Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2025-10-25 12:03 -0400 (Sat, 25 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4901
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4691
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4637
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4658
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1170/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maaslin3 1.1.2  (landing page)
William Nickols
Snapshot Date: 2025-10-24 13:45 -0400 (Fri, 24 Oct 2025)
git_url: https://git.bioconductor.org/packages/maaslin3
git_branch: devel
git_last_commit: e7106d5
git_last_commit_date: 2025-10-12 11:00:51 -0400 (Sun, 12 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    NA    NA  

CHECK results for maaslin3 on nebbiolo2

To the developers/maintainers of the maaslin3 package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/maaslin3.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: maaslin3
Version: 1.1.2
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings maaslin3_1.1.2.tar.gz
StartedAt: 2025-10-25 01:05:37 -0400 (Sat, 25 Oct 2025)
EndedAt: 2025-10-25 01:27:20 -0400 (Sat, 25 Oct 2025)
EllapsedTime: 1302.5 seconds
RetCode: 0
Status:   OK  
CheckDir: maaslin3.Rcheck
Warnings: 0

Command output

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


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/maaslin3.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘1.1.2’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘maaslin3’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                     user system elapsed
maaslin_plot_results_from_output   43.699  0.247  43.948
maaslin_plot_results               43.497  0.219  43.681
maaslin3                           20.572  0.658  21.232
maaslin_contrast_test              18.298  0.311  18.611
maaslin_write_results_lefse_format 14.773  0.120  14.894
maaslin_write_results              13.672  0.234  13.907
maaslin_fit                        12.481  0.097  12.579
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

maaslin3.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL maaslin3
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘maaslin3’ ...
** this is package ‘maaslin3’ version ‘1.1.2’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (maaslin3)

Tests output

maaslin3.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(maaslin3)
> 
> test_check("maaslin3")
2025-10-25 01:11:52.057678 WARNING::Fitting problem for feature 50 returning NA
2025-10-25 01:11:52.137056 WARNING::Fitting problem for feature 62 returning NA
2025-10-25 01:11:52.234504 WARNING::Fitting problem for feature 74 returning NA
2025-10-25 01:11:52.255577 WARNING::Fitting problem for feature 78 returning NA
2025-10-25 01:11:52.288348 WARNING::Fitting problem for feature 84 returning NA
2025-10-25 01:11:52.36123 WARNING::Fitting problem for feature 96 returning NA
2025-10-25 01:11:52.366338 WARNING::Fitting problem for feature 97 returning NA
2025-10-25 01:11:52.377808 WARNING::Fitting problem for feature 99 returning NA
2025-10-25 01:11:52.476353 WARNING::Fitting problem for feature 114 returning NA
2025-10-25 01:11:52.481695 WARNING::Fitting problem for feature 115 returning NA
2025-10-25 01:11:52.529868 WARNING::Fitting problem for feature 123 returning NA
2025-10-25 01:11:52.56907 WARNING::Fitting problem for feature 130 returning NA
2025-10-25 01:11:52.580502 WARNING::Fitting problem for feature 132 returning NA
2025-10-25 01:11:52.628026 WARNING::Fitting problem for feature 139 returning NA
2025-10-25 01:11:52.697189 WARNING::Fitting problem for feature 150 returning NA
2025-10-25 01:12:08.271211 WARNING::Fitting problem for feature 50 returning NA
2025-10-25 01:12:08.345741 WARNING::Fitting problem for feature 62 returning NA
2025-10-25 01:12:08.434071 WARNING::Fitting problem for feature 74 returning NA
2025-10-25 01:12:08.455986 WARNING::Fitting problem for feature 78 returning NA
2025-10-25 01:12:08.490517 WARNING::Fitting problem for feature 84 returning NA
2025-10-25 01:12:08.566052 WARNING::Fitting problem for feature 96 returning NA
