Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-08-06 13:52 -0400 (Wed, 06 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4813
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4550
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4592
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4534
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 1145/2315HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maaslin3 1.1.0  (landing page)
William Nickols
Snapshot Date: 2025-08-05 13:25 -0400 (Tue, 05 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 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    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 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


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: 2025-08-05 23:47:24 -0400 (Tue, 05 Aug 2025)
EndedAt: 2025-08-06 00:07:07 -0400 (Wed, 06 Aug 2025)
EllapsedTime: 1183.2 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 24.04.2 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_from_output   38.039  0.369  38.416
maaslin_plot_results               36.986  0.234  37.186
maaslin3                           20.386  0.531  20.920
maaslin_contrast_test              19.164  0.334  19.501
maaslin_write_results              15.987  0.236  16.225
maaslin_write_results_lefse_format 14.873  0.089  14.963
maaslin_fit                        13.778  0.131  13.910
* 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")
2025-08-05 23:53:33.310307 WARNING::Fitting problem for feature 50 returning NA
2025-08-05 23:53:33.385604 WARNING::Fitting problem for feature 62 returning NA
2025-08-05 23:53:33.470702 WARNING::Fitting problem for feature 74 returning NA
2025-08-05 23:53:33.492375 WARNING::Fitting problem for feature 78 returning NA
2025-08-05 23:53:33.53359 WARNING::Fitting problem for feature 84 returning NA
2025-08-05 23:53:33.608297 WARNING::Fitting problem for feature 96 returning NA
2025-08-05 23:53:33.613563 WARNING::Fitting problem for feature 97 returning NA
2025-08-05 23:53:33.625259 WARNING::Fitting problem for feature 99 returning NA
2025-08-05 23:53:33.727366 WARNING::Fitting problem for feature 114 returning NA
2025-08-05 23:53:33.732872 WARNING::Fitting problem for feature 115 returning NA
2025-08-05 23:53:33.782752 WARNING::Fitting problem for feature 123 returning NA
2025-08-05 23:53:33.822299 WARNING::Fitting problem for feature 130 returning NA
2025-08-05 23:53:33.834118 WARNING::Fitting problem for feature 132 returning NA
2025-08-05 23:53:33.874647 WARNING::Fitting problem for feature 139 returning NA
2025-08-05 23:53:33.950938 WARNING::Fitting problem for feature 150 returning NA
2025-08-05 23:53:49.431922 WARNING::Fitting problem for feature 50 returning NA
2025-08-05 23:53:49.513074 WARNING::Fitting problem for feature 62 returning NA
2025-08-05 23:53:49.594856 WARNING::Fitting problem for feature 74 returning NA
2025-08-05 23:53:49.620516 WARNING::Fitting problem for feature 78 returning NA
2025-08-05 23:53:49.66023 WARNING::Fitting problem for feature 84 returning NA
2025-08-05 23:53:49.754342 WARNING::Fitting problem for feature 96 returning NA
2025-08-05 23:53:49.760109 WARNING::Fitting problem for feature 97 returning NA
2025-08-05 23:53:49.772593 WARNING::Fitting problem for feature 99 returning NA
2025-08-05 23:53:49.87018 WARNING::Fitting problem for feature 114 returning NA
2025-08-05 23:53:49.875774 WARNING::Fitting problem for feature 115 returning NA
2025-08-05 23:53:49.926208 WARNING::Fitting problem for feature 123 returning NA
2025-08-05 23:53:49.966471 WARNING::Fitting problem for feature 130 returning NA
2025-08-05 23:53:49.97885 WARNING::Fitting problem for feature 132 returning NA
2025-08-05 23:53:50.020469 WARNING::Fitting problem for feature 139 returning NA
2025-08-05 23:53:50.091285 WARNING::Fitting problem for feature 150 returning NA
2025-08-05 23:54:08.700445 WARNING::Fitting problem for feature 50 returning NA
2025-08-05 23:54:08.798653 WARNING::Fitting problem for feature 62 returning NA
2025-08-05 23:54:08.874553 WARNING::Fitting problem for feature 74 returning NA
