Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-10-24 12:03 -0400 (Fri, 24 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4898
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4688
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4634
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4658
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 1169/2359HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maaslin3 1.1.2  (landing page)
William Nickols
Snapshot Date: 2025-10-23 14:17 -0400 (Thu, 23 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    NA  

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: 2025-10-24 00:56:52 -0400 (Fri, 24 Oct 2025)
EndedAt: 2025-10-24 01:18:24 -0400 (Fri, 24 Oct 2025)
EllapsedTime: 1292.3 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               43.998  0.358  44.326
maaslin_plot_results_from_output   43.566  0.312  43.882
maaslin3                           21.402  0.559  21.962
maaslin_contrast_test              16.878  0.447  17.325
maaslin_write_results_lefse_format 14.610  0.133  14.743
maaslin_write_results              13.090  0.125  13.220
maaslin_fit                        12.683  0.045  12.750
* 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")
2025-10-24 01:03:05.949895 WARNING::Fitting problem for feature 50 returning NA
2025-10-24 01:03:06.030227 WARNING::Fitting problem for feature 62 returning NA
2025-10-24 01:03:06.133724 WARNING::Fitting problem for feature 74 returning NA
2025-10-24 01:03:06.15668 WARNING::Fitting problem for feature 78 returning NA
2025-10-24 01:03:06.192286 WARNING::Fitting problem for feature 84 returning NA
2025-10-24 01:03:06.269065 WARNING::Fitting problem for feature 96 returning NA
2025-10-24 01:03:06.274568 WARNING::Fitting problem for feature 97 returning NA
2025-10-24 01:03:06.286192 WARNING::Fitting problem for feature 99 returning NA
2025-10-24 01:03:06.387508 WARNING::Fitting problem for feature 114 returning NA
2025-10-24 01:03:06.392765 WARNING::Fitting problem for feature 115 returning NA
2025-10-24 01:03:06.441509 WARNING::Fitting problem for feature 123 returning NA
2025-10-24 01:03:06.481166 WARNING::Fitting problem for feature 130 returning NA
2025-10-24 01:03:06.492752 WARNING::Fitting problem for feature 132 returning NA
2025-10-24 01:03:06.540405 WARNING::Fitting problem for feature 139 returning NA
2025-10-24 01:03:06.607547 WARNING::Fitting problem for feature 150 returning NA
2025-10-24 01:03:22.139398 WARNING::Fitting problem for feature 50 returning NA
2025-10-24 01:03:22.218466 WARNING::Fitting problem for feature 62 returning NA
2025-10-24 01:03:22.324122 WARNING::Fitting problem for feature 74 returning NA
2025-10-24 01:03:22.346425 WARNING::Fitting problem for feature 78 returning NA
2025-10-24 01:03:22.381753 WARNING::Fitting problem for feature 84 returning NA
2025-10-24 01:03:22.45911 WARNING::Fitting problem for feature 96 returning NA
2025-10-24 01:03:22.464454 WARNING::Fitting problem for feature 97 returning NA
2025-10-24 01:03:22.476326 WARNING::Fitting problem for feature 99 returning NA
2025-10-24 01:03:22.571882 WARNING::Fitting problem for feature 114 returning NA
2025-10-24 01:03:22.577399 WARNING::Fitting problem for feature 115 returning NA
2025-10-24 01:03:22.626899 WARNING::Fitting problem for feature 123 returning NA
2025-10-24 01:03:22.667801 WARNING::Fitting problem for feature 130 returning NA
2025-10-24 01:03:22.679636 WARNING::Fitting problem for feature 132 returning NA
2025-10-24 01:03:22.720108 WARNING::Fitting problem for feature 139 returning NA
2025-10-24 01:03:22.791223 WARNING::Fitting problem for feature 150 returning NA
2025-10-24 01:03:46.951356 WARNING::Fitting problem for feature 50 returning NA
2025-10-24 01:03:47.028087 WARNING::Fitting problem for feature 62 returning NA
2025-10-24 01:03:47.100542 WARNING::Fitting problem for feature 74 returning NA
2025-10-24 01:03:47.121699 WARNING::Fitting problem for feature 78 returning NA
2025-10-24 01:03:47.154868 WARNING::Fitting problem for feature 84 returning NA
