Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-09-11 12:03 -0400 (Thu, 11 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4539
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4474
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4519
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4544
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 1150/2322HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maaslin3 1.1.0  (landing page)
William Nickols
Snapshot Date: 2025-09-10 13:45 -0400 (Wed, 10 Sep 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: 2025-09-11 02:03:16 -0400 (Thu, 11 Sep 2025)
EndedAt: 2025-09-11 02:23:10 -0400 (Thu, 11 Sep 2025)
EllapsedTime: 1194.4 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 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 ‘1.1.0’
* 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               36.787  0.212  36.960
maaslin_plot_results_from_output   36.059  0.270  36.333
maaslin3                           20.488  0.483  20.980
maaslin_contrast_test              18.527  0.338  18.868
maaslin_write_results              14.406  0.250  14.658
maaslin_write_results_lefse_format 14.272  0.070  14.344
maaslin_fit                        12.842  0.142  12.984
* 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 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")
2025-09-11 02:09:26.99377 WARNING::Fitting problem for feature 50 returning NA
2025-09-11 02:09:27.071134 WARNING::Fitting problem for feature 62 returning NA
2025-09-11 02:09:27.157959 WARNING::Fitting problem for feature 74 returning NA
2025-09-11 02:09:27.181545 WARNING::Fitting problem for feature 78 returning NA
2025-09-11 02:09:27.227247 WARNING::Fitting problem for feature 84 returning NA
2025-09-11 02:09:27.303389 WARNING::Fitting problem for feature 96 returning NA
2025-09-11 02:09:27.308623 WARNING::Fitting problem for feature 97 returning NA
2025-09-11 02:09:27.320188 WARNING::Fitting problem for feature 99 returning NA
2025-09-11 02:09:27.424212 WARNING::Fitting problem for feature 114 returning NA
2025-09-11 02:09:27.42961 WARNING::Fitting problem for feature 115 returning NA
2025-09-11 02:09:27.479481 WARNING::Fitting problem for feature 123 returning NA
2025-09-11 02:09:27.519907 WARNING::Fitting problem for feature 130 returning NA
2025-09-11 02:09:27.531775 WARNING::Fitting problem for feature 132 returning NA
2025-09-11 02:09:27.571928 WARNING::Fitting problem for feature 139 returning NA
2025-09-11 02:09:27.64911 WARNING::Fitting problem for feature 150 returning NA
2025-09-11 02:09:43.067603 WARNING::Fitting problem for feature 50 returning NA
2025-09-11 02:09:43.155492 WARNING::Fitting problem for feature 62 returning NA
2025-09-11 02:09:43.257419 WARNING::Fitting problem for feature 74 returning NA
2025-09-11 02:09:43.279947 WARNING::Fitting problem for feature 78 returning NA
2025-09-11 02:09:43.317163 WARNING::Fitting problem for feature 84 returning NA
2025-09-11 02:09:43.394271 WARNING::Fitting problem for feature 96 returning NA
2025-09-11 02:09:43.399582 WARNING::Fitting problem for feature 97 returning NA
2025-09-11 02:09:43.411442 WARNING::Fitting problem for feature 99 returning NA
2025-09-11 02:09:43.505819 WARNING::Fitting problem for feature 114 returning NA
2025-09-11 02:09:43.511218 WARNING::Fitting problem for feature 115 returning NA
2025-09-11 02:09:43.561982 WARNING::Fitting problem for feature 123 returning NA
2025-09-11 02:09:43.602118 WARNING::Fitting problem for feature 130 returning NA
2025-09-11 02:09:43.61407 WARNING::Fitting problem for feature 132 returning NA
2025-09-11 02:09:43.654113 WARNING::Fitting problem for feature 139 returning NA
2025-09-11 02:09:43.72009 WARNING::Fitting problem for feature 150 returning NA
2025-09-11 02:10:02.350192 WARNING::Fitting problem for feature 50 returning NA
2025-09-11 02:10:02.4322 WARNING::Fitting problem for feature 62 returning NA
2025-09-11 02:10:02.50835 WARNING::Fitting problem for feature 74 returning NA
2025-09-11 02:10:02.53103 WARNING::Fitting problem for feature 78 returning NA
