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

This page was generated on 2025-10-20 12:04 -0400 (Mon, 20 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4887
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4677
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4622
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4632
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 1164/2353HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maaslin3 1.1.2  (landing page)
William Nickols
Snapshot Date: 2025-10-19 13:45 -0400 (Sun, 19 Oct 2025)
git_url: https://git.bioconductor.org/packages/maaslin3
git_branch: devel
git_last_commit: e7106d5
git_last_commit_date: 2025-10-12 11:00:51 -0400 (Sun, 12 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    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: 1.1.2
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: 2025-10-20 01:26:05 -0400 (Mon, 20 Oct 2025)
EndedAt: 2025-10-20 01:47:10 -0400 (Mon, 20 Oct 2025)
EllapsedTime: 1265.3 seconds
RetCode: 0
Status:   OK  
CheckDir: maaslin3.Rcheck
Warnings: 0

Command output

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


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/maaslin3.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘1.1.2’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘maaslin3’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                     user system elapsed
maaslin_plot_results_from_output   43.070  0.272  43.346
maaslin_plot_results               42.596  0.234  42.809
maaslin3                           19.803  0.650  20.454
maaslin_contrast_test              16.226  0.437  16.665
maaslin_write_results_lefse_format 13.663  0.100  13.763
maaslin_write_results              12.498  0.127  12.627
maaslin_fit                        12.332  0.115  12.447
* 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")
2025-10-20 01:32:07.488254 WARNING::Fitting problem for feature 50 returning NA
2025-10-20 01:32:07.56995 WARNING::Fitting problem for feature 62 returning NA
2025-10-20 01:32:07.672022 WARNING::Fitting problem for feature 74 returning NA
2025-10-20 01:32:07.694013 WARNING::Fitting problem for feature 78 returning NA
2025-10-20 01:32:07.728392 WARNING::Fitting problem for feature 84 returning NA
2025-10-20 01:32:07.80181 WARNING::Fitting problem for feature 96 returning NA
2025-10-20 01:32:07.806999 WARNING::Fitting problem for feature 97 returning NA
2025-10-20 01:32:07.818511 WARNING::Fitting problem for feature 99 returning NA
2025-10-20 01:32:07.919688 WARNING::Fitting problem for feature 114 returning NA
2025-10-20 01:32:07.925134 WARNING::Fitting problem for feature 115 returning NA
2025-10-20 01:32:07.973867 WARNING::Fitting problem for feature 123 returning NA
2025-10-20 01:32:08.012415 WARNING::Fitting problem for feature 130 returning NA
2025-10-20 01:32:08.02355 WARNING::Fitting problem for feature 132 returning NA
2025-10-20 01:32:08.069807 WARNING::Fitting problem for feature 139 returning NA
2025-10-20 01:32:08.137032 WARNING::Fitting problem for feature 150 returning NA
2025-10-20 01:32:23.069061 WARNING::Fitting problem for feature 50 returning NA
2025-10-20 01:32:23.140605 WARNING::Fitting problem for feature 62 returning NA
2025-10-20 01:32:23.225763 WARNING::Fitting problem for feature 74 returning NA
2025-10-20 01:32:23.246966 WARNING::Fitting problem for feature 78 returning NA