2025-10-24 01:03:47.230038 WARNING::Fitting problem for feature 96 returning NA
2025-10-24 01:03:47.235452 WARNING::Fitting problem for feature 97 returning NA
2025-10-24 01:03:47.247008 WARNING::Fitting problem for feature 99 returning NA
2025-10-24 01:03:47.339737 WARNING::Fitting problem for feature 114 returning NA
2025-10-24 01:03:47.345149 WARNING::Fitting problem for feature 115 returning NA
2025-10-24 01:03:47.393489 WARNING::Fitting problem for feature 123 returning NA
2025-10-24 01:03:47.433743 WARNING::Fitting problem for feature 130 returning NA
2025-10-24 01:03:47.445429 WARNING::Fitting problem for feature 132 returning NA
2025-10-24 01:03:47.485695 WARNING::Fitting problem for feature 139 returning NA
2025-10-24 01:03:47.555082 WARNING::Fitting problem for feature 150 returning NA
2025-10-24 01:04:00.553218 WARNING::Fitting problem for feature 50 returning NA
2025-10-24 01:04:00.630344 WARNING::Fitting problem for feature 62 returning NA
2025-10-24 01:04:00.728485 WARNING::Fitting problem for feature 74 returning NA
2025-10-24 01:04:00.751477 WARNING::Fitting problem for feature 78 returning NA
2025-10-24 01:04:00.787543 WARNING::Fitting problem for feature 84 returning NA
2025-10-24 01:04:00.865325 WARNING::Fitting problem for feature 96 returning NA
2025-10-24 01:04:00.870579 WARNING::Fitting problem for feature 97 returning NA
2025-10-24 01:04:00.882419 WARNING::Fitting problem for feature 99 returning NA
2025-10-24 01:04:00.979581 WARNING::Fitting problem for feature 114 returning NA
2025-10-24 01:04:00.985626 WARNING::Fitting problem for feature 115 returning NA
2025-10-24 01:04:01.037326 WARNING::Fitting problem for feature 123 returning NA
2025-10-24 01:04:01.07885 WARNING::Fitting problem for feature 130 returning NA
2025-10-24 01:04:01.091203 WARNING::Fitting problem for feature 132 returning NA
2025-10-24 01:04:01.132656 WARNING::Fitting problem for feature 139 returning NA
2025-10-24 01:04:01.201754 WARNING::Fitting problem for feature 150 returning NA
2025-10-24 01:04:01.412472 WARNING::Deleting existing residuals file: /tmp/RtmpAxiSYL/file871e634b811bd/fits/residuals_linear.rds
2025-10-24 01:04:01.473854 WARNING::Deleting existing fitted file: /tmp/RtmpAxiSYL/file871e634b811bd/fits/fitted_linear.rds
2025-10-24 01:04:01.536901 WARNING::Deleting existing residuals file: /tmp/RtmpAxiSYL/file871e634b811bd/fits/residuals_logistic.rds
2025-10-24 01:04:01.835515 WARNING::Deleting existing fitted file: /tmp/RtmpAxiSYL/file871e634b811bd/fits/fitted_logistic.rds
2025-10-24 01:04:23.70475 WARNING::Fitting problem for feature 50 returning NA
2025-10-24 01:04:23.787644 WARNING::Fitting problem for feature 62 returning NA
2025-10-24 01:04:23.86472 WARNING::Fitting problem for feature 74 returning NA
2025-10-24 01:04:23.887942 WARNING::Fitting problem for feature 78 returning NA
2025-10-24 01:04:23.922479 WARNING::Fitting problem for feature 84 returning NA
2025-10-24 01:04:23.999921 WARNING::Fitting problem for feature 96 returning NA
2025-10-24 01:04:24.005196 WARNING::Fitting problem for feature 97 returning NA
2025-10-24 01:04:24.017176 WARNING::Fitting problem for feature 99 returning NA
2025-10-24 01:04:24.224598 WARNING::Fitting problem for feature 114 returning NA
2025-10-24 01:04:24.230356 WARNING::Fitting problem for feature 115 returning NA
2025-10-24 01:04:24.282631 WARNING::Fitting problem for feature 123 returning NA
2025-10-24 01:04:24.323932 WARNING::Fitting problem for feature 130 returning NA
2025-10-24 01:04:24.33584 WARNING::Fitting problem for feature 132 returning NA
2025-10-24 01:04:24.376643 WARNING::Fitting problem for feature 139 returning NA
2025-10-24 01:04:24.447598 WARNING::Fitting problem for feature 150 returning NA
2025-10-24 01:04:37.304178 WARNING::Fitting problem for feature 50 returning NA
2025-10-24 01:04:37.384717 WARNING::Fitting problem for feature 62 returning NA
2025-10-24 01:04:37.463414 WARNING::Fitting problem for feature 74 returning NA
2025-10-24 01:04:37.486549 WARNING::Fitting problem for feature 78 returning NA