2025-09-11 02:10:02.56641 WARNING::Fitting problem for feature 84 returning NA
2025-09-11 02:10:02.645417 WARNING::Fitting problem for feature 96 returning NA
2025-09-11 02:10:02.650996 WARNING::Fitting problem for feature 97 returning NA
2025-09-11 02:10:02.66351 WARNING::Fitting problem for feature 99 returning NA
2025-09-11 02:10:02.762269 WARNING::Fitting problem for feature 114 returning NA
2025-09-11 02:10:02.767875 WARNING::Fitting problem for feature 115 returning NA
2025-09-11 02:10:03.771259 WARNING::Fitting problem for feature 123 returning NA
2025-09-11 02:10:03.813212 WARNING::Fitting problem for feature 130 returning NA
2025-09-11 02:10:03.825121 WARNING::Fitting problem for feature 132 returning NA
2025-09-11 02:10:03.866944 WARNING::Fitting problem for feature 139 returning NA
2025-09-11 02:10:03.939165 WARNING::Fitting problem for feature 150 returning NA
2025-09-11 02:10:17.580445 WARNING::Fitting problem for feature 50 returning NA
2025-09-11 02:10:17.664032 WARNING::Fitting problem for feature 62 returning NA
2025-09-11 02:10:17.741135 WARNING::Fitting problem for feature 74 returning NA
2025-09-11 02:10:17.762654 WARNING::Fitting problem for feature 78 returning NA
2025-09-11 02:10:17.796616 WARNING::Fitting problem for feature 84 returning NA
2025-09-11 02:10:17.87327 WARNING::Fitting problem for feature 96 returning NA
2025-09-11 02:10:17.878832 WARNING::Fitting problem for feature 97 returning NA
2025-09-11 02:10:17.890897 WARNING::Fitting problem for feature 99 returning NA
2025-09-11 02:10:17.98924 WARNING::Fitting problem for feature 114 returning NA
2025-09-11 02:10:17.994947 WARNING::Fitting problem for feature 115 returning NA
2025-09-11 02:10:18.046265 WARNING::Fitting problem for feature 123 returning NA
2025-09-11 02:10:18.087798 WARNING::Fitting problem for feature 130 returning NA
2025-09-11 02:10:18.099919 WARNING::Fitting problem for feature 132 returning NA
2025-09-11 02:10:18.141699 WARNING::Fitting problem for feature 139 returning NA
2025-09-11 02:10:18.21224 WARNING::Fitting problem for feature 150 returning NA
2025-09-11 02:10:18.427849 WARNING::Deleting existing residuals file: /tmp/RtmpojcQrH/file2edd943840cc9e/fits/residuals_linear.rds
2025-09-11 02:10:18.488872 WARNING::Deleting existing fitted file: /tmp/RtmpojcQrH/file2edd943840cc9e/fits/fitted_linear.rds
2025-09-11 02:10:18.551379 WARNING::Deleting existing residuals file: /tmp/RtmpojcQrH/file2edd943840cc9e/fits/residuals_logistic.rds
2025-09-11 02:10:18.850252 WARNING::Deleting existing fitted file: /tmp/RtmpojcQrH/file2edd943840cc9e/fits/fitted_logistic.rds
2025-09-11 02:10:35.700443 WARNING::Fitting problem for feature 50 returning NA
2025-09-11 02:10:35.78144 WARNING::Fitting problem for feature 62 returning NA
2025-09-11 02:10:35.86034 WARNING::Fitting problem for feature 74 returning NA
2025-09-11 02:10:35.882975 WARNING::Fitting problem for feature 78 returning NA
2025-09-11 02:10:35.920377 WARNING::Fitting problem for feature 84 returning NA
2025-09-11 02:10:35.998107 WARNING::Fitting problem for feature 96 returning NA
2025-09-11 02:10:36.003682 WARNING::Fitting problem for feature 97 returning NA
2025-09-11 02:10:36.015923 WARNING::Fitting problem for feature 99 returning NA
2025-09-11 02:10:36.114444 WARNING::Fitting problem for feature 114 returning NA
2025-09-11 02:10:36.120225 WARNING::Fitting problem for feature 115 returning NA
2025-09-11 02:10:36.170738 WARNING::Fitting problem for feature 123 returning NA
2025-09-11 02:10:36.212418 WARNING::Fitting problem for feature 130 returning NA
2025-09-11 02:10:36.225305 WARNING::Fitting problem for feature 132 returning NA
2025-09-11 02:10:36.268338 WARNING::Fitting problem for feature 139 returning NA
2025-09-11 02:10:36.342832 WARNING::Fitting problem for feature 150 returning NA
2025-09-11 02:10:48.824533 WARNING::Fitting problem for feature 50 returning NA
2025-09-11 02:10:48.899307 WARNING::Fitting problem for feature 62 returning NA
2025-09-11 02:10:48.973749 WARNING::Fitting problem for feature 74 returning NA