2025-10-25 01:12:08.571389 WARNING::Fitting problem for feature 97 returning NA
2025-10-25 01:12:08.583673 WARNING::Fitting problem for feature 99 returning NA
2025-10-25 01:12:08.678612 WARNING::Fitting problem for feature 114 returning NA
2025-10-25 01:12:08.683815 WARNING::Fitting problem for feature 115 returning NA
2025-10-25 01:12:08.732639 WARNING::Fitting problem for feature 123 returning NA
2025-10-25 01:12:08.772299 WARNING::Fitting problem for feature 130 returning NA
2025-10-25 01:12:08.784163 WARNING::Fitting problem for feature 132 returning NA
2025-10-25 01:12:08.824784 WARNING::Fitting problem for feature 139 returning NA
2025-10-25 01:12:08.893526 WARNING::Fitting problem for feature 150 returning NA
2025-10-25 01:12:33.2652 WARNING::Fitting problem for feature 50 returning NA
2025-10-25 01:12:33.344162 WARNING::Fitting problem for feature 62 returning NA
2025-10-25 01:12:33.418846 WARNING::Fitting problem for feature 74 returning NA
2025-10-25 01:12:33.44068 WARNING::Fitting problem for feature 78 returning NA
2025-10-25 01:12:33.476053 WARNING::Fitting problem for feature 84 returning NA
2025-10-25 01:12:33.555663 WARNING::Fitting problem for feature 96 returning NA
2025-10-25 01:12:33.56152 WARNING::Fitting problem for feature 97 returning NA
2025-10-25 01:12:33.573833 WARNING::Fitting problem for feature 99 returning NA
2025-10-25 01:12:33.672939 WARNING::Fitting problem for feature 114 returning NA
2025-10-25 01:12:33.67848 WARNING::Fitting problem for feature 115 returning NA
2025-10-25 01:12:33.72962 WARNING::Fitting problem for feature 123 returning NA
2025-10-25 01:12:33.772171 WARNING::Fitting problem for feature 130 returning NA
2025-10-25 01:12:33.784267 WARNING::Fitting problem for feature 132 returning NA
2025-10-25 01:12:33.826959 WARNING::Fitting problem for feature 139 returning NA
2025-10-25 01:12:33.899195 WARNING::Fitting problem for feature 150 returning NA
2025-10-25 01:12:46.725955 WARNING::Fitting problem for feature 50 returning NA
2025-10-25 01:12:46.819874 WARNING::Fitting problem for feature 62 returning NA
2025-10-25 01:12:46.896072 WARNING::Fitting problem for feature 74 returning NA
2025-10-25 01:12:46.91794 WARNING::Fitting problem for feature 78 returning NA
2025-10-25 01:12:46.952604 WARNING::Fitting problem for feature 84 returning NA
2025-10-25 01:12:47.029151 WARNING::Fitting problem for feature 96 returning NA
2025-10-25 01:12:47.035015 WARNING::Fitting problem for feature 97 returning NA
2025-10-25 01:12:47.047277 WARNING::Fitting problem for feature 99 returning NA
2025-10-25 01:12:47.143637 WARNING::Fitting problem for feature 114 returning NA
2025-10-25 01:12:47.149111 WARNING::Fitting problem for feature 115 returning NA
2025-10-25 01:12:47.199636 WARNING::Fitting problem for feature 123 returning NA
2025-10-25 01:12:47.241055 WARNING::Fitting problem for feature 130 returning NA
2025-10-25 01:12:47.253163 WARNING::Fitting problem for feature 132 returning NA
2025-10-25 01:12:47.294684 WARNING::Fitting problem for feature 139 returning NA
2025-10-25 01:12:47.366462 WARNING::Fitting problem for feature 150 returning NA
2025-10-25 01:12:47.578298 WARNING::Deleting existing residuals file: /tmp/RtmpjFbmtJ/file3f0ec01e4a8e02/fits/residuals_linear.rds
2025-10-25 01:12:47.639788 WARNING::Deleting existing fitted file: /tmp/RtmpjFbmtJ/file3f0ec01e4a8e02/fits/fitted_linear.rds
2025-10-25 01:12:47.702632 WARNING::Deleting existing residuals file: /tmp/RtmpjFbmtJ/file3f0ec01e4a8e02/fits/residuals_logistic.rds
2025-10-25 01:12:48.000864 WARNING::Deleting existing fitted file: /tmp/RtmpjFbmtJ/file3f0ec01e4a8e02/fits/fitted_logistic.rds
2025-10-25 01:13:09.932797 WARNING::Fitting problem for feature 50 returning NA
2025-10-25 01:13:10.011324 WARNING::Fitting problem for feature 62 returning NA
2025-10-25 01:13:10.087461 WARNING::Fitting problem for feature 74 returning NA
2025-10-25 01:13:10.110807 WARNING::Fitting problem for feature 78 returning NA
2025-10-25 01:13:10.146262 WARNING::Fitting problem for feature 84 returning NA
2025-10-25 01:13:10.222329 WARNING::Fitting problem for feature 96 returning NA
2025-10-25 01:13:10.227926 WARNING::Fitting problem for feature 97 returning NA
