Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-10-18 12:03 -0400 (Sat, 18 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4887
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4677
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4622
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4632
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 1164/2353HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maaslin3 1.1.2  (landing page)
William Nickols
Snapshot Date: 2025-10-17 13:45 -0400 (Fri, 17 Oct 2025)
git_url: https://git.bioconductor.org/packages/maaslin3
git_branch: devel
git_last_commit: e7106d5
git_last_commit_date: 2025-10-12 11:00:51 -0400 (Sun, 12 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for maaslin3 on nebbiolo2

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: 1.1.2
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings maaslin3_1.1.2.tar.gz
StartedAt: 2025-10-18 01:21:04 -0400 (Sat, 18 Oct 2025)
EndedAt: 2025-10-18 01:42:17 -0400 (Sat, 18 Oct 2025)
EllapsedTime: 1273.1 seconds
RetCode: 0
Status:   OK  
CheckDir: maaslin3.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings maaslin3_1.1.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/maaslin3.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 ‘1.1.2’
* 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_from_output   43.052  0.415  43.472
maaslin_plot_results               43.004  0.383  43.347
maaslin3                           19.878  0.658  20.539
maaslin_contrast_test              16.241  0.469  16.710
maaslin_write_results_lefse_format 14.277  0.054  14.332
maaslin_write_results              13.313  0.196  13.510
maaslin_fit                        12.469  0.104  12.573
* 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-3.22-bioc/R/bin/R CMD INSTALL maaslin3
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘maaslin3’ ...
** this is package ‘maaslin3’ version ‘1.1.2’
** 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 Patched (2025-08-23 r88802) -- "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")
2025-10-18 01:27:09.897661 WARNING::Fitting problem for feature 50 returning NA
2025-10-18 01:27:09.97729 WARNING::Fitting problem for feature 62 returning NA
2025-10-18 01:27:10.075946 WARNING::Fitting problem for feature 74 returning NA
2025-10-18 01:27:10.097046 WARNING::Fitting problem for feature 78 returning NA
2025-10-18 01:27:10.129766 WARNING::Fitting problem for feature 84 returning NA
2025-10-18 01:27:10.202651 WARNING::Fitting problem for feature 96 returning NA
2025-10-18 01:27:10.207879 WARNING::Fitting problem for feature 97 returning NA
2025-10-18 01:27:10.219372 WARNING::Fitting problem for feature 99 returning NA
2025-10-18 01:27:10.317144 WARNING::Fitting problem for feature 114 returning NA
2025-10-18 01:27:10.322215 WARNING::Fitting problem for feature 115 returning NA
2025-10-18 01:27:10.368974 WARNING::Fitting problem for feature 123 returning NA
2025-10-18 01:27:10.407215 WARNING::Fitting problem for feature 130 returning NA
2025-10-18 01:27:10.418585 WARNING::Fitting problem for feature 132 returning NA
2025-10-18 01:27:10.463525 WARNING::Fitting problem for feature 139 returning NA
2025-10-18 01:27:10.52911 WARNING::Fitting problem for feature 150 returning NA
2025-10-18 01:27:25.254452 WARNING::Fitting problem for feature 50 returning NA
2025-10-18 01:27:25.327765 WARNING::Fitting problem for feature 62 returning NA
2025-10-18 01:27:25.411576 WARNING::Fitting problem for feature 74 returning NA
2025-10-18 01:27:25.432251 WARNING::Fitting problem for feature 78 returning NA
2025-10-18 01:27:25.464696 WARNING::Fitting problem for feature 84 returning NA
2025-10-18 01:27:25.537022 WARNING::Fitting problem for feature 96 returning NA
2025-10-18 01:27:25.542184 WARNING::Fitting problem for feature 97 returning NA
2025-10-18 01:27:25.553482 WARNING::Fitting problem for feature 99 returning NA
2025-10-18 01:27:25.645285 WARNING::Fitting problem for feature 114 returning NA
2025-10-18 01:27:25.650477 WARNING::Fitting problem for feature 115 returning NA
2025-10-18 01:27:25.698528 WARNING::Fitting problem for feature 123 returning NA
2025-10-18 01:27:25.737553 WARNING::Fitting problem for feature 130 returning NA