2025-09-11 02:10:48.995469 WARNING::Fitting problem for feature 78 returning NA
2025-09-11 02:10:49.029866 WARNING::Fitting problem for feature 84 returning NA
2025-09-11 02:10:49.108059 WARNING::Fitting problem for feature 96 returning NA
2025-09-11 02:10:49.113863 WARNING::Fitting problem for feature 97 returning NA
2025-09-11 02:10:49.126053 WARNING::Fitting problem for feature 99 returning NA
2025-09-11 02:10:49.22442 WARNING::Fitting problem for feature 114 returning NA
2025-09-11 02:10:49.229879 WARNING::Fitting problem for feature 115 returning NA
2025-09-11 02:10:49.280571 WARNING::Fitting problem for feature 123 returning NA
2025-09-11 02:10:49.321667 WARNING::Fitting problem for feature 130 returning NA
2025-09-11 02:10:49.336053 WARNING::Fitting problem for feature 132 returning NA
2025-09-11 02:10:49.386902 WARNING::Fitting problem for feature 139 returning NA
2025-09-11 02:10:49.494332 WARNING::Fitting problem for feature 150 returning NA
2025-09-11 02:10:49.689303 WARNING::Deleting existing residuals file: /tmp/RtmpojcQrH/file2edd943840cc9e/fits/residuals_linear.rds
2025-09-11 02:10:49.749655 WARNING::Deleting existing fitted file: /tmp/RtmpojcQrH/file2edd943840cc9e/fits/fitted_linear.rds
2025-09-11 02:10:49.811954 WARNING::Deleting existing residuals file: /tmp/RtmpojcQrH/file2edd943840cc9e/fits/residuals_logistic.rds
2025-09-11 02:10:50.110002 WARNING::Deleting existing fitted file: /tmp/RtmpojcQrH/file2edd943840cc9e/fits/fitted_logistic.rds
2025-09-11 02:11:06.929551 WARNING::Fitting problem for feature 50 returning NA
2025-09-11 02:11:07.01279 WARNING::Fitting problem for feature 62 returning NA
2025-09-11 02:11:07.126804 WARNING::Fitting problem for feature 74 returning NA
2025-09-11 02:11:07.149762 WARNING::Fitting problem for feature 78 returning NA
2025-09-11 02:11:07.185887 WARNING::Fitting problem for feature 84 returning NA
2025-09-11 02:11:07.266578 WARNING::Fitting problem for feature 96 returning NA
2025-09-11 02:11:07.272832 WARNING::Fitting problem for feature 97 returning NA
2025-09-11 02:11:07.286433 WARNING::Fitting problem for feature 99 returning NA
2025-09-11 02:11:07.390769 WARNING::Fitting problem for feature 114 returning NA
2025-09-11 02:11:07.396434 WARNING::Fitting problem for feature 115 returning NA
2025-09-11 02:11:07.44782 WARNING::Fitting problem for feature 123 returning NA
2025-09-11 02:11:07.490992 WARNING::Fitting problem for feature 130 returning NA
2025-09-11 02:11:07.504499 WARNING::Fitting problem for feature 132 returning NA
2025-09-11 02:11:07.551512 WARNING::Fitting problem for feature 139 returning NA
2025-09-11 02:11:07.622882 WARNING::Fitting problem for feature 150 returning NA
2025-09-11 02:11:19.745528 WARNING::Fitting problem for feature 50 returning NA
2025-09-11 02:11:19.821132 WARNING::Fitting problem for feature 62 returning NA
2025-09-11 02:11:19.897519 WARNING::Fitting problem for feature 74 returning NA
2025-09-11 02:11:19.920012 WARNING::Fitting problem for feature 78 returning NA
2025-09-11 02:11:19.955117 WARNING::Fitting problem for feature 84 returning NA
2025-09-11 02:11:20.032222 WARNING::Fitting problem for feature 96 returning NA
2025-09-11 02:11:20.038099 WARNING::Fitting problem for feature 97 returning NA
2025-09-11 02:11:20.05067 WARNING::Fitting problem for feature 99 returning NA
2025-09-11 02:11:20.150238 WARNING::Fitting problem for feature 114 returning NA
2025-09-11 02:11:20.156151 WARNING::Fitting problem for feature 115 returning NA
2025-09-11 02:11:20.2096 WARNING::Fitting problem for feature 123 returning NA
2025-09-11 02:11:20.251928 WARNING::Fitting problem for feature 130 returning NA
2025-09-11 02:11:20.26421 WARNING::Fitting problem for feature 132 returning NA
2025-09-11 02:11:20.306311 WARNING::Fitting problem for feature 139 returning NA
2025-09-11 02:11:20.426054 WARNING::Fitting problem for feature 150 returning NA
2025-09-11 02:11:20.636532 WARNING::Deleting existing residuals file: /tmp/RtmpojcQrH/file2edd943840cc9e/fits/residuals_linear.rds
2025-09-11 02:11:20.697787 WARNING::Deleting existing fitted file: /tmp/RtmpojcQrH/file2edd943840cc9e/fits/fitted_linear.rds