2025-08-05 23:54:08.896911 WARNING::Fitting problem for feature 78 returning NA
2025-08-05 23:54:08.933512 WARNING::Fitting problem for feature 84 returning NA
2025-08-05 23:54:09.012125 WARNING::Fitting problem for feature 96 returning NA
2025-08-05 23:54:09.01753 WARNING::Fitting problem for feature 97 returning NA
2025-08-05 23:54:09.029561 WARNING::Fitting problem for feature 99 returning NA
2025-08-05 23:54:09.126241 WARNING::Fitting problem for feature 114 returning NA
2025-08-05 23:54:09.131681 WARNING::Fitting problem for feature 115 returning NA
2025-08-05 23:54:09.207441 WARNING::Fitting problem for feature 123 returning NA
2025-08-05 23:54:09.250974 WARNING::Fitting problem for feature 130 returning NA
2025-08-05 23:54:09.26344 WARNING::Fitting problem for feature 132 returning NA
2025-08-05 23:54:09.304491 WARNING::Fitting problem for feature 139 returning NA
2025-08-05 23:54:09.372844 WARNING::Fitting problem for feature 150 returning NA
2025-08-05 23:54:22.839667 WARNING::Fitting problem for feature 50 returning NA
2025-08-05 23:54:22.937644 WARNING::Fitting problem for feature 62 returning NA
2025-08-05 23:54:23.012348 WARNING::Fitting problem for feature 74 returning NA
2025-08-05 23:54:23.034228 WARNING::Fitting problem for feature 78 returning NA
2025-08-05 23:54:23.068933 WARNING::Fitting problem for feature 84 returning NA
2025-08-05 23:54:23.144814 WARNING::Fitting problem for feature 96 returning NA
2025-08-05 23:54:23.150164 WARNING::Fitting problem for feature 97 returning NA
2025-08-05 23:54:23.161904 WARNING::Fitting problem for feature 99 returning NA
2025-08-05 23:54:23.258343 WARNING::Fitting problem for feature 114 returning NA
2025-08-05 23:54:23.263952 WARNING::Fitting problem for feature 115 returning NA
2025-08-05 23:54:23.314786 WARNING::Fitting problem for feature 123 returning NA
2025-08-05 23:54:23.356196 WARNING::Fitting problem for feature 130 returning NA
2025-08-05 23:54:23.368596 WARNING::Fitting problem for feature 132 returning NA
2025-08-05 23:54:23.409988 WARNING::Fitting problem for feature 139 returning NA
2025-08-05 23:54:23.480612 WARNING::Fitting problem for feature 150 returning NA
2025-08-05 23:54:23.697991 WARNING::Deleting existing residuals file: /tmp/RtmpUzPRea/file11eb6467c1caec/fits/residuals_linear.rds
2025-08-05 23:54:23.758842 WARNING::Deleting existing fitted file: /tmp/RtmpUzPRea/file11eb6467c1caec/fits/fitted_linear.rds
2025-08-05 23:54:23.821644 WARNING::Deleting existing residuals file: /tmp/RtmpUzPRea/file11eb6467c1caec/fits/residuals_logistic.rds
2025-08-05 23:54:24.119201 WARNING::Deleting existing fitted file: /tmp/RtmpUzPRea/file11eb6467c1caec/fits/fitted_logistic.rds
2025-08-05 23:54:40.882466 WARNING::Fitting problem for feature 50 returning NA
2025-08-05 23:54:40.980469 WARNING::Fitting problem for feature 62 returning NA
2025-08-05 23:54:41.055121 WARNING::Fitting problem for feature 74 returning NA
2025-08-05 23:54:41.077539 WARNING::Fitting problem for feature 78 returning NA
2025-08-05 23:54:41.112425 WARNING::Fitting problem for feature 84 returning NA
2025-08-05 23:54:41.189872 WARNING::Fitting problem for feature 96 returning NA
2025-08-05 23:54:41.195409 WARNING::Fitting problem for feature 97 returning NA
2025-08-05 23:54:41.207692 WARNING::Fitting problem for feature 99 returning NA
2025-08-05 23:54:41.304795 WARNING::Fitting problem for feature 114 returning NA
2025-08-05 23:54:41.310676 WARNING::Fitting problem for feature 115 returning NA
2025-08-05 23:54:41.36128 WARNING::Fitting problem for feature 123 returning NA
2025-08-05 23:54:41.401139 WARNING::Fitting problem for feature 130 returning NA
2025-08-05 23:54:41.41296 WARNING::Fitting problem for feature 132 returning NA
2025-08-05 23:54:41.452494 WARNING::Fitting problem for feature 139 returning NA
2025-08-05 23:54:41.520253 WARNING::Fitting problem for feature 150 returning NA
2025-08-05 23:54:53.987146 WARNING::Fitting problem for feature 50 returning NA
2025-08-05 23:54:54.07282 WARNING::Fitting problem for feature 62 returning NA