2025-10-18 01:27:25.749034 WARNING::Fitting problem for feature 132 returning NA
2025-10-18 01:27:25.788396 WARNING::Fitting problem for feature 139 returning NA
2025-10-18 01:27:25.858129 WARNING::Fitting problem for feature 150 returning NA
2025-10-18 01:27:49.635885 WARNING::Fitting problem for feature 50 returning NA
2025-10-18 01:27:49.717067 WARNING::Fitting problem for feature 62 returning NA
2025-10-18 01:27:49.789736 WARNING::Fitting problem for feature 74 returning NA
2025-10-18 01:27:49.810908 WARNING::Fitting problem for feature 78 returning NA
2025-10-18 01:27:49.844217 WARNING::Fitting problem for feature 84 returning NA
2025-10-18 01:27:49.917231 WARNING::Fitting problem for feature 96 returning NA
2025-10-18 01:27:49.922627 WARNING::Fitting problem for feature 97 returning NA
2025-10-18 01:27:49.934035 WARNING::Fitting problem for feature 99 returning NA
2025-10-18 01:27:50.02629 WARNING::Fitting problem for feature 114 returning NA
2025-10-18 01:27:50.031673 WARNING::Fitting problem for feature 115 returning NA
2025-10-18 01:27:50.07977 WARNING::Fitting problem for feature 123 returning NA
2025-10-18 01:27:50.119776 WARNING::Fitting problem for feature 130 returning NA
2025-10-18 01:27:50.131419 WARNING::Fitting problem for feature 132 returning NA
2025-10-18 01:27:50.171812 WARNING::Fitting problem for feature 139 returning NA
2025-10-18 01:27:50.241455 WARNING::Fitting problem for feature 150 returning NA
2025-10-18 01:28:02.464649 WARNING::Fitting problem for feature 50 returning NA
2025-10-18 01:28:02.55608 WARNING::Fitting problem for feature 62 returning NA
2025-10-18 01:28:02.629767 WARNING::Fitting problem for feature 74 returning NA
2025-10-18 01:28:02.651009 WARNING::Fitting problem for feature 78 returning NA
2025-10-18 01:28:02.685019 WARNING::Fitting problem for feature 84 returning NA
2025-10-18 01:28:02.758214 WARNING::Fitting problem for feature 96 returning NA
2025-10-18 01:28:02.763419 WARNING::Fitting problem for feature 97 returning NA
2025-10-18 01:28:02.774846 WARNING::Fitting problem for feature 99 returning NA
2025-10-18 01:28:02.868984 WARNING::Fitting problem for feature 114 returning NA
2025-10-18 01:28:02.874436 WARNING::Fitting problem for feature 115 returning NA
2025-10-18 01:28:02.922746 WARNING::Fitting problem for feature 123 returning NA
2025-10-18 01:28:02.961816 WARNING::Fitting problem for feature 130 returning NA
2025-10-18 01:28:02.973245 WARNING::Fitting problem for feature 132 returning NA
2025-10-18 01:28:03.012214 WARNING::Fitting problem for feature 139 returning NA
2025-10-18 01:28:03.077754 WARNING::Fitting problem for feature 150 returning NA
2025-10-18 01:28:03.279281 WARNING::Deleting existing residuals file: /tmp/Rtmp4fC4dU/file140955508fb4a6/fits/residuals_linear.rds
2025-10-18 01:28:03.340638 WARNING::Deleting existing fitted file: /tmp/Rtmp4fC4dU/file140955508fb4a6/fits/fitted_linear.rds
2025-10-18 01:28:03.403321 WARNING::Deleting existing residuals file: /tmp/Rtmp4fC4dU/file140955508fb4a6/fits/residuals_logistic.rds
2025-10-18 01:28:03.701983 WARNING::Deleting existing fitted file: /tmp/Rtmp4fC4dU/file140955508fb4a6/fits/fitted_logistic.rds
2025-10-18 01:28:25.063559 WARNING::Fitting problem for feature 50 returning NA
2025-10-18 01:28:25.141425 WARNING::Fitting problem for feature 62 returning NA
2025-10-18 01:28:25.217178 WARNING::Fitting problem for feature 74 returning NA
2025-10-18 01:28:25.238906 WARNING::Fitting problem for feature 78 returning NA
2025-10-18 01:28:25.274683 WARNING::Fitting problem for feature 84 returning NA
2025-10-18 01:28:25.350612 WARNING::Fitting problem for feature 96 returning NA
2025-10-18 01:28:25.356145 WARNING::Fitting problem for feature 97 returning NA
2025-10-18 01:28:25.367955 WARNING::Fitting problem for feature 99 returning NA
2025-10-18 01:28:25.462054 WARNING::Fitting problem for feature 114 returning NA
2025-10-18 01:28:25.467451 WARNING::Fitting problem for feature 115 returning NA
2025-10-18 01:28:25.517456 WARNING::Fitting problem for feature 123 returning NA
2025-10-18 01:28:25.5577 WARNING::Fitting problem for feature 130 returning NA
2025-10-18 01:28:25.569614 WARNING::Fitting problem for feature 132 returning NA