2025-10-25 01:13:10.24029 WARNING::Fitting problem for feature 99 returning NA
2025-10-25 01:13:10.336648 WARNING::Fitting problem for feature 114 returning NA
2025-10-25 01:13:10.342148 WARNING::Fitting problem for feature 115 returning NA
2025-10-25 01:13:10.393034 WARNING::Fitting problem for feature 123 returning NA
2025-10-25 01:13:10.433794 WARNING::Fitting problem for feature 130 returning NA
2025-10-25 01:13:10.445658 WARNING::Fitting problem for feature 132 returning NA
2025-10-25 01:13:10.485989 WARNING::Fitting problem for feature 139 returning NA
2025-10-25 01:13:11.618934 WARNING::Fitting problem for feature 150 returning NA
2025-10-25 01:13:23.302348 WARNING::Fitting problem for feature 50 returning NA
2025-10-25 01:13:23.378038 WARNING::Fitting problem for feature 62 returning NA
2025-10-25 01:13:23.452605 WARNING::Fitting problem for feature 74 returning NA
2025-10-25 01:13:23.474288 WARNING::Fitting problem for feature 78 returning NA
2025-10-25 01:13:23.508399 WARNING::Fitting problem for feature 84 returning NA
2025-10-25 01:13:23.590609 WARNING::Fitting problem for feature 96 returning NA
2025-10-25 01:13:23.595986 WARNING::Fitting problem for feature 97 returning NA
2025-10-25 01:13:23.607815 WARNING::Fitting problem for feature 99 returning NA
2025-10-25 01:13:23.736132 WARNING::Fitting problem for feature 114 returning NA
2025-10-25 01:13:23.741767 WARNING::Fitting problem for feature 115 returning NA
2025-10-25 01:13:23.792204 WARNING::Fitting problem for feature 123 returning NA
2025-10-25 01:13:23.833057 WARNING::Fitting problem for feature 130 returning NA
2025-10-25 01:13:23.844986 WARNING::Fitting problem for feature 132 returning NA
2025-10-25 01:13:23.886243 WARNING::Fitting problem for feature 139 returning NA
2025-10-25 01:13:23.95772 WARNING::Fitting problem for feature 150 returning NA
2025-10-25 01:13:24.168519 WARNING::Deleting existing residuals file: /tmp/RtmpjFbmtJ/file3f0ec01e4a8e02/fits/residuals_linear.rds
2025-10-25 01:13:24.229431 WARNING::Deleting existing fitted file: /tmp/RtmpjFbmtJ/file3f0ec01e4a8e02/fits/fitted_linear.rds
2025-10-25 01:13:24.291968 WARNING::Deleting existing residuals file: /tmp/RtmpjFbmtJ/file3f0ec01e4a8e02/fits/residuals_logistic.rds
2025-10-25 01:13:24.590411 WARNING::Deleting existing fitted file: /tmp/RtmpjFbmtJ/file3f0ec01e4a8e02/fits/fitted_logistic.rds
2025-10-25 01:13:47.37273 WARNING::Fitting problem for feature 50 returning NA
2025-10-25 01:13:47.449022 WARNING::Fitting problem for feature 62 returning NA
2025-10-25 01:13:47.523814 WARNING::Fitting problem for feature 74 returning NA
2025-10-25 01:13:47.545234 WARNING::Fitting problem for feature 78 returning NA
2025-10-25 01:13:47.57932 WARNING::Fitting problem for feature 84 returning NA
2025-10-25 01:13:47.654216 WARNING::Fitting problem for feature 96 returning NA
2025-10-25 01:13:47.659545 WARNING::Fitting problem for feature 97 returning NA
2025-10-25 01:13:47.671295 WARNING::Fitting problem for feature 99 returning NA
2025-10-25 01:13:47.767218 WARNING::Fitting problem for feature 114 returning NA
2025-10-25 01:13:47.772748 WARNING::Fitting problem for feature 115 returning NA
2025-10-25 01:13:47.824976 WARNING::Fitting problem for feature 123 returning NA
2025-10-25 01:13:47.870395 WARNING::Fitting problem for feature 130 returning NA
2025-10-25 01:13:47.883559 WARNING::Fitting problem for feature 132 returning NA
2025-10-25 01:13:47.929386 WARNING::Fitting problem for feature 139 returning NA
2025-10-25 01:13:48.011328 WARNING::Fitting problem for feature 150 returning NA
2025-10-25 01:13:58.798655 WARNING::Fitting problem for feature 50 returning NA
2025-10-25 01:13:58.874819 WARNING::Fitting problem for feature 62 returning NA
2025-10-25 01:13:58.950377 WARNING::Fitting problem for feature 74 returning NA
2025-10-25 01:13:58.973018 WARNING::Fitting problem for feature 78 returning NA
2025-10-25 01:13:59.008332 WARNING::Fitting problem for feature 84 returning NA
2025-10-25 01:13:59.115161 WARNING::Fitting problem for feature 96 returning NA
2025-10-25 01:13:59.120667 WARNING::Fitting problem for feature 97 returning NA