2025-10-20 01:32:23.280647 WARNING::Fitting problem for feature 84 returning NA
2025-10-20 01:32:23.354025 WARNING::Fitting problem for feature 96 returning NA
2025-10-20 01:32:23.359177 WARNING::Fitting problem for feature 97 returning NA
2025-10-20 01:32:23.370685 WARNING::Fitting problem for feature 99 returning NA
2025-10-20 01:32:23.464499 WARNING::Fitting problem for feature 114 returning NA
2025-10-20 01:32:23.46996 WARNING::Fitting problem for feature 115 returning NA
2025-10-20 01:32:23.520906 WARNING::Fitting problem for feature 123 returning NA
2025-10-20 01:32:23.55964 WARNING::Fitting problem for feature 130 returning NA
2025-10-20 01:32:23.571037 WARNING::Fitting problem for feature 132 returning NA
2025-10-20 01:32:23.609982 WARNING::Fitting problem for feature 139 returning NA
2025-10-20 01:32:23.677016 WARNING::Fitting problem for feature 150 returning NA
2025-10-20 01:32:47.348192 WARNING::Fitting problem for feature 50 returning NA
2025-10-20 01:32:47.429268 WARNING::Fitting problem for feature 62 returning NA
2025-10-20 01:32:47.503206 WARNING::Fitting problem for feature 74 returning NA
2025-10-20 01:32:47.52489 WARNING::Fitting problem for feature 78 returning NA
2025-10-20 01:32:47.559345 WARNING::Fitting problem for feature 84 returning NA
2025-10-20 01:32:47.635377 WARNING::Fitting problem for feature 96 returning NA
2025-10-20 01:32:47.640772 WARNING::Fitting problem for feature 97 returning NA
2025-10-20 01:32:47.652385 WARNING::Fitting problem for feature 99 returning NA
2025-10-20 01:32:47.745104 WARNING::Fitting problem for feature 114 returning NA
2025-10-20 01:32:47.750502 WARNING::Fitting problem for feature 115 returning NA
2025-10-20 01:32:47.799295 WARNING::Fitting problem for feature 123 returning NA
2025-10-20 01:32:47.839143 WARNING::Fitting problem for feature 130 returning NA
2025-10-20 01:32:47.850786 WARNING::Fitting problem for feature 132 returning NA
2025-10-20 01:32:47.891715 WARNING::Fitting problem for feature 139 returning NA
2025-10-20 01:32:47.961983 WARNING::Fitting problem for feature 150 returning NA
2025-10-20 01:33:00.404464 WARNING::Fitting problem for feature 50 returning NA
2025-10-20 01:33:00.493935 WARNING::Fitting problem for feature 62 returning NA
2025-10-20 01:33:00.567072 WARNING::Fitting problem for feature 74 returning NA
2025-10-20 01:33:00.588474 WARNING::Fitting problem for feature 78 returning NA
2025-10-20 01:33:00.622989 WARNING::Fitting problem for feature 84 returning NA
2025-10-20 01:33:00.696562 WARNING::Fitting problem for feature 96 returning NA
2025-10-20 01:33:00.701854 WARNING::Fitting problem for feature 97 returning NA
2025-10-20 01:33:00.713533 WARNING::Fitting problem for feature 99 returning NA
2025-10-20 01:33:00.807002 WARNING::Fitting problem for feature 114 returning NA
2025-10-20 01:33:00.81269 WARNING::Fitting problem for feature 115 returning NA
2025-10-20 01:33:00.8634 WARNING::Fitting problem for feature 123 returning NA
2025-10-20 01:33:00.903207 WARNING::Fitting problem for feature 130 returning NA
2025-10-20 01:33:00.914775 WARNING::Fitting problem for feature 132 returning NA
2025-10-20 01:33:00.954383 WARNING::Fitting problem for feature 139 returning NA
2025-10-20 01:33:01.021527 WARNING::Fitting problem for feature 150 returning NA
2025-10-20 01:33:01.222492 WARNING::Deleting existing residuals file: /tmp/Rtmpe3IAd8/file3438e724bb2875/fits/residuals_linear.rds