2025-10-18 01:28:25.609692 WARNING::Fitting problem for feature 139 returning NA
2025-10-18 01:28:26.673459 WARNING::Fitting problem for feature 150 returning NA
2025-10-18 01:28:38.139148 WARNING::Fitting problem for feature 50 returning NA
2025-10-18 01:28:38.219508 WARNING::Fitting problem for feature 62 returning NA
2025-10-18 01:28:38.296274 WARNING::Fitting problem for feature 74 returning NA
2025-10-18 01:28:38.318175 WARNING::Fitting problem for feature 78 returning NA
2025-10-18 01:28:38.352494 WARNING::Fitting problem for feature 84 returning NA
2025-10-18 01:28:38.430268 WARNING::Fitting problem for feature 96 returning NA
2025-10-18 01:28:38.435977 WARNING::Fitting problem for feature 97 returning NA
2025-10-18 01:28:38.448069 WARNING::Fitting problem for feature 99 returning NA
2025-10-18 01:28:38.583548 WARNING::Fitting problem for feature 114 returning NA
2025-10-18 01:28:38.589064 WARNING::Fitting problem for feature 115 returning NA
2025-10-18 01:28:38.640851 WARNING::Fitting problem for feature 123 returning NA
2025-10-18 01:28:38.682113 WARNING::Fitting problem for feature 130 returning NA
2025-10-18 01:28:38.694762 WARNING::Fitting problem for feature 132 returning NA
2025-10-18 01:28:38.73853 WARNING::Fitting problem for feature 139 returning NA
2025-10-18 01:28:38.811785 WARNING::Fitting problem for feature 150 returning NA
2025-10-18 01:28:39.020591 WARNING::Deleting existing residuals file: /tmp/Rtmp4fC4dU/file140955508fb4a6/fits/residuals_linear.rds
2025-10-18 01:28:39.081413 WARNING::Deleting existing fitted file: /tmp/Rtmp4fC4dU/file140955508fb4a6/fits/fitted_linear.rds
2025-10-18 01:28:39.143567 WARNING::Deleting existing residuals file: /tmp/Rtmp4fC4dU/file140955508fb4a6/fits/residuals_logistic.rds
2025-10-18 01:28:39.441585 WARNING::Deleting existing fitted file: /tmp/Rtmp4fC4dU/file140955508fb4a6/fits/fitted_logistic.rds
2025-10-18 01:29:01.538628 WARNING::Fitting problem for feature 50 returning NA
2025-10-18 01:29:01.619474 WARNING::Fitting problem for feature 62 returning NA
2025-10-18 01:29:01.697038 WARNING::Fitting problem for feature 74 returning NA
2025-10-18 01:29:01.719694 WARNING::Fitting problem for feature 78 returning NA
2025-10-18 01:29:01.755188 WARNING::Fitting problem for feature 84 returning NA
2025-10-18 01:29:01.834092 WARNING::Fitting problem for feature 96 returning NA
2025-10-18 01:29:01.839592 WARNING::Fitting problem for feature 97 returning NA
2025-10-18 01:29:01.851819 WARNING::Fitting problem for feature 99 returning NA
2025-10-18 01:29:01.96538 WARNING::Fitting problem for feature 114 returning NA
2025-10-18 01:29:01.971048 WARNING::Fitting problem for feature 115 returning NA
2025-10-18 01:29:02.026881 WARNING::Fitting problem for feature 123 returning NA
2025-10-18 01:29:02.072153 WARNING::Fitting problem for feature 130 returning NA
2025-10-18 01:29:02.085312 WARNING::Fitting problem for feature 132 returning NA
2025-10-18 01:29:02.130194 WARNING::Fitting problem for feature 139 returning NA
2025-10-18 01:29:02.205811 WARNING::Fitting problem for feature 150 returning NA
2025-10-18 01:29:12.760824 WARNING::Fitting problem for feature 50 returning NA
2025-10-18 01:29:12.835791 WARNING::Fitting problem for feature 62 returning NA
2025-10-18 01:29:12.909961 WARNING::Fitting problem for feature 74 returning NA
2025-10-18 01:29:12.931359 WARNING::Fitting problem for feature 78 returning NA
2025-10-18 01:29:12.965017 WARNING::Fitting problem for feature 84 returning NA
2025-10-18 01:29:13.070978 WARNING::Fitting problem for feature 96 returning NA
2025-10-18 01:29:13.07662 WARNING::Fitting problem for feature 97 returning NA
2025-10-18 01:29:13.088908 WARNING::Fitting problem for feature 99 returning NA
2025-10-18 01:29:13.190223 WARNING::Fitting problem for feature 114 returning NA
2025-10-18 01:29:13.196441 WARNING::Fitting problem for feature 115 returning NA
2025-10-18 01:29:13.246398 WARNING::Fitting problem for feature 123 returning NA
2025-10-18 01:29:13.287195 WARNING::Fitting problem for feature 130 returning NA
2025-10-18 01:29:13.299407 WARNING::Fitting problem for feature 132 returning NA
2025-10-18 01:29:13.340602 WARNING::Fitting problem for feature 139 returning NA