2025-10-25 01:13:59.132853 WARNING::Fitting problem for feature 99 returning NA
2025-10-25 01:13:59.229149 WARNING::Fitting problem for feature 114 returning NA
2025-10-25 01:13:59.234652 WARNING::Fitting problem for feature 115 returning NA
2025-10-25 01:13:59.283998 WARNING::Fitting problem for feature 123 returning NA
2025-10-25 01:13:59.324256 WARNING::Fitting problem for feature 130 returning NA
2025-10-25 01:13:59.336141 WARNING::Fitting problem for feature 132 returning NA
2025-10-25 01:13:59.376321 WARNING::Fitting problem for feature 139 returning NA
2025-10-25 01:13:59.445161 WARNING::Fitting problem for feature 150 returning NA
2025-10-25 01:13:59.647363 WARNING::Deleting existing residuals file: /tmp/RtmpjFbmtJ/file3f0ec01e4a8e02/fits/residuals_linear.rds
2025-10-25 01:13:59.70831 WARNING::Deleting existing fitted file: /tmp/RtmpjFbmtJ/file3f0ec01e4a8e02/fits/fitted_linear.rds
2025-10-25 01:13:59.771021 WARNING::Deleting existing residuals file: /tmp/RtmpjFbmtJ/file3f0ec01e4a8e02/fits/residuals_logistic.rds
2025-10-25 01:14:00.072337 WARNING::Deleting existing fitted file: /tmp/RtmpjFbmtJ/file3f0ec01e4a8e02/fits/fitted_logistic.rds
2025-10-25 01:14:21.443468 WARNING::Fitting problem for feature 50 returning NA
2025-10-25 01:14:21.525755 WARNING::Fitting problem for feature 62 returning NA
2025-10-25 01:14:21.608941 WARNING::Fitting problem for feature 74 returning NA
2025-10-25 01:14:21.63423 WARNING::Fitting problem for feature 78 returning NA
2025-10-25 01:14:21.672112 WARNING::Fitting problem for feature 84 returning NA
2025-10-25 01:14:21.751924 WARNING::Fitting problem for feature 96 returning NA
2025-10-25 01:14:21.757496 WARNING::Fitting problem for feature 97 returning NA
2025-10-25 01:14:21.789214 WARNING::Fitting problem for feature 99 returning NA
2025-10-25 01:14:21.895195 WARNING::Fitting problem for feature 114 returning NA
2025-10-25 01:14:21.900873 WARNING::Fitting problem for feature 115 returning NA
2025-10-25 01:14:21.962755 WARNING::Fitting problem for feature 123 returning NA
2025-10-25 01:14:22.005252 WARNING::Fitting problem for feature 130 returning NA
2025-10-25 01:14:22.017988 WARNING::Fitting problem for feature 132 returning NA
2025-10-25 01:14:22.059769 WARNING::Fitting problem for feature 139 returning NA
2025-10-25 01:14:22.132152 WARNING::Fitting problem for feature 150 returning NA
2025-10-25 01:14:35.18356 WARNING::Fitting problem for feature 50 returning NA
2025-10-25 01:14:35.262923 WARNING::Fitting problem for feature 62 returning NA
2025-10-25 01:14:35.343175 WARNING::Fitting problem for feature 74 returning NA
2025-10-25 01:14:35.365375 WARNING::Fitting problem for feature 78 returning NA
2025-10-25 01:14:35.401275 WARNING::Fitting problem for feature 84 returning NA
2025-10-25 01:14:35.476808 WARNING::Fitting problem for feature 96 returning NA
2025-10-25 01:14:35.482111 WARNING::Fitting problem for feature 97 returning NA
2025-10-25 01:14:35.493927 WARNING::Fitting problem for feature 99 returning NA
2025-10-25 01:14:35.589207 WARNING::Fitting problem for feature 114 returning NA
2025-10-25 01:14:35.594822 WARNING::Fitting problem for feature 115 returning NA
2025-10-25 01:14:35.693948 WARNING::Fitting problem for feature 123 returning NA
2025-10-25 01:14:35.735517 WARNING::Fitting problem for feature 130 returning NA
2025-10-25 01:14:35.747781 WARNING::Fitting problem for feature 132 returning NA
2025-10-25 01:14:35.790162 WARNING::Fitting problem for feature 139 returning NA
2025-10-25 01:14:35.863837 WARNING::Fitting problem for feature 150 returning NA
2025-10-25 01:14:59.736969 WARNING::Fitting problem for feature 124 returning NA
2025-10-25 01:15:08.562951 WARNING::Fitting problem for feature 124 returning NA
2025-10-25 01:15:34.582466 WARNING::Fitting problem for feature 124 returning NA
2025-10-25 01:15:43.319105 WARNING::Fitting problem for feature 124 returning NA
2025-10-25 01:15:43.963455 WARNING::Deleting existing residuals file: /tmp/RtmpjFbmtJ/file3f0ec03ea0a7a1/fits/residuals_linear.rds
2025-10-25 01:15:44.024746 WARNING::Deleting existing fitted file: /tmp/RtmpjFbmtJ/file3f0ec03ea0a7a1/fits/fitted_linear.rds