2025-09-11 02:11:20.760417 WARNING::Deleting existing residuals file: /tmp/RtmpojcQrH/file2edd943840cc9e/fits/residuals_logistic.rds
2025-09-11 02:11:21.058593 WARNING::Deleting existing fitted file: /tmp/RtmpojcQrH/file2edd943840cc9e/fits/fitted_logistic.rds
2025-09-11 02:11:37.692468 WARNING::Fitting problem for feature 50 returning NA
2025-09-11 02:11:37.769711 WARNING::Fitting problem for feature 62 returning NA
2025-09-11 02:11:37.866397 WARNING::Fitting problem for feature 74 returning NA
2025-09-11 02:11:37.8889 WARNING::Fitting problem for feature 78 returning NA
2025-09-11 02:11:37.924313 WARNING::Fitting problem for feature 84 returning NA
2025-09-11 02:11:38.001133 WARNING::Fitting problem for feature 96 returning NA
2025-09-11 02:11:38.006627 WARNING::Fitting problem for feature 97 returning NA
2025-09-11 02:11:38.018522 WARNING::Fitting problem for feature 99 returning NA
2025-09-11 02:11:38.114763 WARNING::Fitting problem for feature 114 returning NA
2025-09-11 02:11:38.120244 WARNING::Fitting problem for feature 115 returning NA
2025-09-11 02:11:38.172386 WARNING::Fitting problem for feature 123 returning NA
2025-09-11 02:11:38.213216 WARNING::Fitting problem for feature 130 returning NA
2025-09-11 02:11:38.225529 WARNING::Fitting problem for feature 132 returning NA
2025-09-11 02:11:38.267603 WARNING::Fitting problem for feature 139 returning NA
2025-09-11 02:11:38.33582 WARNING::Fitting problem for feature 150 returning NA
2025-09-11 02:11:50.124606 WARNING::Fitting problem for feature 50 returning NA
2025-09-11 02:11:50.202665 WARNING::Fitting problem for feature 62 returning NA
2025-09-11 02:11:50.280066 WARNING::Fitting problem for feature 74 returning NA
2025-09-11 02:11:50.303766 WARNING::Fitting problem for feature 78 returning NA
2025-09-11 02:11:50.341503 WARNING::Fitting problem for feature 84 returning NA
2025-09-11 02:11:50.425067 WARNING::Fitting problem for feature 96 returning NA
2025-09-11 02:11:50.430764 WARNING::Fitting problem for feature 97 returning NA
2025-09-11 02:11:50.44344 WARNING::Fitting problem for feature 99 returning NA
2025-09-11 02:11:50.540707 WARNING::Fitting problem for feature 114 returning NA
2025-09-11 02:11:50.546066 WARNING::Fitting problem for feature 115 returning NA
2025-09-11 02:11:50.595461 WARNING::Fitting problem for feature 123 returning NA
2025-09-11 02:11:50.636171 WARNING::Fitting problem for feature 130 returning NA
2025-09-11 02:11:50.648263 WARNING::Fitting problem for feature 132 returning NA
2025-09-11 02:11:50.689371 WARNING::Fitting problem for feature 139 returning NA
2025-09-11 02:11:50.760627 WARNING::Fitting problem for feature 150 returning NA
2025-09-11 02:12:09.546897 WARNING::Fitting problem for feature 124 returning NA
2025-09-11 02:12:19.187015 WARNING::Fitting problem for feature 124 returning NA
2025-09-11 02:12:39.570653 WARNING::Fitting problem for feature 124 returning NA
2025-09-11 02:12:49.5473 WARNING::Fitting problem for feature 124 returning NA
2025-09-11 02:12:50.213145 WARNING::Deleting existing residuals file: /tmp/RtmpojcQrH/file2edd941a8d403e/fits/residuals_linear.rds
2025-09-11 02:12:50.274563 WARNING::Deleting existing fitted file: /tmp/RtmpojcQrH/file2edd941a8d403e/fits/fitted_linear.rds
2025-09-11 02:12:50.312967 WARNING::Deleting existing residuals file: /tmp/RtmpojcQrH/file2edd941a8d403e/fits/residuals_logistic.rds
2025-09-11 02:12:50.381211 WARNING::Deleting existing fitted file: /tmp/RtmpojcQrH/file2edd941a8d403e/fits/fitted_logistic.rds
2025-09-11 02:13:09.218883 WARNING::Fitting problem for feature 124 returning NA
2025-09-11 02:13:14.369552 WARNING::Fitting problem for feature 124 returning NA
2025-09-11 02:13:14.692908 WARNING::Deleting existing residuals file: /tmp/RtmpojcQrH/file2edd941a8d403e/fits/residuals_linear.rds
2025-09-11 02:13:14.755529 WARNING::Deleting existing fitted file: /tmp/RtmpojcQrH/file2edd941a8d403e/fits/fitted_linear.rds
2025-09-11 02:13:14.794464 WARNING::Deleting existing residuals file: /tmp/RtmpojcQrH/file2edd941a8d403e/fits/residuals_logistic.rds