2025-10-18 01:29:13.411178 WARNING::Fitting problem for feature 150 returning NA
2025-10-18 01:29:13.607296 WARNING::Deleting existing residuals file: /tmp/Rtmp4fC4dU/file140955508fb4a6/fits/residuals_linear.rds
2025-10-18 01:29:13.667694 WARNING::Deleting existing fitted file: /tmp/Rtmp4fC4dU/file140955508fb4a6/fits/fitted_linear.rds
2025-10-18 01:29:13.730135 WARNING::Deleting existing residuals file: /tmp/Rtmp4fC4dU/file140955508fb4a6/fits/residuals_logistic.rds
2025-10-18 01:29:14.027813 WARNING::Deleting existing fitted file: /tmp/Rtmp4fC4dU/file140955508fb4a6/fits/fitted_logistic.rds
2025-10-18 01:29:35.081537 WARNING::Fitting problem for feature 50 returning NA
2025-10-18 01:29:35.15887 WARNING::Fitting problem for feature 62 returning NA
2025-10-18 01:29:35.236236 WARNING::Fitting problem for feature 74 returning NA
2025-10-18 01:29:35.258329 WARNING::Fitting problem for feature 78 returning NA
2025-10-18 01:29:35.293063 WARNING::Fitting problem for feature 84 returning NA
2025-10-18 01:29:35.369976 WARNING::Fitting problem for feature 96 returning NA
2025-10-18 01:29:35.375575 WARNING::Fitting problem for feature 97 returning NA
2025-10-18 01:29:35.412902 WARNING::Fitting problem for feature 99 returning NA
2025-10-18 01:29:35.511389 WARNING::Fitting problem for feature 114 returning NA
2025-10-18 01:29:35.516968 WARNING::Fitting problem for feature 115 returning NA
2025-10-18 01:29:35.567348 WARNING::Fitting problem for feature 123 returning NA
2025-10-18 01:29:35.608211 WARNING::Fitting problem for feature 130 returning NA
2025-10-18 01:29:35.620182 WARNING::Fitting problem for feature 132 returning NA
2025-10-18 01:29:35.659847 WARNING::Fitting problem for feature 139 returning NA
2025-10-18 01:29:35.728708 WARNING::Fitting problem for feature 150 returning NA
2025-10-18 01:29:47.332795 WARNING::Fitting problem for feature 50 returning NA
2025-10-18 01:29:47.408992 WARNING::Fitting problem for feature 62 returning NA
2025-10-18 01:29:47.484787 WARNING::Fitting problem for feature 74 returning NA
2025-10-18 01:29:47.507052 WARNING::Fitting problem for feature 78 returning NA
2025-10-18 01:29:47.541946 WARNING::Fitting problem for feature 84 returning NA
2025-10-18 01:29:47.617741 WARNING::Fitting problem for feature 96 returning NA
2025-10-18 01:29:47.623019 WARNING::Fitting problem for feature 97 returning NA
2025-10-18 01:29:47.63469 WARNING::Fitting problem for feature 99 returning NA
2025-10-18 01:29:47.730232 WARNING::Fitting problem for feature 114 returning NA
2025-10-18 01:29:47.735841 WARNING::Fitting problem for feature 115 returning NA
2025-10-18 01:29:47.786048 WARNING::Fitting problem for feature 123 returning NA
2025-10-18 01:29:47.827068 WARNING::Fitting problem for feature 130 returning NA
2025-10-18 01:29:47.839486 WARNING::Fitting problem for feature 132 returning NA
2025-10-18 01:29:47.883188 WARNING::Fitting problem for feature 139 returning NA
2025-10-18 01:29:47.955522 WARNING::Fitting problem for feature 150 returning NA
2025-10-18 01:30:11.519332 WARNING::Fitting problem for feature 124 returning NA
2025-10-18 01:30:20.161853 WARNING::Fitting problem for feature 124 returning NA
2025-10-18 01:30:45.706707 WARNING::Fitting problem for feature 124 returning NA
2025-10-18 01:30:54.215306 WARNING::Fitting problem for feature 124 returning NA
2025-10-18 01:30:54.848927 WARNING::Deleting existing residuals file: /tmp/Rtmp4fC4dU/file140955cd66fac/fits/residuals_linear.rds
2025-10-18 01:30:54.909888 WARNING::Deleting existing fitted file: /tmp/Rtmp4fC4dU/file140955cd66fac/fits/fitted_linear.rds
2025-10-18 01:30:54.948673 WARNING::Deleting existing residuals file: /tmp/Rtmp4fC4dU/file140955cd66fac/fits/residuals_logistic.rds
2025-10-18 01:30:55.01628 WARNING::Deleting existing fitted file: /tmp/Rtmp4fC4dU/file140955cd66fac/fits/fitted_logistic.rds
2025-10-18 01:31:17.700257 WARNING::Fitting problem for feature 124 returning NA
2025-10-18 01:31:24.072983 WARNING::Fitting problem for feature 124 returning NA
2025-10-18 01:31:24.437165 WARNING::Deleting existing residuals file: /tmp/Rtmp4fC4dU/file140955cd66fac/fits/residuals_linear.rds
2025-10-18 01:31:24.499044 WARNING::Deleting existing fitted file: /tmp/Rtmp4fC4dU/file140955cd66fac/fits/fitted_linear.rds