2025-10-25 01:15:44.063064 WARNING::Deleting existing residuals file: /tmp/RtmpjFbmtJ/file3f0ec03ea0a7a1/fits/residuals_logistic.rds
2025-10-25 01:15:44.13133 WARNING::Deleting existing fitted file: /tmp/RtmpjFbmtJ/file3f0ec03ea0a7a1/fits/fitted_logistic.rds
2025-10-25 01:16:06.959965 WARNING::Fitting problem for feature 124 returning NA
2025-10-25 01:16:13.475924 WARNING::Fitting problem for feature 124 returning NA
2025-10-25 01:16:13.794246 WARNING::Deleting existing residuals file: /tmp/RtmpjFbmtJ/file3f0ec03ea0a7a1/fits/residuals_linear.rds
2025-10-25 01:16:13.856062 WARNING::Deleting existing fitted file: /tmp/RtmpjFbmtJ/file3f0ec03ea0a7a1/fits/fitted_linear.rds
2025-10-25 01:16:13.894496 WARNING::Deleting existing residuals file: /tmp/RtmpjFbmtJ/file3f0ec03ea0a7a1/fits/residuals_logistic.rds
2025-10-25 01:16:13.962876 WARNING::Deleting existing fitted file: /tmp/RtmpjFbmtJ/file3f0ec03ea0a7a1/fits/fitted_logistic.rds
2025-10-25 01:16:32.712945 WARNING::Fitting problem for feature 124 returning NA
2025-10-25 01:16:39.120809 WARNING::Fitting problem for feature 124 returning NA
2025-10-25 01:16:39.466369 WARNING::Deleting existing residuals file: /tmp/RtmpjFbmtJ/file3f0ec03ea0a7a1/fits/residuals_linear.rds
2025-10-25 01:16:39.528346 WARNING::Deleting existing fitted file: /tmp/RtmpjFbmtJ/file3f0ec03ea0a7a1/fits/fitted_linear.rds
2025-10-25 01:16:39.566716 WARNING::Deleting existing residuals file: /tmp/RtmpjFbmtJ/file3f0ec03ea0a7a1/fits/residuals_logistic.rds
2025-10-25 01:16:39.634805 WARNING::Deleting existing fitted file: /tmp/RtmpjFbmtJ/file3f0ec03ea0a7a1/fits/fitted_logistic.rds
2025-10-25 01:16:57.836711 WARNING::Fitting problem for feature 50 returning NA
2025-10-25 01:16:57.914353 WARNING::Fitting problem for feature 62 returning NA
2025-10-25 01:16:57.991764 WARNING::Fitting problem for feature 74 returning NA
2025-10-25 01:16:58.014838 WARNING::Fitting problem for feature 78 returning NA
2025-10-25 01:16:58.051325 WARNING::Fitting problem for feature 84 returning NA
2025-10-25 01:16:58.129138 WARNING::Fitting problem for feature 96 returning NA
2025-10-25 01:16:58.134542 WARNING::Fitting problem for feature 97 returning NA
2025-10-25 01:16:58.146482 WARNING::Fitting problem for feature 99 returning NA
2025-10-25 01:16:58.244087 WARNING::Fitting problem for feature 114 returning NA
2025-10-25 01:16:58.249715 WARNING::Fitting problem for feature 115 returning NA
2025-10-25 01:16:58.299655 WARNING::Fitting problem for feature 123 returning NA
2025-10-25 01:16:58.340445 WARNING::Fitting problem for feature 130 returning NA
2025-10-25 01:16:58.35233 WARNING::Fitting problem for feature 132 returning NA
2025-10-25 01:16:58.392448 WARNING::Fitting problem for feature 139 returning NA
2025-10-25 01:16:58.461132 WARNING::Fitting problem for feature 150 returning NA
2025-10-25 01:17:11.344811 WARNING::Fitting problem for feature 50 returning NA
2025-10-25 01:17:11.421713 WARNING::Fitting problem for feature 62 returning NA
2025-10-25 01:17:11.526542 WARNING::Fitting problem for feature 74 returning NA
2025-10-25 01:17:11.549346 WARNING::Fitting problem for feature 78 returning NA
2025-10-25 01:17:11.585201 WARNING::Fitting problem for feature 84 returning NA
2025-10-25 01:17:11.663199 WARNING::Fitting problem for feature 96 returning NA
2025-10-25 01:17:11.668562 WARNING::Fitting problem for feature 97 returning NA
2025-10-25 01:17:11.68053 WARNING::Fitting problem for feature 99 returning NA
2025-10-25 01:17:11.776325 WARNING::Fitting problem for feature 114 returning NA
2025-10-25 01:17:11.781754 WARNING::Fitting problem for feature 115 returning NA
2025-10-25 01:17:11.83152 WARNING::Fitting problem for feature 123 returning NA
2025-10-25 01:17:11.871303 WARNING::Fitting problem for feature 130 returning NA
2025-10-25 01:17:11.883131 WARNING::Fitting problem for feature 132 returning NA
2025-10-25 01:17:11.923512 WARNING::Fitting problem for feature 139 returning NA
2025-10-25 01:17:11.992488 WARNING::Fitting problem for feature 150 returning NA
2025-10-25 01:17:12.259569 WARNING::Deleting existing residuals file: /tmp/RtmpjFbmtJ/file3f0ec03ea0a7a1/fits/residuals_linear.rds
