Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-08-30 12:04 -0400 (Sat, 30 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4615
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4541
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 1149/2320HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maaslin3 1.1.0  (landing page)
William Nickols
Snapshot Date: 2025-08-29 13:45 -0400 (Fri, 29 Aug 2025)
git_url: https://git.bioconductor.org/packages/maaslin3
git_branch: devel
git_last_commit: ed6ae28
git_last_commit_date: 2025-04-15 13:45:33 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 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: 1.1.0
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_1.1.0.tar.gz
StartedAt: 2025-08-30 00:05:45 -0400 (Sat, 30 Aug 2025)
EndedAt: 2025-08-30 00:25:06 -0400 (Sat, 30 Aug 2025)
EllapsedTime: 1161.1 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_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-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 ‘1.1.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘maaslin3’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... 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               40.194  0.263  36.242
maaslin_plot_results_from_output   39.971  0.223  35.842
maaslin_contrast_test              23.539  0.363  18.207
maaslin3                           22.974  0.415  19.161
maaslin_write_results_lefse_format 18.191  0.094  14.052
maaslin_write_results              17.780  0.231  14.730
maaslin_fit                        15.895  0.032  12.567
* 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 ‘1.1.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (maaslin3)

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")
2025-08-30 00:11:34.976626 WARNING::Fitting problem for feature 50 returning NA
2025-08-30 00:11:35.0509 WARNING::Fitting problem for feature 62 returning NA
2025-08-30 00:11:35.133421 WARNING::Fitting problem for feature 74 returning NA
2025-08-30 00:11:35.155235 WARNING::Fitting problem for feature 78 returning NA
2025-08-30 00:11:35.196915 WARNING::Fitting problem for feature 84 returning NA
2025-08-30 00:11:35.271345 WARNING::Fitting problem for feature 96 returning NA
2025-08-30 00:11:35.276599 WARNING::Fitting problem for feature 97 returning NA
2025-08-30 00:11:35.288248 WARNING::Fitting problem for feature 99 returning NA
2025-08-30 00:11:35.390458 WARNING::Fitting problem for feature 114 returning NA
2025-08-30 00:11:35.395694 WARNING::Fitting problem for feature 115 returning NA
2025-08-30 00:11:35.4443 WARNING::Fitting problem for feature 123 returning NA
2025-08-30 00:11:35.483402 WARNING::Fitting problem for feature 130 returning NA
2025-08-30 00:11:35.494891 WARNING::Fitting problem for feature 132 returning NA
2025-08-30 00:11:35.53404 WARNING::Fitting problem for feature 139 returning NA
2025-08-30 00:11:35.609595 WARNING::Fitting problem for feature 150 returning NA
2025-08-30 00:11:50.807359 WARNING::Fitting problem for feature 50 returning NA
2025-08-30 00:11:50.881281 WARNING::Fitting problem for feature 62 returning NA
2025-08-30 00:11:50.95978 WARNING::Fitting problem for feature 74 returning NA
2025-08-30 00:11:50.98385 WARNING::Fitting problem for feature 78 returning NA
2025-08-30 00:11:51.022292 WARNING::Fitting problem for feature 84 returning NA
2025-08-30 00:11:51.115077 WARNING::Fitting problem for feature 96 returning NA
2025-08-30 00:11:51.120236 WARNING::Fitting problem for feature 97 returning NA
2025-08-30 00:11:51.131801 WARNING::Fitting problem for feature 99 returning NA
2025-08-30 00:11:51.225552 WARNING::Fitting problem for feature 114 returning NA
2025-08-30 00:11:51.230686 WARNING::Fitting problem for feature 115 returning NA
2025-08-30 00:11:51.278981 WARNING::Fitting problem for feature 123 returning NA
2025-08-30 00:11:51.317854 WARNING::Fitting problem for feature 130 returning NA
2025-08-30 00:11:51.329685 WARNING::Fitting problem for feature 132 returning NA