2025-10-24 01:04:37.521352 WARNING::Fitting problem for feature 84 returning NA
2025-10-24 01:04:37.59693 WARNING::Fitting problem for feature 96 returning NA
2025-10-24 01:04:37.602328 WARNING::Fitting problem for feature 97 returning NA
2025-10-24 01:04:37.614335 WARNING::Fitting problem for feature 99 returning NA
2025-10-24 01:04:37.71315 WARNING::Fitting problem for feature 114 returning NA
2025-10-24 01:04:37.718827 WARNING::Fitting problem for feature 115 returning NA
2025-10-24 01:04:37.770944 WARNING::Fitting problem for feature 123 returning NA
2025-10-24 01:04:37.841718 WARNING::Fitting problem for feature 130 returning NA
2025-10-24 01:04:37.854168 WARNING::Fitting problem for feature 132 returning NA
2025-10-24 01:04:37.896135 WARNING::Fitting problem for feature 139 returning NA
2025-10-24 01:04:37.967014 WARNING::Fitting problem for feature 150 returning NA
2025-10-24 01:04:38.171452 WARNING::Deleting existing residuals file: /tmp/RtmpAxiSYL/file871e634b811bd/fits/residuals_linear.rds
2025-10-24 01:04:38.232282 WARNING::Deleting existing fitted file: /tmp/RtmpAxiSYL/file871e634b811bd/fits/fitted_linear.rds
2025-10-24 01:04:38.295331 WARNING::Deleting existing residuals file: /tmp/RtmpAxiSYL/file871e634b811bd/fits/residuals_logistic.rds
2025-10-24 01:04:38.594743 WARNING::Deleting existing fitted file: /tmp/RtmpAxiSYL/file871e634b811bd/fits/fitted_logistic.rds
2025-10-24 01:05:00.858341 WARNING::Fitting problem for feature 50 returning NA
2025-10-24 01:05:00.935433 WARNING::Fitting problem for feature 62 returning NA
2025-10-24 01:05:01.010417 WARNING::Fitting problem for feature 74 returning NA
2025-10-24 01:05:01.03221 WARNING::Fitting problem for feature 78 returning NA
2025-10-24 01:05:01.066828 WARNING::Fitting problem for feature 84 returning NA
2025-10-24 01:05:01.143822 WARNING::Fitting problem for feature 96 returning NA
2025-10-24 01:05:01.149459 WARNING::Fitting problem for feature 97 returning NA
2025-10-24 01:05:01.161658 WARNING::Fitting problem for feature 99 returning NA
2025-10-24 01:05:01.257064 WARNING::Fitting problem for feature 114 returning NA
2025-10-24 01:05:01.26237 WARNING::Fitting problem for feature 115 returning NA
2025-10-24 01:05:01.311282 WARNING::Fitting problem for feature 123 returning NA
2025-10-24 01:05:01.351217 WARNING::Fitting problem for feature 130 returning NA
2025-10-24 01:05:01.363073 WARNING::Fitting problem for feature 132 returning NA
2025-10-24 01:05:01.405671 WARNING::Fitting problem for feature 139 returning NA
2025-10-24 01:05:01.484698 WARNING::Fitting problem for feature 150 returning NA
2025-10-24 01:05:12.317271 WARNING::Fitting problem for feature 50 returning NA
2025-10-24 01:05:12.394306 WARNING::Fitting problem for feature 62 returning NA
2025-10-24 01:05:12.50682 WARNING::Fitting problem for feature 74 returning NA
2025-10-24 01:05:12.53058 WARNING::Fitting problem for feature 78 returning NA
2025-10-24 01:05:12.566316 WARNING::Fitting problem for feature 84 returning NA
2025-10-24 01:05:12.642951 WARNING::Fitting problem for feature 96 returning NA
2025-10-24 01:05:12.64843 WARNING::Fitting problem for feature 97 returning NA
2025-10-24 01:05:12.660529 WARNING::Fitting problem for feature 99 returning NA
2025-10-24 01:05:12.757194 WARNING::Fitting problem for feature 114 returning NA
2025-10-24 01:05:12.762627 WARNING::Fitting problem for feature 115 returning NA
2025-10-24 01:05:12.812476 WARNING::Fitting problem for feature 123 returning NA
2025-10-24 01:05:12.85254 WARNING::Fitting problem for feature 130 returning NA
2025-10-24 01:05:12.864416 WARNING::Fitting problem for feature 132 returning NA
2025-10-24 01:05:12.905195 WARNING::Fitting problem for feature 139 returning NA
2025-10-24 01:05:12.975357 WARNING::Fitting problem for feature 150 returning NA
2025-10-24 01:05:13.175023 WARNING::Deleting existing residuals file: /tmp/RtmpAxiSYL/file871e634b811bd/fits/residuals_linear.rds
2025-10-24 01:05:13.235613 WARNING::Deleting existing fitted file: /tmp/RtmpAxiSYL/file871e634b811bd/fits/fitted_linear.rds