2025-08-05 23:54:54.158015 WARNING::Fitting problem for feature 74 returning NA
2025-08-05 23:54:54.181477 WARNING::Fitting problem for feature 78 returning NA
2025-08-05 23:54:54.21839 WARNING::Fitting problem for feature 84 returning NA
2025-08-05 23:54:54.294889 WARNING::Fitting problem for feature 96 returning NA
2025-08-05 23:54:54.300438 WARNING::Fitting problem for feature 97 returning NA
2025-08-05 23:54:54.312347 WARNING::Fitting problem for feature 99 returning NA
2025-08-05 23:54:54.408117 WARNING::Fitting problem for feature 114 returning NA
2025-08-05 23:54:54.413477 WARNING::Fitting problem for feature 115 returning NA
2025-08-05 23:54:54.462779 WARNING::Fitting problem for feature 123 returning NA
2025-08-05 23:54:54.5036 WARNING::Fitting problem for feature 130 returning NA
2025-08-05 23:54:54.515627 WARNING::Fitting problem for feature 132 returning NA
2025-08-05 23:54:54.556403 WARNING::Fitting problem for feature 139 returning NA
2025-08-05 23:54:54.62604 WARNING::Fitting problem for feature 150 returning NA
2025-08-05 23:54:54.872591 WARNING::Deleting existing residuals file: /tmp/RtmpUzPRea/file11eb6467c1caec/fits/residuals_linear.rds
2025-08-05 23:54:54.934814 WARNING::Deleting existing fitted file: /tmp/RtmpUzPRea/file11eb6467c1caec/fits/fitted_linear.rds
2025-08-05 23:54:54.998739 WARNING::Deleting existing residuals file: /tmp/RtmpUzPRea/file11eb6467c1caec/fits/residuals_logistic.rds
2025-08-05 23:54:55.302588 WARNING::Deleting existing fitted file: /tmp/RtmpUzPRea/file11eb6467c1caec/fits/fitted_logistic.rds
2025-08-05 23:55:12.127415 WARNING::Fitting problem for feature 50 returning NA
2025-08-05 23:55:12.212302 WARNING::Fitting problem for feature 62 returning NA
2025-08-05 23:55:12.294833 WARNING::Fitting problem for feature 74 returning NA
2025-08-05 23:55:12.320033 WARNING::Fitting problem for feature 78 returning NA
2025-08-05 23:55:12.359506 WARNING::Fitting problem for feature 84 returning NA
2025-08-05 23:55:12.446599 WARNING::Fitting problem for feature 96 returning NA
2025-08-05 23:55:12.452381 WARNING::Fitting problem for feature 97 returning NA
2025-08-05 23:55:12.466188 WARNING::Fitting problem for feature 99 returning NA
2025-08-05 23:55:12.571864 WARNING::Fitting problem for feature 114 returning NA
2025-08-05 23:55:12.577792 WARNING::Fitting problem for feature 115 returning NA
2025-08-05 23:55:12.630762 WARNING::Fitting problem for feature 123 returning NA
2025-08-05 23:55:12.695689 WARNING::Fitting problem for feature 130 returning NA
2025-08-05 23:55:12.713819 WARNING::Fitting problem for feature 132 returning NA
2025-08-05 23:55:12.757347 WARNING::Fitting problem for feature 139 returning NA
2025-08-05 23:55:12.831937 WARNING::Fitting problem for feature 150 returning NA
2025-08-05 23:55:25.199434 WARNING::Fitting problem for feature 50 returning NA
2025-08-05 23:55:25.286296 WARNING::Fitting problem for feature 62 returning NA
2025-08-05 23:55:25.372673 WARNING::Fitting problem for feature 74 returning NA
2025-08-05 23:55:25.39913 WARNING::Fitting problem for feature 78 returning NA
2025-08-05 23:55:25.440151 WARNING::Fitting problem for feature 84 returning NA
2025-08-05 23:55:25.522906 WARNING::Fitting problem for feature 96 returning NA
2025-08-05 23:55:25.529102 WARNING::Fitting problem for feature 97 returning NA
2025-08-05 23:55:25.542972 WARNING::Fitting problem for feature 99 returning NA
2025-08-05 23:55:25.648149 WARNING::Fitting problem for feature 114 returning NA
2025-08-05 23:55:25.654386 WARNING::Fitting problem for feature 115 returning NA
2025-08-05 23:55:25.709848 WARNING::Fitting problem for feature 123 returning NA
2025-08-05 23:55:25.754887 WARNING::Fitting problem for feature 130 returning NA
2025-08-05 23:55:25.768326 WARNING::Fitting problem for feature 132 returning NA
2025-08-05 23:55:25.814722 WARNING::Fitting problem for feature 139 returning NA
2025-08-05 23:55:25.894385 WARNING::Fitting problem for feature 150 returning NA
2025-08-05 23:55:26.18795 WARNING::Deleting existing residuals file: /tmp/RtmpUzPRea/file11eb6467c1caec/fits/residuals_linear.rds