2025-08-30 00:11:51.369036 WARNING::Fitting problem for feature 139 returning NA
2025-08-30 00:11:51.435658 WARNING::Fitting problem for feature 150 returning NA
2025-08-30 00:12:09.91997 WARNING::Fitting problem for feature 50 returning NA
2025-08-30 00:12:10.021 WARNING::Fitting problem for feature 62 returning NA
2025-08-30 00:12:10.102719 WARNING::Fitting problem for feature 74 returning NA
2025-08-30 00:12:10.12675 WARNING::Fitting problem for feature 78 returning NA
2025-08-30 00:12:10.161783 WARNING::Fitting problem for feature 84 returning NA
2025-08-30 00:12:10.238194 WARNING::Fitting problem for feature 96 returning NA
2025-08-30 00:12:10.243599 WARNING::Fitting problem for feature 97 returning NA
2025-08-30 00:12:10.255456 WARNING::Fitting problem for feature 99 returning NA
2025-08-30 00:12:10.350121 WARNING::Fitting problem for feature 114 returning NA
2025-08-30 00:12:10.355949 WARNING::Fitting problem for feature 115 returning NA
2025-08-30 00:12:10.441348 WARNING::Fitting problem for feature 123 returning NA
2025-08-30 00:12:10.487007 WARNING::Fitting problem for feature 130 returning NA
2025-08-30 00:12:10.499754 WARNING::Fitting problem for feature 132 returning NA
2025-08-30 00:12:10.543408 WARNING::Fitting problem for feature 139 returning NA
2025-08-30 00:12:10.615367 WARNING::Fitting problem for feature 150 returning NA
2025-08-30 00:12:24.827998 WARNING::Fitting problem for feature 50 returning NA
2025-08-30 00:12:24.933727 WARNING::Fitting problem for feature 62 returning NA
2025-08-30 00:12:25.016402 WARNING::Fitting problem for feature 74 returning NA
2025-08-30 00:12:25.038701 WARNING::Fitting problem for feature 78 returning NA
2025-08-30 00:12:25.073467 WARNING::Fitting problem for feature 84 returning NA
2025-08-30 00:12:25.148545 WARNING::Fitting problem for feature 96 returning NA
2025-08-30 00:12:25.153695 WARNING::Fitting problem for feature 97 returning NA
2025-08-30 00:12:25.165259 WARNING::Fitting problem for feature 99 returning NA
2025-08-30 00:12:25.260742 WARNING::Fitting problem for feature 114 returning NA
2025-08-30 00:12:25.266189 WARNING::Fitting problem for feature 115 returning NA
2025-08-30 00:12:25.316687 WARNING::Fitting problem for feature 123 returning NA
2025-08-30 00:12:25.357336 WARNING::Fitting problem for feature 130 returning NA
2025-08-30 00:12:25.369545 WARNING::Fitting problem for feature 132 returning NA
2025-08-30 00:12:25.411386 WARNING::Fitting problem for feature 139 returning NA
2025-08-30 00:12:25.482437 WARNING::Fitting problem for feature 150 returning NA
2025-08-30 00:12:25.688445 WARNING::Deleting existing residuals file: /tmp/RtmpmBI8Qb/filee401c2eb3397f/fits/residuals_linear.rds
2025-08-30 00:12:25.749312 WARNING::Deleting existing fitted file: /tmp/RtmpmBI8Qb/filee401c2eb3397f/fits/fitted_linear.rds
2025-08-30 00:12:25.8117 WARNING::Deleting existing residuals file: /tmp/RtmpmBI8Qb/filee401c2eb3397f/fits/residuals_logistic.rds
2025-08-30 00:12:26.108867 WARNING::Deleting existing fitted file: /tmp/RtmpmBI8Qb/filee401c2eb3397f/fits/fitted_logistic.rds
2025-08-30 00:12:42.83065 WARNING::Fitting problem for feature 50 returning NA
2025-08-30 00:12:42.90834 WARNING::Fitting problem for feature 62 returning NA
2025-08-30 00:12:42.987564 WARNING::Fitting problem for feature 74 returning NA
2025-08-30 00:12:43.011614 WARNING::Fitting problem for feature 78 returning NA
2025-08-30 00:12:43.050037 WARNING::Fitting problem for feature 84 returning NA
2025-08-30 00:12:43.13644 WARNING::Fitting problem for feature 96 returning NA
2025-08-30 00:12:43.14249 WARNING::Fitting problem for feature 97 returning NA
2025-08-30 00:12:43.156228 WARNING::Fitting problem for feature 99 returning NA
2025-08-30 00:12:43.265236 WARNING::Fitting problem for feature 114 returning NA
2025-08-30 00:12:43.271318 WARNING::Fitting problem for feature 115 returning NA
2025-08-30 00:12:43.327663 WARNING::Fitting problem for feature 123 returning NA
2025-08-30 00:12:43.374212 WARNING::Fitting problem for feature 130 returning NA
