025-10-16 00:48:46.255108 WARNING::Fitting problem for feature 123 returning NA
2025-10-16 00:48:46.294992 WARNING::Fitting problem for feature 130 returning NA
2025-10-16 00:48:46.306641 WARNING::Fitting problem for feature 132 returning NA
2025-10-16 00:48:46.346238 WARNING::Fitting problem for feature 139 returning NA
2025-10-16 00:48:46.417391 WARNING::Fitting problem for feature 150 returning NA
2025-10-16 00:48:46.680358 WARNING::Deleting existing residuals file: /tmp/RtmpXly8xD/file1b21ef96c2231/fits/residuals_linear.rds
2025-10-16 00:48:46.741288 WARNING::Deleting existing fitted file: /tmp/RtmpXly8xD/file1b21ef96c2231/fits/fitted_linear.rds
2025-10-16 00:48:46.804548 WARNING::Deleting existing residuals file: /tmp/RtmpXly8xD/file1b21ef96c2231/fits/residuals_logistic.rds
2025-10-16 00:48:47.10457 WARNING::Deleting existing fitted file: /tmp/RtmpXly8xD/file1b21ef96c2231/fits/fitted_logistic.rds
2025-10-16 00:49:07.629554 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-10-16 00:49:07.647648 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-10-16 00:49:07.660264 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-10-16 00:49:07.713413 ERROR::No fixed, group, or
                        ordered effects included in formula.
2025-10-16 00:49:07.742869 ERROR::Effect name not found in metadata: d
2025-10-16 00:49:07.75503 ERROR::No user formula provided
2025-10-16 00:49:07.784824 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-10-16 00:49:07.796365 ERROR::No fixed/group/ordered/
                        feature-specific effects provided.
2025-10-16 00:49:10.847891 INFO::Writing function arguments to log file
2025-10-16 00:49:10.86244 INFO::Verifying options selected are valid
2025-10-16 00:49:13.21307 INFO::Writing function arguments to log file
2025-10-16 00:49:13.225396 INFO::Verifying options selected are valid
2025-10-16 00:49:13.226607 INFO::Determining format of input files
2025-10-16 00:49:13.227654 INFO::Input format is data samples as rows and metadata samples as rows
2025-10-16 00:49:13.230076 INFO::Running selected normalization method: TSS
2025-10-16 00:49:13.231608 INFO::Creating output feature tables folder
2025-10-16 00:49:13.232655 INFO::Writing normalized data to file /tmp/RtmpXly8xD/file1b21ef56207d00/features/data_norm.tsv
2025-10-16 00:49:13.234169 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-10-16 00:49:13.235137 INFO::Total samples in data: 16
2025-10-16 00:49:13.236025 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-10-16 00:49:13.236915 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-10-16 00:49:13.238896 INFO::Total filtered features: 0
2025-10-16 00:49:13.239904 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-10-16 00:49:13.241184 INFO::Total features filtered by non-zero variance filtering: 0
2025-10-16 00:49:13.242262 INFO::Filtered feature names from variance filtering:
2025-10-16 00:49:13.243246 INFO::Writing filtered data to file /tmp/RtmpXly8xD/file1b21ef56207d00/features/filtered_data.tsv
2025-10-16 00:49:13.245081 INFO::Running selected transform method: LOG
2025-10-16 00:49:13.246656 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpXly8xD/file1b21ef56207d00/features/data_transformed.tsv
2025-10-16 00:49:13.248767 INFO::Applying z-score to standardize continuous metadata
2025-10-16 00:49:13.256234 INFO::Running the linear model component
2025-10-16 00:49:13.272408 INFO::Fitting model to feature number 1, a
2025-10-16 00:49:13.277585 INFO::Fitting model to feature number 2, b
2025-10-16 00:49:13.281999 INFO::Fitting model to feature number 3, c
2025-10-16 00:49:13.289166 INFO::Counting total values for each feature
2025-10-16 00:49:13.291046 INFO::Running the logistic model component
2025-10-16 00:49:13.304709 INFO::Fitting model to feature number 1, a
2025-10-16 00:49:13.311308 INFO::Fitting model to feature number 2, b
2025-10-16 00:49:13.317551 INFO::Fitting model to feature number 3, c
2025-10-16 00:49:13.326595 INFO::Counting total values for each feature
2025-10-16 00:49:13.328822 INFO::Re-running abundances for warn_prevalence
2025-10-16 00:49:13.329812 INFO::Running selected normalization method: TSS
2025-10-16 00:49:13.331333 INFO::Running selected transform method: LOG
2025-10-16 00:49:13.346045 INFO::Fitting model to feature number 1, a
2025-10-16 00:49:13.350614 INFO::Fitting model to feature number 2, b