2025-10-20 01:33:01.282903 WARNING::Deleting existing fitted file: /tmp/Rtmpe3IAd8/file3438e724bb2875/fits/fitted_linear.rds
2025-10-20 01:33:01.345178 WARNING::Deleting existing residuals file: /tmp/Rtmpe3IAd8/file3438e724bb2875/fits/residuals_logistic.rds
2025-10-20 01:33:01.642387 WARNING::Deleting existing fitted file: /tmp/Rtmpe3IAd8/file3438e724bb2875/fits/fitted_logistic.rds
2025-10-20 01:33:23.003008 WARNING::Fitting problem for feature 50 returning NA
2025-10-20 01:33:23.077221 WARNING::Fitting problem for feature 62 returning NA
2025-10-20 01:33:23.150458 WARNING::Fitting problem for feature 74 returning NA
2025-10-20 01:33:23.172182 WARNING::Fitting problem for feature 78 returning NA
2025-10-20 01:33:23.206795 WARNING::Fitting problem for feature 84 returning NA
2025-10-20 01:33:23.28806 WARNING::Fitting problem for feature 96 returning NA
2025-10-20 01:33:23.294032 WARNING::Fitting problem for feature 97 returning NA
2025-10-20 01:33:23.30729 WARNING::Fitting problem for feature 99 returning NA
2025-10-20 01:33:23.404302 WARNING::Fitting problem for feature 114 returning NA
2025-10-20 01:33:23.409686 WARNING::Fitting problem for feature 115 returning NA
2025-10-20 01:33:23.459224 WARNING::Fitting problem for feature 123 returning NA
2025-10-20 01:33:23.498911 WARNING::Fitting problem for feature 130 returning NA
2025-10-20 01:33:23.510838 WARNING::Fitting problem for feature 132 returning NA
2025-10-20 01:33:23.551838 WARNING::Fitting problem for feature 139 returning NA
2025-10-20 01:33:24.593317 WARNING::Fitting problem for feature 150 returning NA
2025-10-20 01:33:36.099147 WARNING::Fitting problem for feature 50 returning NA
2025-10-20 01:33:36.175915 WARNING::Fitting problem for feature 62 returning NA
2025-10-20 01:33:36.251809 WARNING::Fitting problem for feature 74 returning NA
2025-10-20 01:33:36.273896 WARNING::Fitting problem for feature 78 returning NA
2025-10-20 01:33:36.307954 WARNING::Fitting problem for feature 84 returning NA
2025-10-20 01:33:36.384699 WARNING::Fitting problem for feature 96 returning NA
2025-10-20 01:33:36.390148 WARNING::Fitting problem for feature 97 returning NA
2025-10-20 01:33:36.402083 WARNING::Fitting problem for feature 99 returning NA
2025-10-20 01:33:36.519628 WARNING::Fitting problem for feature 114 returning NA
2025-10-20 01:33:36.525033 WARNING::Fitting problem for feature 115 returning NA
2025-10-20 01:33:36.575367 WARNING::Fitting problem for feature 123 returning NA
2025-10-20 01:33:36.615299 WARNING::Fitting problem for feature 130 returning NA
2025-10-20 01:33:36.627033 WARNING::Fitting problem for feature 132 returning NA
2025-10-20 01:33:36.66758 WARNING::Fitting problem for feature 139 returning NA
2025-10-20 01:33:36.73673 WARNING::Fitting problem for feature 150 returning NA
2025-10-20 01:33:36.936967 WARNING::Deleting existing residuals file: /tmp/Rtmpe3IAd8/file3438e724bb2875/fits/residuals_linear.rds
2025-10-20 01:33:36.998015 WARNING::Deleting existing fitted file: /tmp/Rtmpe3IAd8/file3438e724bb2875/fits/fitted_linear.rds
2025-10-20 01:33:37.061348 WARNING::Deleting existing residuals file: /tmp/Rtmpe3IAd8/file3438e724bb2875/fits/residuals_logistic.rds
2025-10-20 01:33:37.359039 WARNING::Deleting existing fitted file: /tmp/Rtmpe3IAd8/file3438e724bb2875/fits/fitted_logistic.rds
2025-10-20 01:33:59.441912 WARNING::Fitting problem for feature 50 returning NA