2025-08-30 00:12:43.387768 WARNING::Fitting problem for feature 132 returning NA
2025-08-30 00:12:43.449892 WARNING::Fitting problem for feature 139 returning NA
2025-08-30 00:12:43.518868 WARNING::Fitting problem for feature 150 returning NA
2025-08-30 00:12:55.997858 WARNING::Fitting problem for feature 50 returning NA
2025-08-30 00:12:56.074126 WARNING::Fitting problem for feature 62 returning NA
2025-08-30 00:12:56.149986 WARNING::Fitting problem for feature 74 returning NA
2025-08-30 00:12:56.172544 WARNING::Fitting problem for feature 78 returning NA
2025-08-30 00:12:56.20862 WARNING::Fitting problem for feature 84 returning NA
2025-08-30 00:12:56.289422 WARNING::Fitting problem for feature 96 returning NA
2025-08-30 00:12:56.29525 WARNING::Fitting problem for feature 97 returning NA
2025-08-30 00:12:56.308141 WARNING::Fitting problem for feature 99 returning NA
2025-08-30 00:12:56.412193 WARNING::Fitting problem for feature 114 returning NA
2025-08-30 00:12:56.418011 WARNING::Fitting problem for feature 115 returning NA
2025-08-30 00:12:56.469763 WARNING::Fitting problem for feature 123 returning NA
2025-08-30 00:12:56.511018 WARNING::Fitting problem for feature 130 returning NA
2025-08-30 00:12:56.523342 WARNING::Fitting problem for feature 132 returning NA
2025-08-30 00:12:56.565608 WARNING::Fitting problem for feature 139 returning NA
2025-08-30 00:12:56.638186 WARNING::Fitting problem for feature 150 returning NA
2025-08-30 00:12:56.879832 WARNING::Deleting existing residuals file: /tmp/RtmpmBI8Qb/filee401c2eb3397f/fits/residuals_linear.rds
2025-08-30 00:12:56.941161 WARNING::Deleting existing fitted file: /tmp/RtmpmBI8Qb/filee401c2eb3397f/fits/fitted_linear.rds
2025-08-30 00:12:57.004029 WARNING::Deleting existing residuals file: /tmp/RtmpmBI8Qb/filee401c2eb3397f/fits/residuals_logistic.rds
2025-08-30 00:12:57.306222 WARNING::Deleting existing fitted file: /tmp/RtmpmBI8Qb/filee401c2eb3397f/fits/fitted_logistic.rds
2025-08-30 00:13:13.987998 WARNING::Fitting problem for feature 50 returning NA
2025-08-30 00:13:14.069999 WARNING::Fitting problem for feature 62 returning NA
2025-08-30 00:13:14.147901 WARNING::Fitting problem for feature 74 returning NA
2025-08-30 00:13:14.170241 WARNING::Fitting problem for feature 78 returning NA
2025-08-30 00:13:14.205414 WARNING::Fitting problem for feature 84 returning NA
2025-08-30 00:13:14.284222 WARNING::Fitting problem for feature 96 returning NA
2025-08-30 00:13:14.289776 WARNING::Fitting problem for feature 97 returning NA
2025-08-30 00:13:14.302147 WARNING::Fitting problem for feature 99 returning NA
2025-08-30 00:13:14.430734 WARNING::Fitting problem for feature 114 returning NA
2025-08-30 00:13:14.436378 WARNING::Fitting problem for feature 115 returning NA
2025-08-30 00:13:14.490083 WARNING::Fitting problem for feature 123 returning NA
2025-08-30 00:13:14.530713 WARNING::Fitting problem for feature 130 returning NA
2025-08-30 00:13:14.54287 WARNING::Fitting problem for feature 132 returning NA
2025-08-30 00:13:14.584124 WARNING::Fitting problem for feature 139 returning NA
2025-08-30 00:13:14.656238 WARNING::Fitting problem for feature 150 returning NA
2025-08-30 00:13:26.613902 WARNING::Fitting problem for feature 50 returning NA
2025-08-30 00:13:26.690741 WARNING::Fitting problem for feature 62 returning NA
2025-08-30 00:13:26.768455 WARNING::Fitting problem for feature 74 returning NA
2025-08-30 00:13:26.791102 WARNING::Fitting problem for feature 78 returning NA
2025-08-30 00:13:26.827113 WARNING::Fitting problem for feature 84 returning NA
2025-08-30 00:13:26.906467 WARNING::Fitting problem for feature 96 returning NA
2025-08-30 00:13:26.911764 WARNING::Fitting problem for feature 97 returning NA
2025-08-30 00:13:26.923526 WARNING::Fitting problem for feature 99 returning NA
2025-08-30 00:13:27.019578 WARNING::Fitting problem for feature 114 returning NA
2025-08-30 00:13:27.02496 WARNING::Fitting problem for feature 115 returning NA
2025-08-30 00:13:27.074977 WARNING::Fitting problem for feature 123 returning NA