2025-10-18 01:31:24.537537 WARNING::Deleting existing residuals file: /tmp/Rtmp4fC4dU/file140955cd66fac/fits/residuals_logistic.rds
2025-10-18 01:31:24.605873 WARNING::Deleting existing fitted file: /tmp/Rtmp4fC4dU/file140955cd66fac/fits/fitted_logistic.rds
2025-10-18 01:31:43.212592 WARNING::Fitting problem for feature 124 returning NA
2025-10-18 01:31:49.566486 WARNING::Fitting problem for feature 124 returning NA
2025-10-18 01:31:49.885898 WARNING::Deleting existing residuals file: /tmp/Rtmp4fC4dU/file140955cd66fac/fits/residuals_linear.rds
2025-10-18 01:31:49.947663 WARNING::Deleting existing fitted file: /tmp/Rtmp4fC4dU/file140955cd66fac/fits/fitted_linear.rds
2025-10-18 01:31:49.986332 WARNING::Deleting existing residuals file: /tmp/Rtmp4fC4dU/file140955cd66fac/fits/residuals_logistic.rds
2025-10-18 01:31:50.056487 WARNING::Deleting existing fitted file: /tmp/Rtmp4fC4dU/file140955cd66fac/fits/fitted_logistic.rds
2025-10-18 01:32:08.144715 WARNING::Fitting problem for feature 50 returning NA
2025-10-18 01:32:08.247344 WARNING::Fitting problem for feature 62 returning NA
2025-10-18 01:32:08.324943 WARNING::Fitting problem for feature 74 returning NA
2025-10-18 01:32:08.34666 WARNING::Fitting problem for feature 78 returning NA
2025-10-18 01:32:08.381188 WARNING::Fitting problem for feature 84 returning NA
2025-10-18 01:32:08.460402 WARNING::Fitting problem for feature 96 returning NA
2025-10-18 01:32:08.46582 WARNING::Fitting problem for feature 97 returning NA
2025-10-18 01:32:08.477836 WARNING::Fitting problem for feature 99 returning NA
2025-10-18 01:32:08.573921 WARNING::Fitting problem for feature 114 returning NA
2025-10-18 01:32:08.579302 WARNING::Fitting problem for feature 115 returning NA
2025-10-18 01:32:08.628727 WARNING::Fitting problem for feature 123 returning NA
2025-10-18 01:32:08.668216 WARNING::Fitting problem for feature 130 returning NA
2025-10-18 01:32:08.679927 WARNING::Fitting problem for feature 132 returning NA
2025-10-18 01:32:08.719543 WARNING::Fitting problem for feature 139 returning NA
2025-10-18 01:32:08.788245 WARNING::Fitting problem for feature 150 returning NA
2025-10-18 01:32:20.884881 WARNING::Fitting problem for feature 50 returning NA
2025-10-18 01:32:20.962983 WARNING::Fitting problem for feature 62 returning NA
2025-10-18 01:32:21.038687 WARNING::Fitting problem for feature 74 returning NA
2025-10-18 01:32:21.060986 WARNING::Fitting problem for feature 78 returning NA
2025-10-18 01:32:21.095754 WARNING::Fitting problem for feature 84 returning NA
2025-10-18 01:32:21.173106 WARNING::Fitting problem for feature 96 returning NA
2025-10-18 01:32:21.178415 WARNING::Fitting problem for feature 97 returning NA
2025-10-18 01:32:21.19 WARNING::Fitting problem for feature 99 returning NA
2025-10-18 01:32:21.283501 WARNING::Fitting problem for feature 114 returning NA
2025-10-18 01:32:21.288994 WARNING::Fitting problem for feature 115 returning NA
2025-10-18 01:32:21.337832 WARNING::Fitting problem for feature 123 returning NA
2025-10-18 01:32:21.377331 WARNING::Fitting problem for feature 130 returning NA
2025-10-18 01:32:21.389006 WARNING::Fitting problem for feature 132 returning NA
2025-10-18 01:32:21.429556 WARNING::Fitting problem for feature 139 returning NA
2025-10-18 01:32:21.499186 WARNING::Fitting problem for feature 150 returning NA
2025-10-18 01:32:21.790047 WARNING::Deleting existing residuals file: /tmp/Rtmp4fC4dU/file140955cd66fac/fits/residuals_linear.rds
2025-10-18 01:32:21.851866 WARNING::Deleting existing fitted file: /tmp/Rtmp4fC4dU/file140955cd66fac/fits/fitted_linear.rds
2025-10-18 01:32:21.914599 WARNING::Deleting existing residuals file: /tmp/Rtmp4fC4dU/file140955cd66fac/fits/residuals_logistic.rds
2025-10-18 01:32:22.21167 WARNING::Deleting existing fitted file: /tmp/Rtmp4fC4dU/file140955cd66fac/fits/fitted_logistic.rds
2025-10-18 01:32:42.592979 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-10-18 01:32:42.61016 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-10-18 01:32:42.621572 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-10-18 01:32:42.671621 ERROR::No fixed, group, or
                        ordered effects included in formula.