2025-10-24 01:05:13.298559 WARNING::Deleting existing residuals file: /tmp/RtmpAxiSYL/file871e634b811bd/fits/residuals_logistic.rds
2025-10-24 01:05:13.599477 WARNING::Deleting existing fitted file: /tmp/RtmpAxiSYL/file871e634b811bd/fits/fitted_logistic.rds
2025-10-24 01:05:35.178361 WARNING::Fitting problem for feature 50 returning NA
2025-10-24 01:05:35.258731 WARNING::Fitting problem for feature 62 returning NA
2025-10-24 01:05:35.337594 WARNING::Fitting problem for feature 74 returning NA
2025-10-24 01:05:35.360066 WARNING::Fitting problem for feature 78 returning NA
2025-10-24 01:05:35.41788 WARNING::Fitting problem for feature 84 returning NA
2025-10-24 01:05:35.498349 WARNING::Fitting problem for feature 96 returning NA
2025-10-24 01:05:35.503989 WARNING::Fitting problem for feature 97 returning NA
2025-10-24 01:05:35.516211 WARNING::Fitting problem for feature 99 returning NA
2025-10-24 01:05:35.618336 WARNING::Fitting problem for feature 114 returning NA
2025-10-24 01:05:35.624291 WARNING::Fitting problem for feature 115 returning NA
2025-10-24 01:05:35.677098 WARNING::Fitting problem for feature 123 returning NA
2025-10-24 01:05:35.717641 WARNING::Fitting problem for feature 130 returning NA
2025-10-24 01:05:35.729967 WARNING::Fitting problem for feature 132 returning NA
2025-10-24 01:05:35.772414 WARNING::Fitting problem for feature 139 returning NA
2025-10-24 01:05:35.845014 WARNING::Fitting problem for feature 150 returning NA
2025-10-24 01:05:47.952752 WARNING::Fitting problem for feature 50 returning NA
2025-10-24 01:05:48.028971 WARNING::Fitting problem for feature 62 returning NA
2025-10-24 01:05:48.105836 WARNING::Fitting problem for feature 74 returning NA
2025-10-24 01:05:48.128332 WARNING::Fitting problem for feature 78 returning NA
2025-10-24 01:05:48.163126 WARNING::Fitting problem for feature 84 returning NA
2025-10-24 01:05:48.239898 WARNING::Fitting problem for feature 96 returning NA
2025-10-24 01:05:48.245434 WARNING::Fitting problem for feature 97 returning NA
2025-10-24 01:05:48.257379 WARNING::Fitting problem for feature 99 returning NA
2025-10-24 01:05:48.354318 WARNING::Fitting problem for feature 114 returning NA
2025-10-24 01:05:48.359826 WARNING::Fitting problem for feature 115 returning NA
2025-10-24 01:05:48.409971 WARNING::Fitting problem for feature 123 returning NA
2025-10-24 01:05:48.450662 WARNING::Fitting problem for feature 130 returning NA
2025-10-24 01:05:48.462803 WARNING::Fitting problem for feature 132 returning NA
2025-10-24 01:05:48.503834 WARNING::Fitting problem for feature 139 returning NA
2025-10-24 01:05:48.578257 WARNING::Fitting problem for feature 150 returning NA
2025-10-24 01:06:12.975932 WARNING::Fitting problem for feature 124 returning NA
2025-10-24 01:06:22.34278 WARNING::Fitting problem for feature 124 returning NA
2025-10-24 01:06:48.747931 WARNING::Fitting problem for feature 124 returning NA
2025-10-24 01:06:57.432835 WARNING::Fitting problem for feature 124 returning NA
2025-10-24 01:06:58.060368 WARNING::Deleting existing residuals file: /tmp/RtmpAxiSYL/file871e66e80ffa8/fits/residuals_linear.rds
2025-10-24 01:06:58.121988 WARNING::Deleting existing fitted file: /tmp/RtmpAxiSYL/file871e66e80ffa8/fits/fitted_linear.rds
2025-10-24 01:06:58.161061 WARNING::Deleting existing residuals file: /tmp/RtmpAxiSYL/file871e66e80ffa8/fits/residuals_logistic.rds
2025-10-24 01:06:58.230114 WARNING::Deleting existing fitted file: /tmp/RtmpAxiSYL/file871e66e80ffa8/fits/fitted_logistic.rds
2025-10-24 01:07:21.57768 WARNING::Fitting problem for feature 124 returning NA
2025-10-24 01:07:28.135226 WARNING::Fitting problem for feature 124 returning NA
2025-10-24 01:07:28.48272 WARNING::Deleting existing residuals file: /tmp/RtmpAxiSYL/file871e66e80ffa8/fits/residuals_linear.rds
2025-10-24 01:07:28.544233 WARNING::Deleting existing fitted file: /tmp/RtmpAxiSYL/file871e66e80ffa8/fits/fitted_linear.rds
2025-10-24 01:07:28.582567 WARNING::Deleting existing residuals file: /tmp/RtmpAxiSYL/file871e66e80ffa8/fits/residuals_logistic.rds