2025-08-30 00:13:27.116082 WARNING::Fitting problem for feature 130 returning NA
2025-08-30 00:13:27.128356 WARNING::Fitting problem for feature 132 returning NA
2025-08-30 00:13:27.17181 WARNING::Fitting problem for feature 139 returning NA
2025-08-30 00:13:27.245189 WARNING::Fitting problem for feature 150 returning NA
2025-08-30 00:13:27.450465 WARNING::Deleting existing residuals file: /tmp/RtmpmBI8Qb/filee401c2eb3397f/fits/residuals_linear.rds
2025-08-30 00:13:27.511807 WARNING::Deleting existing fitted file: /tmp/RtmpmBI8Qb/filee401c2eb3397f/fits/fitted_linear.rds
2025-08-30 00:13:27.574293 WARNING::Deleting existing residuals file: /tmp/RtmpmBI8Qb/filee401c2eb3397f/fits/residuals_logistic.rds
2025-08-30 00:13:27.871631 WARNING::Deleting existing fitted file: /tmp/RtmpmBI8Qb/filee401c2eb3397f/fits/fitted_logistic.rds
2025-08-30 00:13:45.39744 WARNING::Fitting problem for feature 50 returning NA
2025-08-30 00:13:45.478227 WARNING::Fitting problem for feature 62 returning NA
2025-08-30 00:13:45.554148 WARNING::Fitting problem for feature 74 returning NA
2025-08-30 00:13:45.576071 WARNING::Fitting problem for feature 78 returning NA
2025-08-30 00:13:45.611864 WARNING::Fitting problem for feature 84 returning NA
2025-08-30 00:13:45.690855 WARNING::Fitting problem for feature 96 returning NA
2025-08-30 00:13:45.696388 WARNING::Fitting problem for feature 97 returning NA
2025-08-30 00:13:45.708367 WARNING::Fitting problem for feature 99 returning NA
2025-08-30 00:13:45.807256 WARNING::Fitting problem for feature 114 returning NA
2025-08-30 00:13:45.81284 WARNING::Fitting problem for feature 115 returning NA
2025-08-30 00:13:45.864132 WARNING::Fitting problem for feature 123 returning NA
2025-08-30 00:13:45.904407 WARNING::Fitting problem for feature 130 returning NA
2025-08-30 00:13:45.916252 WARNING::Fitting problem for feature 132 returning NA
2025-08-30 00:13:45.956477 WARNING::Fitting problem for feature 139 returning NA
2025-08-30 00:13:46.027026 WARNING::Fitting problem for feature 150 returning NA
2025-08-30 00:13:58.012627 WARNING::Fitting problem for feature 50 returning NA
2025-08-30 00:13:58.093002 WARNING::Fitting problem for feature 62 returning NA
2025-08-30 00:13:58.16884 WARNING::Fitting problem for feature 74 returning NA
2025-08-30 00:13:58.19082 WARNING::Fitting problem for feature 78 returning NA
2025-08-30 00:13:58.225565 WARNING::Fitting problem for feature 84 returning NA
2025-08-30 00:13:58.302827 WARNING::Fitting problem for feature 96 returning NA
2025-08-30 00:13:58.30832 WARNING::Fitting problem for feature 97 returning NA
2025-08-30 00:13:58.320466 WARNING::Fitting problem for feature 99 returning NA
2025-08-30 00:13:58.418598 WARNING::Fitting problem for feature 114 returning NA
2025-08-30 00:13:58.424236 WARNING::Fitting problem for feature 115 returning NA
2025-08-30 00:13:58.477717 WARNING::Fitting problem for feature 123 returning NA
2025-08-30 00:13:58.522263 WARNING::Fitting problem for feature 130 returning NA
2025-08-30 00:13:58.535593 WARNING::Fitting problem for feature 132 returning NA
2025-08-30 00:13:58.580856 WARNING::Fitting problem for feature 139 returning NA
2025-08-30 00:13:58.658207 WARNING::Fitting problem for feature 150 returning NA
2025-08-30 00:14:17.688977 WARNING::Fitting problem for feature 124 returning NA
2025-08-30 00:14:27.633163 WARNING::Fitting problem for feature 124 returning NA
2025-08-30 00:14:47.673317 WARNING::Fitting problem for feature 124 returning NA
2025-08-30 00:14:57.512342 WARNING::Fitting problem for feature 124 returning NA
2025-08-30 00:14:58.191681 WARNING::Deleting existing residuals file: /tmp/RtmpmBI8Qb/filee401cf3d95ad/fits/residuals_linear.rds
2025-08-30 00:14:58.25343 WARNING::Deleting existing fitted file: /tmp/RtmpmBI8Qb/filee401cf3d95ad/fits/fitted_linear.rds
2025-08-30 00:14:58.29227 WARNING::Deleting existing residuals file: /tmp/RtmpmBI8Qb/filee401cf3d95ad/fits/residuals_logistic.rds
2025-08-30 00:14:58.360949 WARNING::Deleting existing fitted file: /tmp/RtmpmBI8Qb/filee401cf3d95ad/fits/fitted_logistic.rds