2025-10-18 01:32:42.687961 ERROR::Effect name not found in metadata: d
2025-10-18 01:32:42.699106 ERROR::No user formula provided
2025-10-18 01:32:42.72805 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-10-18 01:32:42.739823 ERROR::No fixed/group/ordered/
                        feature-specific effects provided.
2025-10-18 01:32:45.775066 INFO::Writing function arguments to log file
2025-10-18 01:32:45.790296 INFO::Verifying options selected are valid
2025-10-18 01:32:48.105907 INFO::Writing function arguments to log file
2025-10-18 01:32:48.118306 INFO::Verifying options selected are valid
2025-10-18 01:32:48.11939 INFO::Determining format of input files
2025-10-18 01:32:48.120379 INFO::Input format is data samples as rows and metadata samples as rows
2025-10-18 01:32:48.12269 INFO::Running selected normalization method: TSS
2025-10-18 01:32:48.12411 INFO::Creating output feature tables folder
2025-10-18 01:32:48.125062 INFO::Writing normalized data to file /tmp/Rtmp4fC4dU/file1409554d91feb6/features/data_norm.tsv
2025-10-18 01:32:48.126534 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-10-18 01:32:48.127422 INFO::Total samples in data: 16
2025-10-18 01:32:48.128279 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-10-18 01:32:48.129155 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-10-18 01:32:48.131044 INFO::Total filtered features: 0
2025-10-18 01:32:48.132002 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-10-18 01:32:48.133162 INFO::Total features filtered by non-zero variance filtering: 0
2025-10-18 01:32:48.134139 INFO::Filtered feature names from variance filtering:
2025-10-18 01:32:48.13502 INFO::Writing filtered data to file /tmp/Rtmp4fC4dU/file1409554d91feb6/features/filtered_data.tsv
2025-10-18 01:32:48.136501 INFO::Running selected transform method: LOG
2025-10-18 01:32:48.137689 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp4fC4dU/file1409554d91feb6/features/data_transformed.tsv
2025-10-18 01:32:48.139362 INFO::Applying z-score to standardize continuous metadata
2025-10-18 01:32:48.144526 INFO::Running the linear model component
2025-10-18 01:32:48.158649 INFO::Fitting model to feature number 1, a
2025-10-18 01:32:48.163286 INFO::Fitting model to feature number 2, b
2025-10-18 01:32:48.167603 INFO::Fitting model to feature number 3, c
2025-10-18 01:32:48.174788 INFO::Counting total values for each feature
2025-10-18 01:32:48.176638 INFO::Running the logistic model component
2025-10-18 01:32:48.190511 INFO::Fitting model to feature number 1, a
2025-10-18 01:32:48.197142 INFO::Fitting model to feature number 2, b
2025-10-18 01:32:48.203401 INFO::Fitting model to feature number 3, c
2025-10-18 01:32:48.21238 INFO::Counting total values for each feature
2025-10-18 01:32:48.214629 INFO::Re-running abundances for warn_prevalence
2025-10-18 01:32:48.215611 INFO::Running selected normalization method: TSS
2025-10-18 01:32:48.217123 INFO::Running selected transform method: LOG
2025-10-18 01:32:48.231174 INFO::Fitting model to feature number 1, a
2025-10-18 01:32:48.235698 INFO::Fitting model to feature number 2, b
2025-10-18 01:32:48.239894 INFO::Fitting model to feature number 3, c
2025-10-18 01:32:48.32537 INFO::Creating fits folder
2025-10-18 01:32:48.326598 INFO::Writing residuals to file /tmp/Rtmp4fC4dU/file1409554d91feb6/fits/residuals_linear.rds
2025-10-18 01:32:48.327788 INFO::Writing fitted values to file /tmp/Rtmp4fC4dU/file1409554d91feb6/fits/fitted_linear.rds
2025-10-18 01:32:48.329014 INFO::Writing residuals to file /tmp/Rtmp4fC4dU/file1409554d91feb6/fits/residuals_logistic.rds
2025-10-18 01:32:48.330218 INFO::Writing fitted values to file /tmp/Rtmp4fC4dU/file1409554d91feb6/fits/fitted_logistic.rds
2025-10-18 01:32:48.332871 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /tmp/Rtmp4fC4dU/file1409554d91feb6/all_results.tsv
2025-10-18 01:32:48.334498 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/Rtmp4fC4dU/file1409554d91feb6/significant_results.tsv