2025-10-20 01:33:59.524437 WARNING::Fitting problem for feature 62 returning NA
2025-10-20 01:33:59.602708 WARNING::Fitting problem for feature 74 returning NA
2025-10-20 01:33:59.626578 WARNING::Fitting problem for feature 78 returning NA
2025-10-20 01:33:59.664186 WARNING::Fitting problem for feature 84 returning NA
2025-10-20 01:33:59.749055 WARNING::Fitting problem for feature 96 returning NA
2025-10-20 01:33:59.754875 WARNING::Fitting problem for feature 97 returning NA
2025-10-20 01:33:59.768134 WARNING::Fitting problem for feature 99 returning NA
2025-10-20 01:33:59.872037 WARNING::Fitting problem for feature 114 returning NA
2025-10-20 01:33:59.87778 WARNING::Fitting problem for feature 115 returning NA
2025-10-20 01:33:59.930461 WARNING::Fitting problem for feature 123 returning NA
2025-10-20 01:33:59.97403 WARNING::Fitting problem for feature 130 returning NA
2025-10-20 01:33:59.986667 WARNING::Fitting problem for feature 132 returning NA
2025-10-20 01:34:00.029852 WARNING::Fitting problem for feature 139 returning NA
2025-10-20 01:34:00.104556 WARNING::Fitting problem for feature 150 returning NA
2025-10-20 01:34:10.680938 WARNING::Fitting problem for feature 50 returning NA
2025-10-20 01:34:10.756304 WARNING::Fitting problem for feature 62 returning NA
2025-10-20 01:34:10.829989 WARNING::Fitting problem for feature 74 returning NA
2025-10-20 01:34:10.852041 WARNING::Fitting problem for feature 78 returning NA
2025-10-20 01:34:10.886016 WARNING::Fitting problem for feature 84 returning NA
2025-10-20 01:34:10.988281 WARNING::Fitting problem for feature 96 returning NA
2025-10-20 01:34:10.99362 WARNING::Fitting problem for feature 97 returning NA
2025-10-20 01:34:11.005329 WARNING::Fitting problem for feature 99 returning NA
2025-10-20 01:34:11.101685 WARNING::Fitting problem for feature 114 returning NA
2025-10-20 01:34:11.107331 WARNING::Fitting problem for feature 115 returning NA
2025-10-20 01:34:11.156989 WARNING::Fitting problem for feature 123 returning NA
2025-10-20 01:34:11.196899 WARNING::Fitting problem for feature 130 returning NA
2025-10-20 01:34:11.20863 WARNING::Fitting problem for feature 132 returning NA
2025-10-20 01:34:11.249249 WARNING::Fitting problem for feature 139 returning NA
2025-10-20 01:34:11.317581 WARNING::Fitting problem for feature 150 returning NA
2025-10-20 01:34:11.51871 WARNING::Deleting existing residuals file: /tmp/Rtmpe3IAd8/file3438e724bb2875/fits/residuals_linear.rds
2025-10-20 01:34:11.579405 WARNING::Deleting existing fitted file: /tmp/Rtmpe3IAd8/file3438e724bb2875/fits/fitted_linear.rds
2025-10-20 01:34:11.64225 WARNING::Deleting existing residuals file: /tmp/Rtmpe3IAd8/file3438e724bb2875/fits/residuals_logistic.rds
2025-10-20 01:34:11.940405 WARNING::Deleting existing fitted file: /tmp/Rtmpe3IAd8/file3438e724bb2875/fits/fitted_logistic.rds
2025-10-20 01:34:32.814404 WARNING::Fitting problem for feature 50 returning NA
2025-10-20 01:34:32.890759 WARNING::Fitting problem for feature 62 returning NA
2025-10-20 01:34:32.967495 WARNING::Fitting problem for feature 74 returning NA
2025-10-20 01:34:32.989483 WARNING::Fitting problem for feature 78 returning NA
2025-10-20 01:34:33.02509 WARNING::Fitting problem for feature 84 returning NA
2025-10-20 01:34:33.100901 WARNING::Fitting problem for feature 96 returning NA
2025-10-20 01:34:33.106319 WARNING::Fitting problem for feature 97 returning NA
2025-10-20 01:34:33.139938 WARNING::Fitting problem for feature 99 returning NA