2025-10-16 00:49:13.354941 INFO::Fitting model to feature number 3, c
2025-10-16 00:49:13.43898 INFO::Creating fits folder
2025-10-16 00:49:13.440251 INFO::Writing residuals to file /tmp/RtmpXly8xD/file1b21ef56207d00/fits/residuals_linear.rds
2025-10-16 00:49:13.441474 INFO::Writing fitted values to file /tmp/RtmpXly8xD/file1b21ef56207d00/fits/fitted_linear.rds
2025-10-16 00:49:13.442715 INFO::Writing residuals to file /tmp/RtmpXly8xD/file1b21ef56207d00/fits/residuals_logistic.rds
2025-10-16 00:49:13.443892 INFO::Writing fitted values to file /tmp/RtmpXly8xD/file1b21ef56207d00/fits/fitted_logistic.rds
2025-10-16 00:49:13.447195 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /tmp/RtmpXly8xD/file1b21ef56207d00/all_results.tsv
2025-10-16 00:49:13.448878 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/RtmpXly8xD/file1b21ef56207d00/significant_results.tsv
2025-10-16 00:49:13.450263 INFO::Creating output figures folder
2025-10-16 00:49:13.451658 INFO::Writing summary plot of significant
                        results to file: /tmp/RtmpXly8xD/file1b21ef56207d00/figures/summary_plot.pdf
2025-10-16 00:49:15.062141 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpXly8xD/file1b21ef56207d00/figures
2025-10-16 00:49:15.064114 INFO::Plotting associations from most to least significant, grouped by metadata
2025-10-16 00:49:15.069203 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-10-16 00:49:15.661414 INFO::Writing summary plot of
                        significant results to file: /tmp/RtmpXly8xD/file1b21ef56207d00/figures/summary_plot.pdf
2025-10-16 00:49:17.294886 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpXly8xD/file1b21ef56207d00/figures
2025-10-16 00:49:17.296494 INFO::Plotting associations from most to least significant, grouped by metadata
2025-10-16 00:49:17.301346 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-10-16 00:49:17.814097 INFO::Running the linear model component
2025-10-16 00:49:17.823075 INFO::Fitting model to feature number 1, a
2025-10-16 00:49:17.827521 INFO::Fitting model to feature number 2, b
2025-10-16 00:49:17.831644 INFO::Fitting model to feature number 3, c
2025-10-16 00:49:17.838508 INFO::Counting total values for each feature
2025-10-16 00:49:17.840169 INFO::Running the logistic model component
2025-10-16 00:49:17.848443 INFO::Fitting model to feature number 1, a
2025-10-16 00:49:17.854645 INFO::Fitting model to feature number 2, b
2025-10-16 00:49:17.860464 INFO::Fitting model to feature number 3, c
2025-10-16 00:49:17.871871 INFO::Counting total values for each feature
2025-10-16 00:49:17.874542 INFO::Re-running abundances for warn_prevalence
2025-10-16 00:49:17.875434 INFO::Running selected normalization method: TSS
2025-10-16 00:49:17.876844 INFO::Running selected transform method: LOG
2025-10-16 00:49:17.885333 INFO::Fitting model to feature number 1, a
2025-10-16 00:49:17.889604 INFO::Fitting model to feature number 2, b
2025-10-16 00:49:17.893677 INFO::Fitting model to feature number 3, c
2025-10-16 00:49:17.980216 INFO::Creating output folder
2025-10-16 00:49:17.98123 INFO::Creating output figures folder
2025-10-16 00:49:17.982522 INFO::Writing summary plot of significant
                        results to file: /tmp/RtmpXly8xD/file1b21ef6c09e5a9/figures/summary_plot.pdf
2025-10-16 00:49:19.614304 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpXly8xD/file1b21ef6c09e5a9/figures
2025-10-16 00:49:19.616034 INFO::Plotting associations from most to least significant, grouped by metadata
2025-10-16 00:49:19.621122 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-10-16 00:49:20.61461 INFO::Applying z-score to standardize continuous metadata
2025-10-16 00:49:20.622468 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-10-16 00:49:20.623382 INFO::Bypass z-score application to metadata
2025-10-16 00:49:20.625841 INFO::Bypass z-score application to metadata
2025-10-16 00:49:20.643385 INFO::Determining format of input files
2025-10-16 00:49:20.644438 INFO::Input format is data samples as rows and metadata samples as rows
2025-10-16 00:49:20.645344 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-10-16 00:49:20.65212 INFO::Determining format of input files
2025-10-16 00:49:20.653119 INFO::Input format is data samples as columns and metadata samples as rows