2025-08-30 00:15:16.26836 WARNING::Fitting problem for feature 124 returning NA
2025-08-30 00:15:21.508501 WARNING::Fitting problem for feature 124 returning NA
2025-08-30 00:15:21.826284 WARNING::Deleting existing residuals file: /tmp/RtmpmBI8Qb/filee401cf3d95ad/fits/residuals_linear.rds
2025-08-30 00:15:21.887805 WARNING::Deleting existing fitted file: /tmp/RtmpmBI8Qb/filee401cf3d95ad/fits/fitted_linear.rds
2025-08-30 00:15:21.925977 WARNING::Deleting existing residuals file: /tmp/RtmpmBI8Qb/filee401cf3d95ad/fits/residuals_logistic.rds
2025-08-30 00:15:21.994054 WARNING::Deleting existing fitted file: /tmp/RtmpmBI8Qb/filee401cf3d95ad/fits/fitted_logistic.rds
2025-08-30 00:15:38.535702 WARNING::Fitting problem for feature 124 returning NA
2025-08-30 00:15:43.788415 WARNING::Fitting problem for feature 124 returning NA
2025-08-30 00:15:44.098722 WARNING::Deleting existing residuals file: /tmp/RtmpmBI8Qb/filee401cf3d95ad/fits/residuals_linear.rds
2025-08-30 00:15:44.161034 WARNING::Deleting existing fitted file: /tmp/RtmpmBI8Qb/filee401cf3d95ad/fits/fitted_linear.rds
2025-08-30 00:15:44.200851 WARNING::Deleting existing residuals file: /tmp/RtmpmBI8Qb/filee401cf3d95ad/fits/residuals_logistic.rds
2025-08-30 00:15:44.271532 WARNING::Deleting existing fitted file: /tmp/RtmpmBI8Qb/filee401cf3d95ad/fits/fitted_logistic.rds
2025-08-30 00:15:59.432231 WARNING::Fitting problem for feature 50 returning NA
2025-08-30 00:15:59.513928 WARNING::Fitting problem for feature 62 returning NA
2025-08-30 00:15:59.597111 WARNING::Fitting problem for feature 74 returning NA
2025-08-30 00:15:59.62192 WARNING::Fitting problem for feature 78 returning NA
2025-08-30 00:15:59.659084 WARNING::Fitting problem for feature 84 returning NA
2025-08-30 00:15:59.744701 WARNING::Fitting problem for feature 96 returning NA
2025-08-30 00:15:59.750393 WARNING::Fitting problem for feature 97 returning NA
2025-08-30 00:15:59.763431 WARNING::Fitting problem for feature 99 returning NA
2025-08-30 00:15:59.865527 WARNING::Fitting problem for feature 114 returning NA
2025-08-30 00:15:59.871068 WARNING::Fitting problem for feature 115 returning NA
2025-08-30 00:15:59.923871 WARNING::Fitting problem for feature 123 returning NA
2025-08-30 00:15:59.967069 WARNING::Fitting problem for feature 130 returning NA
2025-08-30 00:15:59.979599 WARNING::Fitting problem for feature 132 returning NA
2025-08-30 00:16:00.02512 WARNING::Fitting problem for feature 139 returning NA
2025-08-30 00:16:00.10232 WARNING::Fitting problem for feature 150 returning NA
2025-08-30 00:16:11.967525 WARNING::Fitting problem for feature 50 returning NA
2025-08-30 00:16:12.045761 WARNING::Fitting problem for feature 62 returning NA
2025-08-30 00:16:12.121641 WARNING::Fitting problem for feature 74 returning NA
2025-08-30 00:16:12.143991 WARNING::Fitting problem for feature 78 returning NA
2025-08-30 00:16:12.179563 WARNING::Fitting problem for feature 84 returning NA
2025-08-30 00:16:12.258378 WARNING::Fitting problem for feature 96 returning NA
2025-08-30 00:16:12.263787 WARNING::Fitting problem for feature 97 returning NA
2025-08-30 00:16:12.27581 WARNING::Fitting problem for feature 99 returning NA
2025-08-30 00:16:12.373071 WARNING::Fitting problem for feature 114 returning NA
2025-08-30 00:16:12.378637 WARNING::Fitting problem for feature 115 returning NA
2025-08-30 00:16:12.429167 WARNING::Fitting problem for feature 123 returning NA
2025-08-30 00:16:12.47102 WARNING::Fitting problem for feature 130 returning NA
2025-08-30 00:16:12.483257 WARNING::Fitting problem for feature 132 returning NA
2025-08-30 00:16:12.524221 WARNING::Fitting problem for feature 139 returning NA
2025-08-30 00:16:12.595737 WARNING::Fitting problem for feature 150 returning NA
2025-08-30 00:16:12.906391 WARNING::Deleting existing residuals file: /tmp/RtmpmBI8Qb/filee401cf3d95ad/fits/residuals_linear.rds
2025-08-30 00:16:12.967078 WARNING::Deleting existing fitted file: /tmp/RtmpmBI8Qb/filee401cf3d95ad/fits/fitted_linear.rds