2025-10-24 01:07:28.650683 WARNING::Deleting existing fitted file: /tmp/RtmpAxiSYL/file871e66e80ffa8/fits/fitted_logistic.rds
2025-10-24 01:07:47.37452 WARNING::Fitting problem for feature 124 returning NA
2025-10-24 01:07:53.639937 WARNING::Fitting problem for feature 124 returning NA
2025-10-24 01:07:53.97792 WARNING::Deleting existing residuals file: /tmp/RtmpAxiSYL/file871e66e80ffa8/fits/residuals_linear.rds
2025-10-24 01:07:54.039554 WARNING::Deleting existing fitted file: /tmp/RtmpAxiSYL/file871e66e80ffa8/fits/fitted_linear.rds
2025-10-24 01:07:54.078141 WARNING::Deleting existing residuals file: /tmp/RtmpAxiSYL/file871e66e80ffa8/fits/residuals_logistic.rds
2025-10-24 01:07:54.1499 WARNING::Deleting existing fitted file: /tmp/RtmpAxiSYL/file871e66e80ffa8/fits/fitted_logistic.rds
2025-10-24 01:08:12.364304 WARNING::Fitting problem for feature 50 returning NA
2025-10-24 01:08:12.440821 WARNING::Fitting problem for feature 62 returning NA
2025-10-24 01:08:12.517158 WARNING::Fitting problem for feature 74 returning NA
2025-10-24 01:08:12.539258 WARNING::Fitting problem for feature 78 returning NA
2025-10-24 01:08:12.574171 WARNING::Fitting problem for feature 84 returning NA
2025-10-24 01:08:12.65248 WARNING::Fitting problem for feature 96 returning NA
2025-10-24 01:08:12.65791 WARNING::Fitting problem for feature 97 returning NA
2025-10-24 01:08:12.669821 WARNING::Fitting problem for feature 99 returning NA
2025-10-24 01:08:12.76769 WARNING::Fitting problem for feature 114 returning NA
2025-10-24 01:08:12.773137 WARNING::Fitting problem for feature 115 returning NA
2025-10-24 01:08:12.823649 WARNING::Fitting problem for feature 123 returning NA
2025-10-24 01:08:12.863748 WARNING::Fitting problem for feature 130 returning NA
2025-10-24 01:08:12.875564 WARNING::Fitting problem for feature 132 returning NA
2025-10-24 01:08:12.916027 WARNING::Fitting problem for feature 139 returning NA
2025-10-24 01:08:12.984598 WARNING::Fitting problem for feature 150 returning NA
2025-10-24 01:08:26.173574 WARNING::Fitting problem for feature 50 returning NA
2025-10-24 01:08:26.252914 WARNING::Fitting problem for feature 62 returning NA
2025-10-24 01:08:26.336028 WARNING::Fitting problem for feature 74 returning NA
2025-10-24 01:08:26.36074 WARNING::Fitting problem for feature 78 returning NA
2025-10-24 01:08:26.399184 WARNING::Fitting problem for feature 84 returning NA
2025-10-24 01:08:26.480583 WARNING::Fitting problem for feature 96 returning NA
2025-10-24 01:08:26.486343 WARNING::Fitting problem for feature 97 returning NA
2025-10-24 01:08:26.499354 WARNING::Fitting problem for feature 99 returning NA
2025-10-24 01:08:26.602973 WARNING::Fitting problem for feature 114 returning NA
2025-10-24 01:08:26.6093 WARNING::Fitting problem for feature 115 returning NA
2025-10-24 01:08:26.704033 WARNING::Fitting problem for feature 123 returning NA
2025-10-24 01:08:26.747566 WARNING::Fitting problem for feature 130 returning NA
2025-10-24 01:08:26.760857 WARNING::Fitting problem for feature 132 returning NA
2025-10-24 01:08:26.806025 WARNING::Fitting problem for feature 139 returning NA
2025-10-24 01:08:26.877681 WARNING::Fitting problem for feature 150 returning NA
2025-10-24 01:08:27.13613 WARNING::Deleting existing residuals file: /tmp/RtmpAxiSYL/file871e66e80ffa8/fits/residuals_linear.rds
2025-10-24 01:08:27.198073 WARNING::Deleting existing fitted file: /tmp/RtmpAxiSYL/file871e66e80ffa8/fits/fitted_linear.rds
2025-10-24 01:08:27.261399 WARNING::Deleting existing residuals file: /tmp/RtmpAxiSYL/file871e66e80ffa8/fits/residuals_logistic.rds
2025-10-24 01:08:27.561309 WARNING::Deleting existing fitted file: /tmp/RtmpAxiSYL/file871e66e80ffa8/fits/fitted_logistic.rds
2025-10-24 01:08:48.089253 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-10-24 01:08:48.105295 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-10-24 01:08:48.116356 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-10-24 01:08:48.164972 ERROR::No fixed, group, or
                        ordered effects included in formula.