2025-10-25 01:17:12.320772 WARNING::Deleting existing fitted file: /tmp/RtmpjFbmtJ/file3f0ec03ea0a7a1/fits/fitted_linear.rds
2025-10-25 01:17:12.383819 WARNING::Deleting existing residuals file: /tmp/RtmpjFbmtJ/file3f0ec03ea0a7a1/fits/residuals_logistic.rds
2025-10-25 01:17:12.681966 WARNING::Deleting existing fitted file: /tmp/RtmpjFbmtJ/file3f0ec03ea0a7a1/fits/fitted_logistic.rds
2025-10-25 01:17:33.373889 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-10-25 01:17:33.390923 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-10-25 01:17:33.402424 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-10-25 01:17:33.454257 ERROR::No fixed, group, or
                        ordered effects included in formula.
2025-10-25 01:17:33.471484 ERROR::Effect name not found in metadata: d
2025-10-25 01:17:33.482524 ERROR::No user formula provided
2025-10-25 01:17:33.511367 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-10-25 01:17:33.522612 ERROR::No fixed/group/ordered/
                        feature-specific effects provided.
2025-10-25 01:17:36.402514 INFO::Writing function arguments to log file
2025-10-25 01:17:36.416862 INFO::Verifying options selected are valid
2025-10-25 01:17:38.950689 INFO::Writing function arguments to log file
2025-10-25 01:17:38.963875 INFO::Verifying options selected are valid
2025-10-25 01:17:38.96514 INFO::Determining format of input files
2025-10-25 01:17:38.966243 INFO::Input format is data samples as rows and metadata samples as rows
2025-10-25 01:17:38.968855 INFO::Running selected normalization method: TSS
2025-10-25 01:17:38.970463 INFO::Creating output feature tables folder
2025-10-25 01:17:38.971497 INFO::Writing normalized data to file /tmp/RtmpjFbmtJ/file3f0ec0274708f/features/data_norm.tsv
2025-10-25 01:17:38.973053 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-10-25 01:17:38.973989 INFO::Total samples in data: 16
2025-10-25 01:17:38.974924 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-10-25 01:17:38.975866 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-10-25 01:17:38.977912 INFO::Total filtered features: 0
2025-10-25 01:17:38.978922 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-10-25 01:17:38.980173 INFO::Total features filtered by non-zero variance filtering: 0
2025-10-25 01:17:38.981162 INFO::Filtered feature names from variance filtering:
2025-10-25 01:17:38.982082 INFO::Writing filtered data to file /tmp/RtmpjFbmtJ/file3f0ec0274708f/features/filtered_data.tsv
2025-10-25 01:17:38.983684 INFO::Running selected transform method: LOG
2025-10-25 01:17:38.984958 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpjFbmtJ/file3f0ec0274708f/features/data_transformed.tsv
2025-10-25 01:17:38.986703 INFO::Applying z-score to standardize continuous metadata
2025-10-25 01:17:38.992529 INFO::Running the linear model component
2025-10-25 01:17:39.007741 INFO::Fitting model to feature number 1, a
2025-10-25 01:17:39.012638 INFO::Fitting model to feature number 2, b
2025-10-25 01:17:39.017267 INFO::Fitting model to feature number 3, c
2025-10-25 01:17:39.025043 INFO::Counting total values for each feature
2025-10-25 01:17:39.027008 INFO::Running the logistic model component
2025-10-25 01:17:39.041525 INFO::Fitting model to feature number 1, a
2025-10-25 01:17:39.048697 INFO::Fitting model to feature number 2, b
2025-10-25 01:17:39.055432 INFO::Fitting model to feature number 3, c
2025-10-25 01:17:39.065226 INFO::Counting total values for each feature
2025-10-25 01:17:39.067554 INFO::Re-running abundances for warn_prevalence
2025-10-25 01:17:39.068567 INFO::Running selected normalization method: TSS
2025-10-25 01:17:39.07016 INFO::Running selected transform method: LOG
2025-10-25 01:17:39.08459 INFO::Fitting model to feature number 1, a
2025-10-25 01:17:39.08936 INFO::Fitting model to feature number 2, b
2025-10-25 01:17:39.093848 INFO::Fitting model to feature number 3, c
2025-10-25 01:17:39.186893 INFO::Creating fits folder
2025-10-25 01:17:39.188267 INFO::Writing residuals to file /tmp/RtmpjFbmtJ/file3f0ec0274708f/fits/residuals_linear.rds
2025-10-25 01:17:39.189529 INFO::Writing fitted values to file /tmp/RtmpjFbmtJ/file3f0ec0274708f/fits/fitted_linear.rds