2025-08-30 00:16:13.029807 WARNING::Deleting existing residuals file: /tmp/RtmpmBI8Qb/filee401cf3d95ad/fits/residuals_logistic.rds
2025-08-30 00:16:13.327339 WARNING::Deleting existing fitted file: /tmp/RtmpmBI8Qb/filee401cf3d95ad/fits/fitted_logistic.rds
2025-08-30 00:16:29.148572 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-08-30 00:16:29.165959 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-08-30 00:16:29.177467 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-08-30 00:16:29.230556 ERROR::No fixed, group, or
                        ordered effects included in formula.
2025-08-30 00:16:29.247499 ERROR::Effect name not found in metadata: d
2025-08-30 00:16:29.258801 ERROR::No user formula provided
2025-08-30 00:16:29.288543 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-08-30 00:16:29.299891 ERROR::No fixed/group/ordered/
                        feature-specific effects provided.
2025-08-30 00:16:32.18962 INFO::Writing function arguments to log file
2025-08-30 00:16:32.203676 INFO::Verifying options selected are valid
2025-08-30 00:16:34.034408 INFO::Writing function arguments to log file
2025-08-30 00:16:34.046881 INFO::Verifying options selected are valid
2025-08-30 00:16:34.04808 INFO::Determining format of input files
2025-08-30 00:16:34.049084 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-30 00:16:34.051468 INFO::Running selected normalization method: TSS
2025-08-30 00:16:34.052962 INFO::Creating output feature tables folder
2025-08-30 00:16:34.053936 INFO::Writing normalized data to file /tmp/RtmpmBI8Qb/filee401c13f6ed4/features/data_norm.tsv
2025-08-30 00:16:34.05546 INFO::Filter data based on min abundance and min prevalence
2025-08-30 00:16:34.056377 INFO::Total samples in data: 16
2025-08-30 00:16:34.057248 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-08-30 00:16:34.059145 INFO::Total filtered features: 0
2025-08-30 00:16:34.060114 INFO::Filtered feature names from abundance and prevalence filtering:
2025-08-30 00:16:34.061309 INFO::Total features filtered by non-zero variance filtering: 0
2025-08-30 00:16:34.062283 INFO::Filtered feature names from variance filtering:
2025-08-30 00:16:34.063162 INFO::Writing filtered data to file /tmp/RtmpmBI8Qb/filee401c13f6ed4/features/filtered_data.tsv
2025-08-30 00:16:34.064705 INFO::Running selected transform method: LOG
2025-08-30 00:16:34.065912 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpmBI8Qb/filee401c13f6ed4/features/data_transformed.tsv
2025-08-30 00:16:34.0676 INFO::Applying z-score to standardize continuous metadata
2025-08-30 00:16:34.073351 INFO::Running the linear model component
2025-08-30 00:16:34.087833 INFO::Fitting model to feature number 1, a
2025-08-30 00:16:34.092401 INFO::Fitting model to feature number 2, b
2025-08-30 00:16:34.096696 INFO::Fitting model to feature number 3, c
2025-08-30 00:16:34.103938 INFO::Counting total values for each feature
2025-08-30 00:16:34.105781 INFO::Running the logistic model component
2025-08-30 00:16:34.119977 INFO::Fitting model to feature number 1, a
2025-08-30 00:16:34.126862 INFO::Fitting model to feature number 2, b
2025-08-30 00:16:34.133231 INFO::Fitting model to feature number 3, c
2025-08-30 00:16:34.142359 INFO::Counting total values for each feature
2025-08-30 00:16:34.14461 INFO::Re-running abundances for warn_prevalence
2025-08-30 00:16:34.145594 INFO::Running selected normalization method: TSS
2025-08-30 00:16:34.14708 INFO::Running selected transform method: LOG
2025-08-30 00:16:34.16111 INFO::Fitting model to feature number 1, a
2025-08-30 00:16:34.165563 INFO::Fitting model to feature number 2, b
2025-08-30 00:16:34.17 INFO::Fitting model to feature number 3, c
2025-08-30 00:16:34.258924 INFO::Creating fits folder
2025-08-30 00:16:34.260092 INFO::Writing residuals to file /tmp/RtmpmBI8Qb/filee401c13f6ed4/fits/residuals_linear.rds
2025-08-30 00:16:34.261261 INFO::Writing fitted values to file /tmp/RtmpmBI8Qb/filee401c13f6ed4/fits/fitted_linear.rds