2025-10-18 01:32:48.33582 INFO::Creating output figures folder
2025-10-18 01:32:48.337166 INFO::Writing summary plot of significant
                        results to file: /tmp/Rtmp4fC4dU/file1409554d91feb6/figures/summary_plot.pdf
2025-10-18 01:32:49.919639 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmp4fC4dU/file1409554d91feb6/figures
2025-10-18 01:32:49.921655 INFO::Plotting associations from most to least significant, grouped by metadata
2025-10-18 01:32:49.926711 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-10-18 01:32:50.502133 INFO::Writing summary plot of
                        significant results to file: /tmp/Rtmp4fC4dU/file1409554d91feb6/figures/summary_plot.pdf
2025-10-18 01:32:52.144037 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmp4fC4dU/file1409554d91feb6/figures
2025-10-18 01:32:52.14563 INFO::Plotting associations from most to least significant, grouped by metadata
2025-10-18 01:32:52.150474 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-10-18 01:32:52.673242 INFO::Running the linear model component
2025-10-18 01:32:52.68219 INFO::Fitting model to feature number 1, a
2025-10-18 01:32:52.686671 INFO::Fitting model to feature number 2, b
2025-10-18 01:32:52.690747 INFO::Fitting model to feature number 3, c
2025-10-18 01:32:52.69798 INFO::Counting total values for each feature
2025-10-18 01:32:52.699688 INFO::Running the logistic model component
2025-10-18 01:32:52.708145 INFO::Fitting model to feature number 1, a
2025-10-18 01:32:52.714432 INFO::Fitting model to feature number 2, b
2025-10-18 01:32:52.720376 INFO::Fitting model to feature number 3, c
2025-10-18 01:32:52.729066 INFO::Counting total values for each feature
2025-10-18 01:32:52.731144 INFO::Re-running abundances for warn_prevalence
2025-10-18 01:32:52.731951 INFO::Running selected normalization method: TSS
2025-10-18 01:32:52.733336 INFO::Running selected transform method: LOG
2025-10-18 01:32:52.741973 INFO::Fitting model to feature number 1, a
2025-10-18 01:32:52.746202 INFO::Fitting model to feature number 2, b
2025-10-18 01:32:52.750196 INFO::Fitting model to feature number 3, c
2025-10-18 01:32:52.836958 INFO::Creating output folder
2025-10-18 01:32:52.837943 INFO::Creating output figures folder
2025-10-18 01:32:52.839187 INFO::Writing summary plot of significant
                        results to file: /tmp/Rtmp4fC4dU/file140955c86c6fa/figures/summary_plot.pdf
2025-10-18 01:32:54.456847 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmp4fC4dU/file140955c86c6fa/figures
2025-10-18 01:32:54.458565 INFO::Plotting associations from most to least significant, grouped by metadata
2025-10-18 01:32:54.463393 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-10-18 01:32:55.430412 INFO::Applying z-score to standardize continuous metadata
2025-10-18 01:32:55.438218 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-10-18 01:32:55.439093 INFO::Bypass z-score application to metadata
2025-10-18 01:32:55.441506 INFO::Bypass z-score application to metadata
2025-10-18 01:32:55.458721 INFO::Determining format of input files
2025-10-18 01:32:55.459671 INFO::Input format is data samples as rows and metadata samples as rows
2025-10-18 01:32:55.460524 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-10-18 01:32:55.467335 INFO::Determining format of input files
2025-10-18 01:32:55.468313 INFO::Input format is data samples as columns and metadata samples as rows
2025-10-18 01:32:55.469584 INFO::Input format is feature_specific_covariate samples as columns
2025-10-18 01:32:55.477133 INFO::Determining format of input files
2025-10-18 01:32:55.47801 INFO::Input format is data samples as rows and metadata samples as rows
2025-10-18 01:32:55.479007 INFO::Input format is feature_specific_covariate samples as columns