2025-10-24 01:08:48.180814 ERROR::Effect name not found in metadata: d
2025-10-24 01:08:48.191596 ERROR::No user formula provided
2025-10-24 01:08:48.220112 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-10-24 01:08:48.231433 ERROR::No fixed/group/ordered/
                        feature-specific effects provided.
2025-10-24 01:08:51.306645 INFO::Writing function arguments to log file
2025-10-24 01:08:51.321466 INFO::Verifying options selected are valid
2025-10-24 01:08:53.675537 INFO::Writing function arguments to log file
2025-10-24 01:08:53.687619 INFO::Verifying options selected are valid
2025-10-24 01:08:53.688716 INFO::Determining format of input files
2025-10-24 01:08:53.689696 INFO::Input format is data samples as rows and metadata samples as rows
2025-10-24 01:08:53.691984 INFO::Running selected normalization method: TSS
2025-10-24 01:08:53.693418 INFO::Creating output feature tables folder
2025-10-24 01:08:53.694364 INFO::Writing normalized data to file /tmp/RtmpAxiSYL/file871e690f52ed/features/data_norm.tsv
2025-10-24 01:08:53.6958 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-10-24 01:08:53.696682 INFO::Total samples in data: 16
2025-10-24 01:08:53.697527 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-10-24 01:08:53.698368 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-10-24 01:08:53.700249 INFO::Total filtered features: 0
2025-10-24 01:08:53.701202 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-10-24 01:08:53.702332 INFO::Total features filtered by non-zero variance filtering: 0
2025-10-24 01:08:53.703257 INFO::Filtered feature names from variance filtering:
2025-10-24 01:08:53.704134 INFO::Writing filtered data to file /tmp/RtmpAxiSYL/file871e690f52ed/features/filtered_data.tsv
2025-10-24 01:08:53.705605 INFO::Running selected transform method: LOG
2025-10-24 01:08:53.70679 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpAxiSYL/file871e690f52ed/features/data_transformed.tsv
2025-10-24 01:08:53.708421 INFO::Applying z-score to standardize continuous metadata
2025-10-24 01:08:53.713653 INFO::Running the linear model component
2025-10-24 01:08:53.727635 INFO::Fitting model to feature number 1, a
2025-10-24 01:08:53.732064 INFO::Fitting model to feature number 2, b
2025-10-24 01:08:53.736269 INFO::Fitting model to feature number 3, c
2025-10-24 01:08:53.743444 INFO::Counting total values for each feature
2025-10-24 01:08:53.745352 INFO::Running the logistic model component
2025-10-24 01:08:53.759191 INFO::Fitting model to feature number 1, a
2025-10-24 01:08:53.76598 INFO::Fitting model to feature number 2, b
2025-10-24 01:08:53.772362 INFO::Fitting model to feature number 3, c
2025-10-24 01:08:53.78139 INFO::Counting total values for each feature
2025-10-24 01:08:53.7836 INFO::Re-running abundances for warn_prevalence
2025-10-24 01:08:53.784565 INFO::Running selected normalization method: TSS
2025-10-24 01:08:53.786067 INFO::Running selected transform method: LOG
2025-10-24 01:08:53.800082 INFO::Fitting model to feature number 1, a
2025-10-24 01:08:53.804569 INFO::Fitting model to feature number 2, b
2025-10-24 01:08:53.808818 INFO::Fitting model to feature number 3, c
2025-10-24 01:08:53.896763 INFO::Creating fits folder
2025-10-24 01:08:53.897904 INFO::Writing residuals to file /tmp/RtmpAxiSYL/file871e690f52ed/fits/residuals_linear.rds
2025-10-24 01:08:53.899021 INFO::Writing fitted values to file /tmp/RtmpAxiSYL/file871e690f52ed/fits/fitted_linear.rds
2025-10-24 01:08:53.900204 INFO::Writing residuals to file /tmp/RtmpAxiSYL/file871e690f52ed/fits/residuals_logistic.rds
2025-10-24 01:08:53.901351 INFO::Writing fitted values to file /tmp/RtmpAxiSYL/file871e690f52ed/fits/fitted_logistic.rds
2025-10-24 01:08:53.90383 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /tmp/RtmpAxiSYL/file871e690f52ed/all_results.tsv
2025-10-24 01:08:53.905457 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/RtmpAxiSYL/file871e690f52ed/significant_results.tsv