2025-09-11 02:13:14.86353 WARNING::Deleting existing fitted file: /tmp/RtmpojcQrH/file2edd941a8d403e/fits/fitted_logistic.rds
2025-09-11 02:13:30.220729 WARNING::Fitting problem for feature 124 returning NA
2025-09-11 02:13:36.668507 WARNING::Fitting problem for feature 124 returning NA
2025-09-11 02:13:37.037249 WARNING::Deleting existing residuals file: /tmp/RtmpojcQrH/file2edd941a8d403e/fits/residuals_linear.rds
2025-09-11 02:13:37.098753 WARNING::Deleting existing fitted file: /tmp/RtmpojcQrH/file2edd941a8d403e/fits/fitted_linear.rds
2025-09-11 02:13:37.136874 WARNING::Deleting existing residuals file: /tmp/RtmpojcQrH/file2edd941a8d403e/fits/residuals_logistic.rds
2025-09-11 02:13:37.204806 WARNING::Deleting existing fitted file: /tmp/RtmpojcQrH/file2edd941a8d403e/fits/fitted_logistic.rds
2025-09-11 02:13:52.489463 WARNING::Fitting problem for feature 50 returning NA
2025-09-11 02:13:52.571847 WARNING::Fitting problem for feature 62 returning NA
2025-09-11 02:13:52.652766 WARNING::Fitting problem for feature 74 returning NA
2025-09-11 02:13:52.676179 WARNING::Fitting problem for feature 78 returning NA
2025-09-11 02:13:52.713052 WARNING::Fitting problem for feature 84 returning NA
2025-09-11 02:13:52.794888 WARNING::Fitting problem for feature 96 returning NA
2025-09-11 02:13:52.800746 WARNING::Fitting problem for feature 97 returning NA
2025-09-11 02:13:52.813545 WARNING::Fitting problem for feature 99 returning NA
2025-09-11 02:13:52.947 WARNING::Fitting problem for feature 114 returning NA
2025-09-11 02:13:52.952761 WARNING::Fitting problem for feature 115 returning NA
2025-09-11 02:13:53.00459 WARNING::Fitting problem for feature 123 returning NA
2025-09-11 02:13:53.047454 WARNING::Fitting problem for feature 130 returning NA
2025-09-11 02:13:53.060565 WARNING::Fitting problem for feature 132 returning NA
2025-09-11 02:13:53.101987 WARNING::Fitting problem for feature 139 returning NA
2025-09-11 02:13:53.173402 WARNING::Fitting problem for feature 150 returning NA
2025-09-11 02:14:05.174212 WARNING::Fitting problem for feature 50 returning NA
2025-09-11 02:14:05.253649 WARNING::Fitting problem for feature 62 returning NA
2025-09-11 02:14:05.333879 WARNING::Fitting problem for feature 74 returning NA
2025-09-11 02:14:05.35719 WARNING::Fitting problem for feature 78 returning NA
2025-09-11 02:14:05.39473 WARNING::Fitting problem for feature 84 returning NA
2025-09-11 02:14:05.479594 WARNING::Fitting problem for feature 96 returning NA
2025-09-11 02:14:05.485761 WARNING::Fitting problem for feature 97 returning NA
2025-09-11 02:14:05.498745 WARNING::Fitting problem for feature 99 returning NA
2025-09-11 02:14:05.595754 WARNING::Fitting problem for feature 114 returning NA
2025-09-11 02:14:05.601342 WARNING::Fitting problem for feature 115 returning NA
2025-09-11 02:14:05.654036 WARNING::Fitting problem for feature 123 returning NA
2025-09-11 02:14:05.69666 WARNING::Fitting problem for feature 130 returning NA
2025-09-11 02:14:05.709527 WARNING::Fitting problem for feature 132 returning NA
2025-09-11 02:14:05.754231 WARNING::Fitting problem for feature 139 returning NA
2025-09-11 02:14:05.866668 WARNING::Fitting problem for feature 150 returning NA
2025-09-11 02:14:06.124543 WARNING::Deleting existing residuals file: /tmp/RtmpojcQrH/file2edd941a8d403e/fits/residuals_linear.rds
2025-09-11 02:14:06.185493 WARNING::Deleting existing fitted file: /tmp/RtmpojcQrH/file2edd941a8d403e/fits/fitted_linear.rds
2025-09-11 02:14:06.248346 WARNING::Deleting existing residuals file: /tmp/RtmpojcQrH/file2edd941a8d403e/fits/residuals_logistic.rds
2025-09-11 02:14:06.547043 WARNING::Deleting existing fitted file: /tmp/RtmpojcQrH/file2edd941a8d403e/fits/fitted_logistic.rds
2025-09-11 02:14:22.541616 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-09-11 02:14:22.55846 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-09-11 02:14:22.569971 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-09-11 02:14:22.620254 ERROR::No fixed, group, or
                        ordered effects included in formula.