2025-08-30 00:16:34.26251 INFO::Writing residuals to file /tmp/RtmpmBI8Qb/filee401c13f6ed4/fits/residuals_logistic.rds
2025-08-30 00:16:34.263715 INFO::Writing fitted values to file /tmp/RtmpmBI8Qb/filee401c13f6ed4/fits/fitted_logistic.rds
2025-08-30 00:16:34.266449 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /tmp/RtmpmBI8Qb/filee401c13f6ed4/all_results.tsv
2025-08-30 00:16:34.268076 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/RtmpmBI8Qb/filee401c13f6ed4/significant_results.tsv
2025-08-30 00:16:34.2694 INFO::Creating output figures folder
2025-08-30 00:16:34.270733 INFO::Writing summary plot of significant
                        results to file: /tmp/RtmpmBI8Qb/filee401c13f6ed4/figures/summary_plot.pdf
2025-08-30 00:16:35.557666 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpmBI8Qb/filee401c13f6ed4/figures
2025-08-30 00:16:35.559863 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-30 00:16:35.565233 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-30 00:16:35.971755 INFO::Writing summary plot of
                        significant results to file: /tmp/RtmpmBI8Qb/filee401c13f6ed4/figures/summary_plot.pdf
2025-08-30 00:16:37.250835 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpmBI8Qb/filee401c13f6ed4/figures
2025-08-30 00:16:37.252438 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-30 00:16:37.257419 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-30 00:16:37.650122 INFO::Running the linear model component
2025-08-30 00:16:37.659078 INFO::Fitting model to feature number 1, a
2025-08-30 00:16:37.663548 INFO::Fitting model to feature number 2, b
2025-08-30 00:16:37.667658 INFO::Fitting model to feature number 3, c
2025-08-30 00:16:37.674691 INFO::Counting total values for each feature
2025-08-30 00:16:37.676418 INFO::Running the logistic model component
2025-08-30 00:16:37.684891 INFO::Fitting model to feature number 1, a
2025-08-30 00:16:37.691201 INFO::Fitting model to feature number 2, b
2025-08-30 00:16:37.697287 INFO::Fitting model to feature number 3, c
2025-08-30 00:16:37.706313 INFO::Counting total values for each feature
2025-08-30 00:16:37.708469 INFO::Re-running abundances for warn_prevalence
2025-08-30 00:16:37.709333 INFO::Running selected normalization method: TSS
2025-08-30 00:16:37.710724 INFO::Running selected transform method: LOG
2025-08-30 00:16:37.719315 INFO::Fitting model to feature number 1, a
2025-08-30 00:16:37.723455 INFO::Fitting model to feature number 2, b
2025-08-30 00:16:37.727365 INFO::Fitting model to feature number 3, c
2025-08-30 00:16:37.813498 INFO::Creating output folder
2025-08-30 00:16:37.814443 INFO::Creating output figures folder
2025-08-30 00:16:37.815665 INFO::Writing summary plot of significant
                        results to file: /tmp/RtmpmBI8Qb/filee401c34db90ab/figures/summary_plot.pdf
2025-08-30 00:16:39.062618 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpmBI8Qb/filee401c34db90ab/figures
2025-08-30 00:16:39.064439 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-30 00:16:39.069326 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-30 00:16:39.903536 INFO::Applying z-score to standardize continuous metadata
2025-08-30 00:16:39.911119 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-08-30 00:16:39.912019 INFO::Bypass z-score application to metadata
2025-08-30 00:16:39.914393 INFO::Bypass z-score application to metadata
2025-08-30 00:16:39.931783 INFO::Determining format of input files
2025-08-30 00:16:39.932822 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-30 00:16:39.933693 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-08-30 00:16:39.940599 INFO::Determining format of input files
2025-08-30 00:16:39.941571 INFO::Input format is data samples as columns and metadata samples as rows
2025-08-30 00:16:39.942835 INFO::Input format is feature_specific_covariate samples as columns
2025-08-30 00:16:39.950326 INFO::Determining format of input files
2025-08-30 00:16:39.951223 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-30 00:16:39.952203 INFO::Input format is feature_specific_covariate samples as columns