2025-10-24 01:08:53.906755 INFO::Creating output figures folder
2025-10-24 01:08:53.908064 INFO::Writing summary plot of significant
                        results to file: /tmp/RtmpAxiSYL/file871e690f52ed/figures/summary_plot.pdf
2025-10-24 01:08:55.503334 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpAxiSYL/file871e690f52ed/figures
2025-10-24 01:08:55.50532 INFO::Plotting associations from most to least significant, grouped by metadata
2025-10-24 01:08:55.510459 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-10-24 01:08:56.103503 INFO::Writing summary plot of
                        significant results to file: /tmp/RtmpAxiSYL/file871e690f52ed/figures/summary_plot.pdf
2025-10-24 01:08:57.792655 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpAxiSYL/file871e690f52ed/figures
2025-10-24 01:08:57.794299 INFO::Plotting associations from most to least significant, grouped by metadata
2025-10-24 01:08:57.799529 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-10-24 01:08:58.379263 INFO::Running the linear model component
2025-10-24 01:08:58.388213 INFO::Fitting model to feature number 1, a
2025-10-24 01:08:58.392607 INFO::Fitting model to feature number 2, b
2025-10-24 01:08:58.396614 INFO::Fitting model to feature number 3, c
2025-10-24 01:08:58.403742 INFO::Counting total values for each feature
2025-10-24 01:08:58.405399 INFO::Running the logistic model component
2025-10-24 01:08:58.413671 INFO::Fitting model to feature number 1, a
2025-10-24 01:08:58.41977 INFO::Fitting model to feature number 2, b
2025-10-24 01:08:58.42552 INFO::Fitting model to feature number 3, c
2025-10-24 01:08:58.434675 INFO::Counting total values for each feature
2025-10-24 01:08:58.436664 INFO::Re-running abundances for warn_prevalence
2025-10-24 01:08:58.437441 INFO::Running selected normalization method: TSS
2025-10-24 01:08:58.438764 INFO::Running selected transform method: LOG
2025-10-24 01:08:58.447218 INFO::Fitting model to feature number 1, a
2025-10-24 01:08:58.451426 INFO::Fitting model to feature number 2, b
2025-10-24 01:08:58.455353 INFO::Fitting model to feature number 3, c
2025-10-24 01:08:58.540337 INFO::Creating output folder
2025-10-24 01:08:58.541264 INFO::Creating output figures folder
2025-10-24 01:08:58.542463 INFO::Writing summary plot of significant
                        results to file: /tmp/RtmpAxiSYL/file871e6e3684b9/figures/summary_plot.pdf
2025-10-24 01:09:00.14084 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpAxiSYL/file871e6e3684b9/figures
2025-10-24 01:09:00.142703 INFO::Plotting associations from most to least significant, grouped by metadata
2025-10-24 01:09:00.147996 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-10-24 01:09:01.136308 INFO::Applying z-score to standardize continuous metadata
2025-10-24 01:09:01.144591 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-10-24 01:09:01.145542 INFO::Bypass z-score application to metadata
2025-10-24 01:09:01.148088 INFO::Bypass z-score application to metadata
2025-10-24 01:09:01.165553 INFO::Determining format of input files
2025-10-24 01:09:01.166535 INFO::Input format is data samples as rows and metadata samples as rows
2025-10-24 01:09:01.167411 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-10-24 01:09:01.174361 INFO::Determining format of input files
2025-10-24 01:09:01.175385 INFO::Input format is data samples as columns and metadata samples as rows
2025-10-24 01:09:01.176672 INFO::Input format is feature_specific_covariate samples as columns
2025-10-24 01:09:01.184428 INFO::Determining format of input files
2025-10-24 01:09:01.185374 INFO::Input format is data samples as rows and metadata samples as rows
2025-10-24 01:09:01.186414 INFO::Input format is feature_specific_covariate samples as columns