2025-08-05 23:55:26.24978 WARNING::Deleting existing fitted file: /tmp/RtmpUzPRea/file11eb6467c1caec/fits/fitted_linear.rds
2025-08-05 23:55:26.312929 WARNING::Deleting existing residuals file: /tmp/RtmpUzPRea/file11eb6467c1caec/fits/residuals_logistic.rds
2025-08-05 23:55:26.612648 WARNING::Deleting existing fitted file: /tmp/RtmpUzPRea/file11eb6467c1caec/fits/fitted_logistic.rds
2025-08-05 23:55:43.955308 WARNING::Fitting problem for feature 50 returning NA
2025-08-05 23:55:44.03826 WARNING::Fitting problem for feature 62 returning NA
2025-08-05 23:55:44.119536 WARNING::Fitting problem for feature 74 returning NA
2025-08-05 23:55:44.143778 WARNING::Fitting problem for feature 78 returning NA
2025-08-05 23:55:44.181695 WARNING::Fitting problem for feature 84 returning NA
2025-08-05 23:55:44.266431 WARNING::Fitting problem for feature 96 returning NA
2025-08-05 23:55:44.272638 WARNING::Fitting problem for feature 97 returning NA
2025-08-05 23:55:44.286715 WARNING::Fitting problem for feature 99 returning NA
2025-08-05 23:55:44.424506 WARNING::Fitting problem for feature 114 returning NA
2025-08-05 23:55:44.430596 WARNING::Fitting problem for feature 115 returning NA
2025-08-05 23:55:44.489599 WARNING::Fitting problem for feature 123 returning NA
2025-08-05 23:55:44.536992 WARNING::Fitting problem for feature 130 returning NA
2025-08-05 23:55:44.550771 WARNING::Fitting problem for feature 132 returning NA
2025-08-05 23:55:44.596565 WARNING::Fitting problem for feature 139 returning NA
2025-08-05 23:55:44.674893 WARNING::Fitting problem for feature 150 returning NA
2025-08-05 23:55:57.656039 WARNING::Fitting problem for feature 50 returning NA
2025-08-05 23:55:57.736583 WARNING::Fitting problem for feature 62 returning NA
2025-08-05 23:55:57.815127 WARNING::Fitting problem for feature 74 returning NA
2025-08-05 23:55:57.838119 WARNING::Fitting problem for feature 78 returning NA
2025-08-05 23:55:57.875216 WARNING::Fitting problem for feature 84 returning NA
2025-08-05 23:55:57.960164 WARNING::Fitting problem for feature 96 returning NA
2025-08-05 23:55:57.965719 WARNING::Fitting problem for feature 97 returning NA
2025-08-05 23:55:57.978076 WARNING::Fitting problem for feature 99 returning NA
2025-08-05 23:55:58.075584 WARNING::Fitting problem for feature 114 returning NA
2025-08-05 23:55:58.081417 WARNING::Fitting problem for feature 115 returning NA
2025-08-05 23:55:58.134786 WARNING::Fitting problem for feature 123 returning NA
2025-08-05 23:55:58.176294 WARNING::Fitting problem for feature 130 returning NA
2025-08-05 23:55:58.188633 WARNING::Fitting problem for feature 132 returning NA
2025-08-05 23:55:58.22992 WARNING::Fitting problem for feature 139 returning NA
2025-08-05 23:55:58.302038 WARNING::Fitting problem for feature 150 returning NA
2025-08-05 23:56:17.106996 WARNING::Fitting problem for feature 124 returning NA
2025-08-05 23:56:25.848856 WARNING::Fitting problem for feature 124 returning NA
2025-08-05 23:56:45.858063 WARNING::Fitting problem for feature 124 returning NA
2025-08-05 23:56:55.266699 WARNING::Fitting problem for feature 124 returning NA
2025-08-05 23:56:55.90468 WARNING::Deleting existing residuals file: /tmp/RtmpUzPRea/file11eb64559162fb/fits/residuals_linear.rds
2025-08-05 23:56:55.966405 WARNING::Deleting existing fitted file: /tmp/RtmpUzPRea/file11eb64559162fb/fits/fitted_linear.rds
2025-08-05 23:56:56.004951 WARNING::Deleting existing residuals file: /tmp/RtmpUzPRea/file11eb64559162fb/fits/residuals_logistic.rds
2025-08-05 23:56:56.073247 WARNING::Deleting existing fitted file: /tmp/RtmpUzPRea/file11eb64559162fb/fits/fitted_logistic.rds
2025-08-05 23:57:14.431411 WARNING::Fitting problem for feature 124 returning NA
2025-08-05 23:57:19.495377 WARNING::Fitting problem for feature 124 returning NA
2025-08-05 23:57:19.822392 WARNING::Deleting existing residuals file: /tmp/RtmpUzPRea/file11eb64559162fb/fits/residuals_linear.rds
2025-08-05 23:57:19.884171 WARNING::Deleting existing fitted file: /tmp/RtmpUzPRea/file11eb64559162fb/fits/fitted_linear.rds
2025-08-05 23:57:19.922896 WARNING::Deleting existing residuals file: /tmp/RtmpUzPRea/file11eb64559162fb/fits/residuals_logistic.rds