2025-10-25 01:17:39.190776 INFO::Writing residuals to file /tmp/RtmpjFbmtJ/file3f0ec0274708f/fits/residuals_logistic.rds
2025-10-25 01:17:39.192029 INFO::Writing fitted values to file /tmp/RtmpjFbmtJ/file3f0ec0274708f/fits/fitted_logistic.rds
2025-10-25 01:17:39.194766 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /tmp/RtmpjFbmtJ/file3f0ec0274708f/all_results.tsv
2025-10-25 01:17:39.196435 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/RtmpjFbmtJ/file3f0ec0274708f/significant_results.tsv
2025-10-25 01:17:39.197832 INFO::Creating output figures folder
2025-10-25 01:17:39.199236 INFO::Writing summary plot of significant
                        results to file: /tmp/RtmpjFbmtJ/file3f0ec0274708f/figures/summary_plot.pdf
2025-10-25 01:17:40.858267 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpjFbmtJ/file3f0ec0274708f/figures
2025-10-25 01:17:40.860216 INFO::Plotting associations from most to least significant, grouped by metadata
2025-10-25 01:17:40.865318 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-10-25 01:17:41.390606 INFO::Writing summary plot of
                        significant results to file: /tmp/RtmpjFbmtJ/file3f0ec0274708f/figures/summary_plot.pdf
2025-10-25 01:17:43.071295 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpjFbmtJ/file3f0ec0274708f/figures
2025-10-25 01:17:43.073023 INFO::Plotting associations from most to least significant, grouped by metadata
2025-10-25 01:17:43.078475 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-10-25 01:17:43.614558 INFO::Running the linear model component
2025-10-25 01:17:43.62334 INFO::Fitting model to feature number 1, a
2025-10-25 01:17:43.627593 INFO::Fitting model to feature number 2, b
2025-10-25 01:17:43.631564 INFO::Fitting model to feature number 3, c
2025-10-25 01:17:43.638455 INFO::Counting total values for each feature
2025-10-25 01:17:43.648004 INFO::Running the logistic model component
2025-10-25 01:17:43.657731 INFO::Fitting model to feature number 1, a
2025-10-25 01:17:43.664646 INFO::Fitting model to feature number 2, b
2025-10-25 01:17:43.671069 INFO::Fitting model to feature number 3, c
2025-10-25 01:17:43.680445 INFO::Counting total values for each feature
2025-10-25 01:17:43.682784 INFO::Re-running abundances for warn_prevalence
2025-10-25 01:17:43.683696 INFO::Running selected normalization method: TSS
2025-10-25 01:17:43.685239 INFO::Running selected transform method: LOG
2025-10-25 01:17:43.696199 INFO::Fitting model to feature number 1, a
2025-10-25 01:17:43.701637 INFO::Fitting model to feature number 2, b
2025-10-25 01:17:43.706509 INFO::Fitting model to feature number 3, c
2025-10-25 01:17:43.797566 INFO::Creating output folder
2025-10-25 01:17:43.79855 INFO::Creating output figures folder
2025-10-25 01:17:43.799794 INFO::Writing summary plot of significant
                        results to file: /tmp/RtmpjFbmtJ/file3f0ec01d24af72/figures/summary_plot.pdf
2025-10-25 01:17:45.441629 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpjFbmtJ/file3f0ec01d24af72/figures
2025-10-25 01:17:45.443378 INFO::Plotting associations from most to least significant, grouped by metadata
2025-10-25 01:17:45.448321 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-10-25 01:17:46.436833 INFO::Applying z-score to standardize continuous metadata
2025-10-25 01:17:46.444751 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-10-25 01:17:46.44566 INFO::Bypass z-score application to metadata
2025-10-25 01:17:46.448106 INFO::Bypass z-score application to metadata
2025-10-25 01:17:46.465487 INFO::Determining format of input files
2025-10-25 01:17:46.466469 INFO::Input format is data samples as rows and metadata samples as rows
2025-10-25 01:17:46.467331 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-10-25 01:17:46.474336 INFO::Determining format of input files
2025-10-25 01:17:46.475345 INFO::Input format is data samples as columns and metadata samples as rows
2025-10-25 01:17:46.476664 INFO::Input format is feature_specific_covariate samples as columns
2025-10-25 01:17:46.484524 INFO::Determining format of input files