2025-10-24 01:09:01.188079 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-10-24 01:09:01.188853 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-10-24 01:09:01.20563 INFO::Running selected transform method: LOG
2025-10-24 01:09:01.206876 INFO::Creating output feature tables folder
2025-10-24 01:09:01.207788 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpAxiSYL/file871e62df8a70e/features/data_transformed.tsv
2025-10-24 01:09:01.211893 INFO::Running selected transform method: LOG
2025-10-24 01:09:01.212976 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpAxiSYL/file871e62df8a70e/features/data_transformed.tsv
2025-10-24 01:09:01.217019 INFO::Running selected transform method: PLOG
2025-10-24 01:09:01.21866 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpAxiSYL/file871e62df8a70e/features/data_transformed.tsv
2025-10-24 01:09:01.221637 INFO::Running selected transform method: NONE
2025-10-24 01:09:01.222404 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpAxiSYL/file871e62df8a70e/features/data_transformed.tsv
2025-10-24 01:09:01.229661 INFO::Running the linear model component
2025-10-24 01:09:01.238719 INFO::Fitting model to feature number 1, a
2025-10-24 01:09:01.243215 INFO::Fitting model to feature number 2, b
2025-10-24 01:09:01.247453 INFO::Fitting model to feature number 3, c
2025-10-24 01:09:01.254755 INFO::Counting total values for each feature
2025-10-24 01:09:01.256551 INFO::Running the logistic model component
2025-10-24 01:09:01.265487 INFO::Fitting model to feature number 1, a
2025-10-24 01:09:01.27207 INFO::Fitting model to feature number 2, b
2025-10-24 01:09:01.278164 INFO::Fitting model to feature number 3, c
2025-10-24 01:09:01.287502 INFO::Counting total values for each feature
2025-10-24 01:09:01.289571 INFO::Re-running abundances for warn_prevalence
2025-10-24 01:09:01.290393 INFO::Running selected normalization method: TSS
2025-10-24 01:09:01.29179 INFO::Running selected transform method: LOG
2025-10-24 01:09:01.300801 INFO::Fitting model to feature number 1, a
2025-10-24 01:09:01.30515 INFO::Fitting model to feature number 2, b
2025-10-24 01:09:01.309293 INFO::Fitting model to feature number 3, c
2025-10-24 01:09:01.39864 INFO::Creating output folder
2025-10-24 01:09:01.399618 INFO::Creating fits folder
2025-10-24 01:09:01.400473 INFO::Writing residuals to file /tmp/RtmpAxiSYL/file871e6788ead13/fits/residuals_linear.rds
2025-10-24 01:09:01.40145 INFO::Writing fitted values to file /tmp/RtmpAxiSYL/file871e6788ead13/fits/fitted_linear.rds
2025-10-24 01:09:01.402514 INFO::Writing residuals to file /tmp/RtmpAxiSYL/file871e6788ead13/fits/residuals_logistic.rds
2025-10-24 01:09:01.403531 INFO::Writing fitted values to file /tmp/RtmpAxiSYL/file871e6788ead13/fits/fitted_logistic.rds
2025-10-24 01:09:01.406001 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /tmp/RtmpAxiSYL/file871e6788ead13/all_results.tsv
2025-10-24 01:09:01.407504 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/RtmpAxiSYL/file871e6788ead13/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]

[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
> 
> 
> proc.time()
   user  system elapsed 
361.622   4.832 366.432

Example timings

maaslin3.Rcheck/maaslin3-Ex.timings

nameusersystemelapsed
maaslin321.402 0.55921.962
maaslin_check_arguments0.1320.0000.132
maaslin_check_formula0.1370.0030.141
maaslin_compute_formula0.1360.0000.136
maaslin_contrast_test16.878 0.44717.325
maaslin_filter0.4410.0080.449
maaslin_fit12.683 0.04512.750
maaslin_log_arguments0.1280.0020.131
maaslin_normalize0.2860.0050.291
maaslin_plot_results43.998 0.35844.326
maaslin_plot_results_from_output43.566 0.31243.882
maaslin_process_metadata0.4290.0060.435
maaslin_read_data0.1220.0010.123
maaslin_reorder_data0.1260.0020.128
maaslin_transform0.5520.0090.561
maaslin_write_results13.090 0.12513.220
maaslin_write_results_lefse_format14.610 0.13314.743
preprocess_dna_mtx0.0040.0000.003
preprocess_taxa_mtx0.0040.0000.004