2025-08-05 23:57:19.991026 WARNING::Deleting existing fitted file: /tmp/RtmpUzPRea/file11eb64559162fb/fits/fitted_logistic.rds
2025-08-05 23:57:34.662782 WARNING::Fitting problem for feature 124 returning NA
2025-08-05 23:57:40.769703 WARNING::Fitting problem for feature 124 returning NA
2025-08-05 23:57:41.074669 WARNING::Deleting existing residuals file: /tmp/RtmpUzPRea/file11eb64559162fb/fits/residuals_linear.rds
2025-08-05 23:57:41.136225 WARNING::Deleting existing fitted file: /tmp/RtmpUzPRea/file11eb64559162fb/fits/fitted_linear.rds
2025-08-05 23:57:41.17473 WARNING::Deleting existing residuals file: /tmp/RtmpUzPRea/file11eb64559162fb/fits/residuals_logistic.rds
2025-08-05 23:57:41.242936 WARNING::Deleting existing fitted file: /tmp/RtmpUzPRea/file11eb64559162fb/fits/fitted_logistic.rds
2025-08-05 23:57:55.423228 WARNING::Fitting problem for feature 50 returning NA
2025-08-05 23:57:55.503506 WARNING::Fitting problem for feature 62 returning NA
2025-08-05 23:57:55.582444 WARNING::Fitting problem for feature 74 returning NA
2025-08-05 23:57:55.60544 WARNING::Fitting problem for feature 78 returning NA
2025-08-05 23:57:55.641145 WARNING::Fitting problem for feature 84 returning NA
2025-08-05 23:57:55.720603 WARNING::Fitting problem for feature 96 returning NA
2025-08-05 23:57:55.726119 WARNING::Fitting problem for feature 97 returning NA
2025-08-05 23:57:55.738553 WARNING::Fitting problem for feature 99 returning NA
2025-08-05 23:57:55.840973 WARNING::Fitting problem for feature 114 returning NA
2025-08-05 23:57:55.846655 WARNING::Fitting problem for feature 115 returning NA
2025-08-05 23:57:55.897528 WARNING::Fitting problem for feature 123 returning NA
2025-08-05 23:57:55.938826 WARNING::Fitting problem for feature 130 returning NA
2025-08-05 23:57:55.951244 WARNING::Fitting problem for feature 132 returning NA
2025-08-05 23:57:55.994106 WARNING::Fitting problem for feature 139 returning NA
2025-08-05 23:57:56.06852 WARNING::Fitting problem for feature 150 returning NA
2025-08-05 23:58:07.913399 WARNING::Fitting problem for feature 50 returning NA
2025-08-05 23:58:07.990183 WARNING::Fitting problem for feature 62 returning NA
2025-08-05 23:58:08.067255 WARNING::Fitting problem for feature 74 returning NA
2025-08-05 23:58:08.091289 WARNING::Fitting problem for feature 78 returning NA
2025-08-05 23:58:08.128122 WARNING::Fitting problem for feature 84 returning NA
2025-08-05 23:58:08.205224 WARNING::Fitting problem for feature 96 returning NA
2025-08-05 23:58:08.21067 WARNING::Fitting problem for feature 97 returning NA
2025-08-05 23:58:08.222672 WARNING::Fitting problem for feature 99 returning NA
2025-08-05 23:58:08.317966 WARNING::Fitting problem for feature 114 returning NA
2025-08-05 23:58:08.323466 WARNING::Fitting problem for feature 115 returning NA
2025-08-05 23:58:08.374939 WARNING::Fitting problem for feature 123 returning NA
2025-08-05 23:58:08.416289 WARNING::Fitting problem for feature 130 returning NA
2025-08-05 23:58:08.428239 WARNING::Fitting problem for feature 132 returning NA
2025-08-05 23:58:08.468966 WARNING::Fitting problem for feature 139 returning NA
2025-08-05 23:58:08.538994 WARNING::Fitting problem for feature 150 returning NA
2025-08-05 23:58:08.800942 WARNING::Deleting existing residuals file: /tmp/RtmpUzPRea/file11eb64559162fb/fits/residuals_linear.rds
2025-08-05 23:58:08.862284 WARNING::Deleting existing fitted file: /tmp/RtmpUzPRea/file11eb64559162fb/fits/fitted_linear.rds
2025-08-05 23:58:08.925361 WARNING::Deleting existing residuals file: /tmp/RtmpUzPRea/file11eb64559162fb/fits/residuals_logistic.rds
2025-08-05 23:58:09.224422 WARNING::Deleting existing fitted file: /tmp/RtmpUzPRea/file11eb64559162fb/fits/fitted_logistic.rds
2025-08-05 23:58:25.14861 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-08-05 23:58:25.166078 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-08-05 23:58:25.178125 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-08-05 23:58:25.22887 ERROR::No fixed, group, or
                        ordered effects included in formula.