2025-10-25 01:17:46.485552 INFO::Input format is data samples as rows and metadata samples as rows
2025-10-25 01:17:46.486606 INFO::Input format is feature_specific_covariate samples as columns
2025-10-25 01:17:46.488346 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-10-25 01:17:46.489145 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-10-25 01:17:46.500197 INFO::Running selected transform method: LOG
2025-10-25 01:17:46.502315 INFO::Creating output feature tables folder
2025-10-25 01:17:46.503582 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpjFbmtJ/file3f0ec05ce0ac8a/features/data_transformed.tsv
2025-10-25 01:17:46.519009 INFO::Running selected transform method: LOG
2025-10-25 01:17:46.520423 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpjFbmtJ/file3f0ec05ce0ac8a/features/data_transformed.tsv
2025-10-25 01:17:46.525257 INFO::Running selected transform method: PLOG
2025-10-25 01:17:46.527258 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpjFbmtJ/file3f0ec05ce0ac8a/features/data_transformed.tsv
2025-10-25 01:17:46.530479 INFO::Running selected transform method: NONE
2025-10-25 01:17:46.531261 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpjFbmtJ/file3f0ec05ce0ac8a/features/data_transformed.tsv
2025-10-25 01:17:46.538428 INFO::Running the linear model component
2025-10-25 01:17:46.547016 INFO::Fitting model to feature number 1, a
2025-10-25 01:17:46.551292 INFO::Fitting model to feature number 2, b
2025-10-25 01:17:46.555326 INFO::Fitting model to feature number 3, c
2025-10-25 01:17:46.562352 INFO::Counting total values for each feature
2025-10-25 01:17:46.564001 INFO::Running the logistic model component
2025-10-25 01:17:46.572759 INFO::Fitting model to feature number 1, a
2025-10-25 01:17:46.579498 INFO::Fitting model to feature number 2, b
2025-10-25 01:17:46.585575 INFO::Fitting model to feature number 3, c
2025-10-25 01:17:46.594426 INFO::Counting total values for each feature
2025-10-25 01:17:46.596385 INFO::Re-running abundances for warn_prevalence
2025-10-25 01:17:46.597157 INFO::Running selected normalization method: TSS
2025-10-25 01:17:46.598485 INFO::Running selected transform method: LOG
2025-10-25 01:17:46.606902 INFO::Fitting model to feature number 1, a
2025-10-25 01:17:46.610956 INFO::Fitting model to feature number 2, b
2025-10-25 01:17:46.614827 INFO::Fitting model to feature number 3, c
2025-10-25 01:17:46.700971 INFO::Creating output folder
2025-10-25 01:17:46.70192 INFO::Creating fits folder
2025-10-25 01:17:46.702732 INFO::Writing residuals to file /tmp/RtmpjFbmtJ/file3f0ec08025e80/fits/residuals_linear.rds
2025-10-25 01:17:46.703676 INFO::Writing fitted values to file /tmp/RtmpjFbmtJ/file3f0ec08025e80/fits/fitted_linear.rds
2025-10-25 01:17:46.704704 INFO::Writing residuals to file /tmp/RtmpjFbmtJ/file3f0ec08025e80/fits/residuals_logistic.rds
2025-10-25 01:17:46.705711 INFO::Writing fitted values to file /tmp/RtmpjFbmtJ/file3f0ec08025e80/fits/fitted_logistic.rds
2025-10-25 01:17:46.708104 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /tmp/RtmpjFbmtJ/file3f0ec08025e80/all_results.tsv
2025-10-25 01:17:46.709558 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/RtmpjFbmtJ/file3f0ec08025e80/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]

[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
> 
> 
> proc.time()
   user  system elapsed 
360.989   4.686 365.667

Example timings

maaslin3.Rcheck/maaslin3-Ex.timings

nameusersystemelapsed
maaslin320.572 0.65821.232
maaslin_check_arguments0.1460.0020.148
maaslin_check_formula0.1390.0010.140
maaslin_compute_formula0.1430.0010.144
maaslin_contrast_test18.298 0.31118.611
maaslin_filter0.4410.0120.453
maaslin_fit12.481 0.09712.579
maaslin_log_arguments0.1290.0010.131
maaslin_normalize0.2580.0030.261
maaslin_plot_results43.497 0.21943.681
maaslin_plot_results_from_output43.699 0.24743.948
maaslin_process_metadata0.4480.0100.459
maaslin_read_data0.1340.0020.136
maaslin_reorder_data0.1430.0010.143
maaslin_transform0.5460.0410.587
maaslin_write_results13.672 0.23413.907
maaslin_write_results_lefse_format14.773 0.12014.894
preprocess_dna_mtx0.0030.0000.003
preprocess_taxa_mtx0.0040.0000.003