2025-09-11 02:14:22.63697 ERROR::Effect name not found in metadata: d
2025-09-11 02:14:22.648975 ERROR::No user formula provided
2025-09-11 02:14:22.679729 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-09-11 02:14:22.692281 ERROR::No fixed/group/ordered/
                        feature-specific effects provided.
2025-09-11 02:14:25.598429 INFO::Writing function arguments to log file
2025-09-11 02:14:25.612766 INFO::Verifying options selected are valid
2025-09-11 02:14:27.484504 INFO::Writing function arguments to log file
2025-09-11 02:14:27.497092 INFO::Verifying options selected are valid
2025-09-11 02:14:27.49827 INFO::Determining format of input files
2025-09-11 02:14:27.499318 INFO::Input format is data samples as rows and metadata samples as rows
2025-09-11 02:14:27.501729 INFO::Running selected normalization method: TSS
2025-09-11 02:14:27.503254 INFO::Creating output feature tables folder
2025-09-11 02:14:27.504243 INFO::Writing normalized data to file /tmp/RtmpojcQrH/file2edd943d2733b2/features/data_norm.tsv
2025-09-11 02:14:27.50574 INFO::Filter data based on min abundance and min prevalence
2025-09-11 02:14:27.506636 INFO::Total samples in data: 16
2025-09-11 02:14:27.507508 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-09-11 02:14:27.509429 INFO::Total filtered features: 0
2025-09-11 02:14:27.510414 INFO::Filtered feature names from abundance and prevalence filtering:
2025-09-11 02:14:27.511594 INFO::Total features filtered by non-zero variance filtering: 0
2025-09-11 02:14:27.512545 INFO::Filtered feature names from variance filtering:
2025-09-11 02:14:27.513431 INFO::Writing filtered data to file /tmp/RtmpojcQrH/file2edd943d2733b2/features/filtered_data.tsv
2025-09-11 02:14:27.514971 INFO::Running selected transform method: LOG
2025-09-11 02:14:27.516186 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpojcQrH/file2edd943d2733b2/features/data_transformed.tsv
2025-09-11 02:14:27.51791 INFO::Applying z-score to standardize continuous metadata
2025-09-11 02:14:27.523486 INFO::Running the linear model component
2025-09-11 02:14:27.537828 INFO::Fitting model to feature number 1, a
2025-09-11 02:14:27.542507 INFO::Fitting model to feature number 2, b
2025-09-11 02:14:27.546954 INFO::Fitting model to feature number 3, c
2025-09-11 02:14:27.554518 INFO::Counting total values for each feature
2025-09-11 02:14:27.556694 INFO::Running the logistic model component
2025-09-11 02:14:27.570885 INFO::Fitting model to feature number 1, a
2025-09-11 02:14:27.589952 INFO::Fitting model to feature number 2, b
2025-09-11 02:14:27.596417 INFO::Fitting model to feature number 3, c
2025-09-11 02:14:27.605973 INFO::Counting total values for each feature
2025-09-11 02:14:27.608474 INFO::Re-running abundances for warn_prevalence
2025-09-11 02:14:27.609593 INFO::Running selected normalization method: TSS
2025-09-11 02:14:27.611197 INFO::Running selected transform method: LOG
2025-09-11 02:14:27.625281 INFO::Fitting model to feature number 1, a
2025-09-11 02:14:27.629908 INFO::Fitting model to feature number 2, b
2025-09-11 02:14:27.634367 INFO::Fitting model to feature number 3, c
2025-09-11 02:14:27.729052 INFO::Creating fits folder
2025-09-11 02:14:27.730374 INFO::Writing residuals to file /tmp/RtmpojcQrH/file2edd943d2733b2/fits/residuals_linear.rds
2025-09-11 02:14:27.731645 INFO::Writing fitted values to file /tmp/RtmpojcQrH/file2edd943d2733b2/fits/fitted_linear.rds
2025-09-11 02:14:27.732945 INFO::Writing residuals to file /tmp/RtmpojcQrH/file2edd943d2733b2/fits/residuals_logistic.rds
2025-09-11 02:14:27.734184 INFO::Writing fitted values to file /tmp/RtmpojcQrH/file2edd943d2733b2/fits/fitted_logistic.rds
2025-09-11 02:14:27.736916 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /tmp/RtmpojcQrH/file2edd943d2733b2/all_results.tsv
2025-09-11 02:14:27.738727 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/RtmpojcQrH/file2edd943d2733b2/significant_results.tsv