2025-08-05 23:58:25.245471 ERROR::Effect name not found in metadata: d
2025-08-05 23:58:25.25662 ERROR::No user formula provided
2025-08-05 23:58:25.285868 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-08-05 23:58:25.297938 ERROR::No fixed/group/ordered/
                        feature-specific effects provided.
2025-08-05 23:58:28.205375 INFO::Writing function arguments to log file
2025-08-05 23:58:28.219314 INFO::Verifying options selected are valid
2025-08-05 23:58:30.085874 INFO::Writing function arguments to log file
2025-08-05 23:58:30.097753 INFO::Verifying options selected are valid
2025-08-05 23:58:30.098864 INFO::Determining format of input files
2025-08-05 23:58:30.099842 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-05 23:58:30.102185 INFO::Running selected normalization method: TSS
2025-08-05 23:58:30.103627 INFO::Creating output feature tables folder
2025-08-05 23:58:30.10459 INFO::Writing normalized data to file /tmp/RtmpUzPRea/file11eb64145eb71d/features/data_norm.tsv
2025-08-05 23:58:30.106059 INFO::Filter data based on min abundance and min prevalence
2025-08-05 23:58:30.106964 INFO::Total samples in data: 16
2025-08-05 23:58:30.107813 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-08-05 23:58:30.109647 INFO::Total filtered features: 0
2025-08-05 23:58:30.110599 INFO::Filtered feature names from abundance and prevalence filtering:
2025-08-05 23:58:30.111738 INFO::Total features filtered by non-zero variance filtering: 0
2025-08-05 23:58:30.112675 INFO::Filtered feature names from variance filtering:
2025-08-05 23:58:30.113551 INFO::Writing filtered data to file /tmp/RtmpUzPRea/file11eb64145eb71d/features/filtered_data.tsv
2025-08-05 23:58:30.115033 INFO::Running selected transform method: LOG
2025-08-05 23:58:30.11624 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpUzPRea/file11eb64145eb71d/features/data_transformed.tsv
2025-08-05 23:58:30.117894 INFO::Applying z-score to standardize continuous metadata
2025-08-05 23:58:30.123282 INFO::Running the linear model component
2025-08-05 23:58:30.137119 INFO::Fitting model to feature number 1, a
2025-08-05 23:58:30.141629 INFO::Fitting model to feature number 2, b
2025-08-05 23:58:30.145892 INFO::Fitting model to feature number 3, c
2025-08-05 23:58:30.153186 INFO::Counting total values for each feature
2025-08-05 23:58:30.155 INFO::Running the logistic model component
2025-08-05 23:58:30.169016 INFO::Fitting model to feature number 1, a
2025-08-05 23:58:30.176026 INFO::Fitting model to feature number 2, b
2025-08-05 23:58:30.182527 INFO::Fitting model to feature number 3, c
2025-08-05 23:58:30.191767 INFO::Counting total values for each feature
2025-08-05 23:58:30.194014 INFO::Re-running abundances for warn_prevalence
2025-08-05 23:58:30.195009 INFO::Running selected normalization method: TSS
2025-08-05 23:58:30.196527 INFO::Running selected transform method: LOG
2025-08-05 23:58:30.210612 INFO::Fitting model to feature number 1, a
2025-08-05 23:58:30.21517 INFO::Fitting model to feature number 2, b
2025-08-05 23:58:30.219467 INFO::Fitting model to feature number 3, c
2025-08-05 23:58:30.306588 INFO::Creating fits folder
2025-08-05 23:58:30.30785 INFO::Writing residuals to file /tmp/RtmpUzPRea/file11eb64145eb71d/fits/residuals_linear.rds
2025-08-05 23:58:30.309075 INFO::Writing fitted values to file /tmp/RtmpUzPRea/file11eb64145eb71d/fits/fitted_linear.rds
2025-08-05 23:58:30.310445 INFO::Writing residuals to file /tmp/RtmpUzPRea/file11eb64145eb71d/fits/residuals_logistic.rds
2025-08-05 23:58:30.311748 INFO::Writing fitted values to file /tmp/RtmpUzPRea/file11eb64145eb71d/fits/fitted_logistic.rds
2025-08-05 23:58:30.314541 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /tmp/RtmpUzPRea/file11eb64145eb71d/all_results.tsv