2025-08-30 00:16:39.953822 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-08-30 00:16:39.954576 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-08-30 00:16:39.964891 INFO::Running selected transform method: LOG
2025-08-30 00:16:39.966006 INFO::Creating output feature tables folder
2025-08-30 00:16:39.966844 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpmBI8Qb/filee401c465f9369/features/data_transformed.tsv
2025-08-30 00:16:39.970651 INFO::Running selected transform method: LOG
2025-08-30 00:16:39.971668 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpmBI8Qb/filee401c465f9369/features/data_transformed.tsv
2025-08-30 00:16:39.975682 INFO::Running selected transform method: PLOG
2025-08-30 00:16:39.977214 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpmBI8Qb/filee401c465f9369/features/data_transformed.tsv
2025-08-30 00:16:39.979977 INFO::Running selected transform method: NONE
2025-08-30 00:16:39.980716 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpmBI8Qb/filee401c465f9369/features/data_transformed.tsv
2025-08-30 00:16:39.987726 INFO::Running the linear model component
2025-08-30 00:16:39.996631 INFO::Fitting model to feature number 1, a
2025-08-30 00:16:40.001197 INFO::Fitting model to feature number 2, b
2025-08-30 00:16:40.005352 INFO::Fitting model to feature number 3, c
2025-08-30 00:16:40.012541 INFO::Counting total values for each feature
2025-08-30 00:16:40.014248 INFO::Running the logistic model component
2025-08-30 00:16:40.022712 INFO::Fitting model to feature number 1, a
2025-08-30 00:16:40.028931 INFO::Fitting model to feature number 2, b
2025-08-30 00:16:40.03485 INFO::Fitting model to feature number 3, c
2025-08-30 00:16:40.043463 INFO::Counting total values for each feature
2025-08-30 00:16:40.045431 INFO::Re-running abundances for warn_prevalence
2025-08-30 00:16:40.046194 INFO::Running selected normalization method: TSS
2025-08-30 00:16:40.047505 INFO::Running selected transform method: LOG
2025-08-30 00:16:40.055906 INFO::Fitting model to feature number 1, a
2025-08-30 00:16:40.059923 INFO::Fitting model to feature number 2, b
2025-08-30 00:16:40.063741 INFO::Fitting model to feature number 3, c
2025-08-30 00:16:40.148092 INFO::Creating output folder
2025-08-30 00:16:40.149048 INFO::Creating fits folder
2025-08-30 00:16:40.149879 INFO::Writing residuals to file /tmp/RtmpmBI8Qb/filee401c1464741c/fits/residuals_linear.rds
2025-08-30 00:16:40.150831 INFO::Writing fitted values to file /tmp/RtmpmBI8Qb/filee401c1464741c/fits/fitted_linear.rds
2025-08-30 00:16:40.151926 INFO::Writing residuals to file /tmp/RtmpmBI8Qb/filee401c1464741c/fits/residuals_logistic.rds
2025-08-30 00:16:40.152987 INFO::Writing fitted values to file /tmp/RtmpmBI8Qb/filee401c1464741c/fits/fitted_logistic.rds
2025-08-30 00:16:40.15542 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /tmp/RtmpmBI8Qb/filee401c1464741c/all_results.tsv
2025-08-30 00:16:40.156852 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/RtmpmBI8Qb/filee401c1464741c/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]

[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
> 
> 
> proc.time()
   user  system elapsed 
362.554   4.305 315.979

Example timings

maaslin3.Rcheck/maaslin3-Ex.timings

nameusersystemelapsed
maaslin322.974 0.41519.161
maaslin_check_arguments0.1410.0000.142
maaslin_check_formula0.1320.0020.134
maaslin_compute_formula0.1320.0020.134
maaslin_contrast_test23.539 0.36318.207
maaslin_filter0.4960.0050.500
maaslin_fit15.895 0.03212.567
maaslin_log_arguments0.1310.0030.134
maaslin_normalize0.2660.0060.272
maaslin_plot_results40.194 0.26336.242
maaslin_plot_results_from_output39.971 0.22335.842
maaslin_process_metadata0.4410.0040.445
maaslin_read_data0.1310.0030.134
maaslin_reorder_data0.1330.0010.134
maaslin_transform0.5640.0070.571
maaslin_write_results17.780 0.23114.730
maaslin_write_results_lefse_format18.191 0.09414.052
preprocess_dna_mtx0.0030.0000.004
preprocess_taxa_mtx0.0030.0000.004