2025-09-11 02:14:27.740127 INFO::Creating output figures folder
2025-09-11 02:14:27.741508 INFO::Writing summary plot of significant
                        results to file: /tmp/RtmpojcQrH/file2edd943d2733b2/figures/summary_plot.pdf
2025-09-11 02:14:29.022166 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpojcQrH/file2edd943d2733b2/figures
2025-09-11 02:14:29.024323 INFO::Plotting associations from most to least significant, grouped by metadata
2025-09-11 02:14:29.029618 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-09-11 02:14:29.441286 INFO::Writing summary plot of
                        significant results to file: /tmp/RtmpojcQrH/file2edd943d2733b2/figures/summary_plot.pdf
2025-09-11 02:14:30.695704 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpojcQrH/file2edd943d2733b2/figures
2025-09-11 02:14:30.697604 INFO::Plotting associations from most to least significant, grouped by metadata
2025-09-11 02:14:30.703084 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-09-11 02:14:31.125292 INFO::Running the linear model component
2025-09-11 02:14:31.134864 INFO::Fitting model to feature number 1, a
2025-09-11 02:14:31.139494 INFO::Fitting model to feature number 2, b
2025-09-11 02:14:31.143545 INFO::Fitting model to feature number 3, c
2025-09-11 02:14:31.150797 INFO::Counting total values for each feature
2025-09-11 02:14:31.152464 INFO::Running the logistic model component
2025-09-11 02:14:31.161141 INFO::Fitting model to feature number 1, a
2025-09-11 02:14:31.167542 INFO::Fitting model to feature number 2, b
2025-09-11 02:14:31.173298 INFO::Fitting model to feature number 3, c
2025-09-11 02:14:31.182086 INFO::Counting total values for each feature
2025-09-11 02:14:31.184124 INFO::Re-running abundances for warn_prevalence
2025-09-11 02:14:31.18493 INFO::Running selected normalization method: TSS
2025-09-11 02:14:31.186347 INFO::Running selected transform method: LOG
2025-09-11 02:14:31.195024 INFO::Fitting model to feature number 1, a
2025-09-11 02:14:31.199243 INFO::Fitting model to feature number 2, b
2025-09-11 02:14:31.203242 INFO::Fitting model to feature number 3, c
2025-09-11 02:14:31.29453 INFO::Creating output folder
2025-09-11 02:14:31.29587 INFO::Creating output figures folder
2025-09-11 02:14:31.297226 INFO::Writing summary plot of significant
                        results to file: /tmp/RtmpojcQrH/file2edd945ec892c0/figures/summary_plot.pdf
2025-09-11 02:14:32.555788 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpojcQrH/file2edd945ec892c0/figures
2025-09-11 02:14:32.557603 INFO::Plotting associations from most to least significant, grouped by metadata
2025-09-11 02:14:32.562979 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-09-11 02:14:33.379293 INFO::Applying z-score to standardize continuous metadata
2025-09-11 02:14:33.386815 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-09-11 02:14:33.387697 INFO::Bypass z-score application to metadata
2025-09-11 02:14:33.390122 INFO::Bypass z-score application to metadata
2025-09-11 02:14:33.407586 INFO::Determining format of input files
2025-09-11 02:14:33.408559 INFO::Input format is data samples as rows and metadata samples as rows
2025-09-11 02:14:33.409419 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-09-11 02:14:33.416229 INFO::Determining format of input files
2025-09-11 02:14:33.417242 INFO::Input format is data samples as columns and metadata samples as rows
2025-09-11 02:14:33.418529 INFO::Input format is feature_specific_covariate samples as columns
2025-09-11 02:14:33.426131 INFO::Determining format of input files
2025-09-11 02:14:33.427057 INFO::Input format is data samples as rows and metadata samples as rows
2025-09-11 02:14:33.428059 INFO::Input format is feature_specific_covariate samples as columns