2025-08-05 23:58:30.316345 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/RtmpUzPRea/file11eb64145eb71d/significant_results.tsv
2025-08-05 23:58:30.317733 INFO::Creating output figures folder
2025-08-05 23:58:30.319174 INFO::Writing summary plot of significant
                        results to file: /tmp/RtmpUzPRea/file11eb64145eb71d/figures/summary_plot.pdf
2025-08-05 23:58:31.599085 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpUzPRea/file11eb64145eb71d/figures
2025-08-05 23:58:31.601205 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-05 23:58:31.60647 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-05 23:58:31.995677 INFO::Writing summary plot of
                        significant results to file: /tmp/RtmpUzPRea/file11eb64145eb71d/figures/summary_plot.pdf
2025-08-05 23:58:33.246976 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpUzPRea/file11eb64145eb71d/figures
2025-08-05 23:58:33.248628 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-05 23:58:33.25377 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-05 23:58:33.648754 INFO::Running the linear model component
2025-08-05 23:58:33.657564 INFO::Fitting model to feature number 1, a
2025-08-05 23:58:33.661828 INFO::Fitting model to feature number 2, b
2025-08-05 23:58:33.665763 INFO::Fitting model to feature number 3, c
2025-08-05 23:58:33.672595 INFO::Counting total values for each feature
2025-08-05 23:58:33.674238 INFO::Running the logistic model component
2025-08-05 23:58:33.682542 INFO::Fitting model to feature number 1, a
2025-08-05 23:58:33.688636 INFO::Fitting model to feature number 2, b
2025-08-05 23:58:33.694446 INFO::Fitting model to feature number 3, c
2025-08-05 23:58:33.703162 INFO::Counting total values for each feature
2025-08-05 23:58:33.705134 INFO::Re-running abundances for warn_prevalence
2025-08-05 23:58:33.705901 INFO::Running selected normalization method: TSS
2025-08-05 23:58:33.707224 INFO::Running selected transform method: LOG
2025-08-05 23:58:33.715832 INFO::Fitting model to feature number 1, a
2025-08-05 23:58:33.72013 INFO::Fitting model to feature number 2, b
2025-08-05 23:58:33.724196 INFO::Fitting model to feature number 3, c
2025-08-05 23:58:33.814022 INFO::Creating output folder
2025-08-05 23:58:33.815053 INFO::Creating output figures folder
2025-08-05 23:58:33.816358 INFO::Writing summary plot of significant
                        results to file: /tmp/RtmpUzPRea/file11eb64263ed351/figures/summary_plot.pdf
2025-08-05 23:58:35.076156 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpUzPRea/file11eb64263ed351/figures
2025-08-05 23:58:35.077968 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-05 23:58:35.082969 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-05 23:58:35.927489 INFO::Applying z-score to standardize continuous metadata
2025-08-05 23:58:35.935233 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-08-05 23:58:35.936131 INFO::Bypass z-score application to metadata
2025-08-05 23:58:35.93859 INFO::Bypass z-score application to metadata
2025-08-05 23:58:35.955671 INFO::Determining format of input files
2025-08-05 23:58:35.956631 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-05 23:58:35.957474 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-08-05 23:58:35.964178 INFO::Determining format of input files
2025-08-05 23:58:35.965138 INFO::Input format is data samples as columns and metadata samples as rows
2025-08-05 23:58:35.966385 INFO::Input format is feature_specific_covariate samples as columns
2025-08-05 23:58:35.973736 INFO::Determining format of input files
2025-08-05 23:58:35.974614 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-05 23:58:35.975578 INFO::Input format is feature_specific_covariate samples as columns
2025-08-05 23:58:35.977154 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-08-05 23:58:35.977894 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-08-05 23:58:35.987983 INFO::Running selected transform method: LOG