2025-10-18 01:32:55.480637 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-10-18 01:32:55.481422 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-10-18 01:32:55.491907 INFO::Running selected transform method: LOG
2025-10-18 01:32:55.493025 INFO::Creating output feature tables folder
2025-10-18 01:32:55.493881 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp4fC4dU/file14095556ed4289/features/data_transformed.tsv
2025-10-18 01:32:55.497497 INFO::Running selected transform method: LOG
2025-10-18 01:32:55.498481 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp4fC4dU/file14095556ed4289/features/data_transformed.tsv
2025-10-18 01:32:55.502186 INFO::Running selected transform method: PLOG
2025-10-18 01:32:55.503866 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp4fC4dU/file14095556ed4289/features/data_transformed.tsv
2025-10-18 01:32:55.508342 INFO::Running selected transform method: NONE
2025-10-18 01:32:55.509067 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp4fC4dU/file14095556ed4289/features/data_transformed.tsv
2025-10-18 01:32:55.516057 INFO::Running the linear model component
2025-10-18 01:32:55.524467 INFO::Fitting model to feature number 1, a
2025-10-18 01:32:55.528606 INFO::Fitting model to feature number 2, b
2025-10-18 01:32:55.532522 INFO::Fitting model to feature number 3, c
2025-10-18 01:32:55.539427 INFO::Counting total values for each feature
2025-10-18 01:32:55.541014 INFO::Running the logistic model component
2025-10-18 01:32:55.549328 INFO::Fitting model to feature number 1, a
2025-10-18 01:32:55.555391 INFO::Fitting model to feature number 2, b
2025-10-18 01:32:55.561398 INFO::Fitting model to feature number 3, c
2025-10-18 01:32:55.570289 INFO::Counting total values for each feature
2025-10-18 01:32:55.572253 INFO::Re-running abundances for warn_prevalence
2025-10-18 01:32:55.573022 INFO::Running selected normalization method: TSS
2025-10-18 01:32:55.574381 INFO::Running selected transform method: LOG
2025-10-18 01:32:55.583018 INFO::Fitting model to feature number 1, a
2025-10-18 01:32:55.593133 INFO::Fitting model to feature number 2, b
2025-10-18 01:32:55.597502 INFO::Fitting model to feature number 3, c
2025-10-18 01:32:55.696091 INFO::Creating output folder
2025-10-18 01:32:55.69722 INFO::Creating fits folder
2025-10-18 01:32:55.698143 INFO::Writing residuals to file /tmp/Rtmp4fC4dU/file140955106a3220/fits/residuals_linear.rds
2025-10-18 01:32:55.699206 INFO::Writing fitted values to file /tmp/Rtmp4fC4dU/file140955106a3220/fits/fitted_linear.rds
2025-10-18 01:32:55.700314 INFO::Writing residuals to file /tmp/Rtmp4fC4dU/file140955106a3220/fits/residuals_logistic.rds
2025-10-18 01:32:55.701354 INFO::Writing fitted values to file /tmp/Rtmp4fC4dU/file140955106a3220/fits/fitted_logistic.rds
2025-10-18 01:32:55.703805 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /tmp/Rtmp4fC4dU/file140955106a3220/all_results.tsv
2025-10-18 01:32:55.705333 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/Rtmp4fC4dU/file140955106a3220/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]

[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
> 
> 
> proc.time()
   user  system elapsed 
351.632   4.701 356.339

Example timings

maaslin3.Rcheck/maaslin3-Ex.timings

nameusersystemelapsed
maaslin319.878 0.65820.539
maaslin_check_arguments0.1140.0010.115
maaslin_check_formula0.1230.0050.128
maaslin_compute_formula0.1290.0020.131
maaslin_contrast_test16.241 0.46916.710
maaslin_filter0.4490.0060.454
maaslin_fit12.469 0.10412.573
maaslin_log_arguments0.1270.0010.128
maaslin_normalize0.2800.0020.282
maaslin_plot_results43.004 0.38343.347
maaslin_plot_results_from_output43.052 0.41543.472
maaslin_process_metadata0.4420.0110.453
maaslin_read_data0.1220.0020.124
maaslin_reorder_data0.1280.0010.129
maaslin_transform0.5550.0120.567
maaslin_write_results13.313 0.19613.510
maaslin_write_results_lefse_format14.277 0.05414.332
preprocess_dna_mtx0.0040.0000.004
preprocess_taxa_mtx0.0040.0000.004