2025-10-16 00:49:20.654398 INFO::Input format is feature_specific_covariate samples as columns
2025-10-16 00:49:20.661954 INFO::Determining format of input files
2025-10-16 00:49:20.662884 INFO::Input format is data samples as rows and metadata samples as rows
2025-10-16 00:49:20.663926 INFO::Input format is feature_specific_covariate samples as columns
2025-10-16 00:49:20.665565 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-10-16 00:49:20.666363 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-10-16 00:49:20.677031 INFO::Running selected transform method: LOG
2025-10-16 00:49:20.678191 INFO::Creating output feature tables folder
2025-10-16 00:49:20.679107 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpXly8xD/file1b21ef4fe7fdaa/features/data_transformed.tsv
2025-10-16 00:49:20.682883 INFO::Running selected transform method: LOG
2025-10-16 00:49:20.683914 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpXly8xD/file1b21ef4fe7fdaa/features/data_transformed.tsv
2025-10-16 00:49:20.687422 INFO::Running selected transform method: PLOG
2025-10-16 00:49:20.688964 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpXly8xD/file1b21ef4fe7fdaa/features/data_transformed.tsv
2025-10-16 00:49:20.691634 INFO::Running selected transform method: NONE
2025-10-16 00:49:20.692383 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpXly8xD/file1b21ef4fe7fdaa/features/data_transformed.tsv
2025-10-16 00:49:20.699265 INFO::Running the linear model component
2025-10-16 00:49:20.707609 INFO::Fitting model to feature number 1, a
2025-10-16 00:49:20.711758 INFO::Fitting model to feature number 2, b
2025-10-16 00:49:20.715669 INFO::Fitting model to feature number 3, c
2025-10-16 00:49:20.722476 INFO::Counting total values for each feature
2025-10-16 00:49:20.724125 INFO::Running the logistic model component
2025-10-16 00:49:20.732356 INFO::Fitting model to feature number 1, a
2025-10-16 00:49:20.7384 INFO::Fitting model to feature number 2, b
2025-10-16 00:49:20.744703 INFO::Fitting model to feature number 3, c
2025-10-16 00:49:20.75364 INFO::Counting total values for each feature
2025-10-16 00:49:20.755637 INFO::Re-running abundances for warn_prevalence
2025-10-16 00:49:20.756402 INFO::Running selected normalization method: TSS
2025-10-16 00:49:20.757775 INFO::Running selected transform method: LOG
2025-10-16 00:49:20.766273 INFO::Fitting model to feature number 1, a
2025-10-16 00:49:20.770378 INFO::Fitting model to feature number 2, b
2025-10-16 00:49:20.774318 INFO::Fitting model to feature number 3, c
2025-10-16 00:49:20.903385 INFO::Creating output folder
2025-10-16 00:49:20.904734 INFO::Creating fits folder
2025-10-16 00:49:20.905846 INFO::Writing residuals to file /tmp/RtmpXly8xD/file1b21ef78b962a0/fits/residuals_linear.rds
2025-10-16 00:49:20.906988 INFO::Writing fitted values to file /tmp/RtmpXly8xD/file1b21ef78b962a0/fits/fitted_linear.rds
2025-10-16 00:49:20.908135 INFO::Writing residuals to file /tmp/RtmpXly8xD/file1b21ef78b962a0/fits/residuals_logistic.rds
2025-10-16 00:49:20.909271 INFO::Writing fitted values to file /tmp/RtmpXly8xD/file1b21ef78b962a0/fits/fitted_logistic.rds
2025-10-16 00:49:20.912226 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /tmp/RtmpXly8xD/file1b21ef78b962a0/all_results.tsv
2025-10-16 00:49:20.91408 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/RtmpXly8xD/file1b21ef78b962a0/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]

[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
> 
> 
> proc.time()
   user  system elapsed 
359.207   5.137 364.338

Example timings

maaslin3.Rcheck/maaslin3-Ex.timings

nameusersystemelapsed
maaslin320.188 0.69720.891
maaslin_check_arguments0.1390.0090.148
maaslin_check_formula0.1380.0040.142
maaslin_compute_formula0.1490.0030.152
maaslin_contrast_test18.889 0.51719.406
maaslin_filter0.4410.0100.450
maaslin_fit13.269 0.25613.527
maaslin_log_arguments0.1280.0040.133
maaslin_normalize0.2660.0070.274
maaslin_plot_results43.365 0.32443.640
maaslin_plot_results_from_output43.345 0.27443.624
maaslin_process_metadata0.4400.0110.451
maaslin_read_data0.1300.0020.132
maaslin_reorder_data0.1660.0030.169
maaslin_transform0.5480.0130.561
maaslin_write_results13.760 0.21613.976
maaslin_write_results_lefse_format14.173 0.16214.337
preprocess_dna_mtx0.0040.0000.004
preprocess_taxa_mtx0.0050.0000.004