2025-08-05 23:58:35.989065 INFO::Creating output feature tables folder
2025-08-05 23:58:35.989909 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpUzPRea/file11eb6430750a69/features/data_transformed.tsv
2025-08-05 23:58:35.993505 INFO::Running selected transform method: LOG
2025-08-05 23:58:35.994494 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpUzPRea/file11eb6430750a69/features/data_transformed.tsv
2025-08-05 23:58:35.99821 INFO::Running selected transform method: PLOG
2025-08-05 23:58:35.999736 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpUzPRea/file11eb6430750a69/features/data_transformed.tsv
2025-08-05 23:58:36.002588 INFO::Running selected transform method: NONE
2025-08-05 23:58:36.003346 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpUzPRea/file11eb6430750a69/features/data_transformed.tsv
2025-08-05 23:58:36.010045 INFO::Running the linear model component
2025-08-05 23:58:36.018411 INFO::Fitting model to feature number 1, a
2025-08-05 23:58:36.022628 INFO::Fitting model to feature number 2, b
2025-08-05 23:58:36.026618 INFO::Fitting model to feature number 3, c
2025-08-05 23:58:36.033544 INFO::Counting total values for each feature
2025-08-05 23:58:36.035164 INFO::Running the logistic model component
2025-08-05 23:58:36.043431 INFO::Fitting model to feature number 1, a
2025-08-05 23:58:36.049586 INFO::Fitting model to feature number 2, b
2025-08-05 23:58:36.055398 INFO::Fitting model to feature number 3, c
2025-08-05 23:58:36.063999 INFO::Counting total values for each feature
2025-08-05 23:58:36.065989 INFO::Re-running abundances for warn_prevalence
2025-08-05 23:58:36.066777 INFO::Running selected normalization method: TSS
2025-08-05 23:58:36.068102 INFO::Running selected transform method: LOG
2025-08-05 23:58:36.076629 INFO::Fitting model to feature number 1, a
2025-08-05 23:58:36.080936 INFO::Fitting model to feature number 2, b
2025-08-05 23:58:36.084964 INFO::Fitting model to feature number 3, c
2025-08-05 23:58:36.172127 INFO::Creating output folder
2025-08-05 23:58:36.173172 INFO::Creating fits folder
2025-08-05 23:58:36.174031 INFO::Writing residuals to file /tmp/RtmpUzPRea/file11eb64302c865b/fits/residuals_linear.rds
2025-08-05 23:58:36.175028 INFO::Writing fitted values to file /tmp/RtmpUzPRea/file11eb64302c865b/fits/fitted_linear.rds
2025-08-05 23:58:36.176224 INFO::Writing residuals to file /tmp/RtmpUzPRea/file11eb64302c865b/fits/residuals_logistic.rds
2025-08-05 23:58:36.177356 INFO::Writing fitted values to file /tmp/RtmpUzPRea/file11eb64302c865b/fits/fitted_logistic.rds
2025-08-05 23:58:36.179856 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /tmp/RtmpUzPRea/file11eb64302c865b/all_results.tsv
2025-08-05 23:58:36.181314 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/RtmpUzPRea/file11eb64302c865b/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]

[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
> 
> 
> proc.time()
   user  system elapsed 
310.306   4.374 314.670 

Example timings

maaslin3.Rcheck/maaslin3-Ex.timings

nameusersystemelapsed
maaslin320.386 0.53120.920
maaslin_check_arguments0.1450.0000.146
maaslin_check_formula0.1330.0020.134
maaslin_compute_formula0.1350.0040.139
maaslin_contrast_test19.164 0.33419.501
maaslin_filter0.4300.0120.442
maaslin_fit13.778 0.13113.910
maaslin_log_arguments0.1440.0020.146
maaslin_normalize0.2910.0030.295
maaslin_plot_results36.986 0.23437.186
maaslin_plot_results_from_output38.039 0.36938.416
maaslin_process_metadata0.4740.0110.486
maaslin_read_data0.1250.0010.127
maaslin_reorder_data0.1300.0010.131
maaslin_transform0.5660.0120.579
maaslin_write_results15.987 0.23616.225
maaslin_write_results_lefse_format14.873 0.08914.963
preprocess_dna_mtx0.0040.0000.004
preprocess_taxa_mtx0.0040.0000.004