2025-09-11 02:14:33.429698 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-09-11 02:14:33.430474 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-09-11 02:14:33.440962 INFO::Running selected transform method: LOG
2025-09-11 02:14:33.442084 INFO::Creating output feature tables folder
2025-09-11 02:14:33.442948 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpojcQrH/file2edd947c172aaa/features/data_transformed.tsv
2025-09-11 02:14:33.446649 INFO::Running selected transform method: LOG
2025-09-11 02:14:33.447654 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpojcQrH/file2edd947c172aaa/features/data_transformed.tsv
2025-09-11 02:14:33.451476 INFO::Running selected transform method: PLOG
2025-09-11 02:14:33.453102 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpojcQrH/file2edd947c172aaa/features/data_transformed.tsv
2025-09-11 02:14:33.455895 INFO::Running selected transform method: NONE
2025-09-11 02:14:33.456627 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpojcQrH/file2edd947c172aaa/features/data_transformed.tsv
2025-09-11 02:14:33.463659 INFO::Running the linear model component
2025-09-11 02:14:33.472371 INFO::Fitting model to feature number 1, a
2025-09-11 02:14:33.476703 INFO::Fitting model to feature number 2, b
2025-09-11 02:14:33.48086 INFO::Fitting model to feature number 3, c
2025-09-11 02:14:33.487971 INFO::Counting total values for each feature
2025-09-11 02:14:33.489648 INFO::Running the logistic model component
2025-09-11 02:14:33.498059 INFO::Fitting model to feature number 1, a
2025-09-11 02:14:33.50454 INFO::Fitting model to feature number 2, b
2025-09-11 02:14:33.510478 INFO::Fitting model to feature number 3, c
2025-09-11 02:14:33.519726 INFO::Counting total values for each feature
2025-09-11 02:14:33.522009 INFO::Re-running abundances for warn_prevalence
2025-09-11 02:14:33.522923 INFO::Running selected normalization method: TSS
2025-09-11 02:14:33.524421 INFO::Running selected transform method: LOG
2025-09-11 02:14:33.544652 INFO::Fitting model to feature number 1, a
2025-09-11 02:14:33.549942 INFO::Fitting model to feature number 2, b
2025-09-11 02:14:33.55401 INFO::Fitting model to feature number 3, c
2025-09-11 02:14:33.640546 INFO::Creating output folder
2025-09-11 02:14:33.641502 INFO::Creating fits folder
2025-09-11 02:14:33.642325 INFO::Writing residuals to file /tmp/RtmpojcQrH/file2edd943df61f5b/fits/residuals_linear.rds
2025-09-11 02:14:33.643327 INFO::Writing fitted values to file /tmp/RtmpojcQrH/file2edd943df61f5b/fits/fitted_linear.rds
2025-09-11 02:14:33.644433 INFO::Writing residuals to file /tmp/RtmpojcQrH/file2edd943df61f5b/fits/residuals_logistic.rds
2025-09-11 02:14:33.645517 INFO::Writing fitted values to file /tmp/RtmpojcQrH/file2edd943df61f5b/fits/fitted_logistic.rds
2025-09-11 02:14:33.648201 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /tmp/RtmpojcQrH/file2edd943df61f5b/all_results.tsv
2025-09-11 02:14:33.649708 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/RtmpojcQrH/file2edd943df61f5b/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]

[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
> 
> 
> proc.time()
   user  system elapsed 
313.575   4.491 318.109

Example timings

maaslin3.Rcheck/maaslin3-Ex.timings

nameusersystemelapsed
maaslin320.488 0.48320.980
maaslin_check_arguments0.1520.0000.151
maaslin_check_formula0.1330.0020.134
maaslin_compute_formula0.1370.0020.139
maaslin_contrast_test18.527 0.33818.868
maaslin_filter0.4230.0050.428
maaslin_fit12.842 0.14212.984
maaslin_log_arguments0.1290.0030.131
maaslin_normalize0.2660.0020.267
maaslin_plot_results36.787 0.21236.960
maaslin_plot_results_from_output36.059 0.27036.333
maaslin_process_metadata0.4690.0110.479
maaslin_read_data0.1220.0050.128
maaslin_reorder_data0.1310.0010.133
maaslin_transform0.5440.0070.550
maaslin_write_results14.406 0.25014.658
maaslin_write_results_lefse_format14.272 0.07014.344
preprocess_dna_mtx0.0040.0000.004
preprocess_taxa_mtx0.0040.0000.004