2025-10-20 01:34:33.236068 WARNING::Fitting problem for feature 114 returning NA
2025-10-20 01:34:33.241545 WARNING::Fitting problem for feature 115 returning NA
2025-10-20 01:34:33.292197 WARNING::Fitting problem for feature 123 returning NA
2025-10-20 01:34:33.33218 WARNING::Fitting problem for feature 130 returning NA
2025-10-20 01:34:33.344064 WARNING::Fitting problem for feature 132 returning NA
2025-10-20 01:34:33.384574 WARNING::Fitting problem for feature 139 returning NA
2025-10-20 01:34:33.453018 WARNING::Fitting problem for feature 150 returning NA
2025-10-20 01:34:45.043105 WARNING::Fitting problem for feature 50 returning NA
2025-10-20 01:34:45.118031 WARNING::Fitting problem for feature 62 returning NA
2025-10-20 01:34:45.192812 WARNING::Fitting problem for feature 74 returning NA
2025-10-20 01:34:45.214406 WARNING::Fitting problem for feature 78 returning NA
2025-10-20 01:34:45.248464 WARNING::Fitting problem for feature 84 returning NA
2025-10-20 01:34:45.336232 WARNING::Fitting problem for feature 96 returning NA
2025-10-20 01:34:45.341751 WARNING::Fitting problem for feature 97 returning NA
2025-10-20 01:34:45.354046 WARNING::Fitting problem for feature 99 returning NA
2025-10-20 01:34:45.451266 WARNING::Fitting problem for feature 114 returning NA
2025-10-20 01:34:45.456716 WARNING::Fitting problem for feature 115 returning NA
2025-10-20 01:34:45.50594 WARNING::Fitting problem for feature 123 returning NA
2025-10-20 01:34:45.544984 WARNING::Fitting problem for feature 130 returning NA
2025-10-20 01:34:45.55655 WARNING::Fitting problem for feature 132 returning NA
2025-10-20 01:34:45.596025 WARNING::Fitting problem for feature 139 returning NA
2025-10-20 01:34:45.664915 WARNING::Fitting problem for feature 150 returning NA
2025-10-20 01:35:09.025178 WARNING::Fitting problem for feature 124 returning NA
2025-10-20 01:35:17.604277 WARNING::Fitting problem for feature 124 returning NA
2025-10-20 01:35:43.608805 WARNING::Fitting problem for feature 124 returning NA
2025-10-20 01:35:51.967721 WARNING::Fitting problem for feature 124 returning NA
2025-10-20 01:35:52.580383 WARNING::Deleting existing residuals file: /tmp/Rtmpe3IAd8/file3438e73909c74e/fits/residuals_linear.rds
2025-10-20 01:35:52.642577 WARNING::Deleting existing fitted file: /tmp/Rtmpe3IAd8/file3438e73909c74e/fits/fitted_linear.rds
2025-10-20 01:35:52.681246 WARNING::Deleting existing residuals file: /tmp/Rtmpe3IAd8/file3438e73909c74e/fits/residuals_logistic.rds
2025-10-20 01:35:52.752404 WARNING::Deleting existing fitted file: /tmp/Rtmpe3IAd8/file3438e73909c74e/fits/fitted_logistic.rds
2025-10-20 01:36:15.401914 WARNING::Fitting problem for feature 124 returning NA
2025-10-20 01:36:21.626073 WARNING::Fitting problem for feature 124 returning NA
2025-10-20 01:36:21.973927 WARNING::Deleting existing residuals file: /tmp/Rtmpe3IAd8/file3438e73909c74e/fits/residuals_linear.rds
2025-10-20 01:36:22.03502 WARNING::Deleting existing fitted file: /tmp/Rtmpe3IAd8/file3438e73909c74e/fits/fitted_linear.rds
2025-10-20 01:36:22.073413 WARNING::Deleting existing residuals file: /tmp/Rtmpe3IAd8/file3438e73909c74e/fits/residuals_logistic.rds
2025-10-20 01:36:22.141493 WARNING::Deleting existing fitted file: /tmp/Rtmpe3IAd8/file3438e73909c74e/fits/fitted_logistic.rds
2025-10-20 01:36:40.624388 WARNING::Fitting problem for feature 124 returning NA
2025-10-20 01:36:46.852275 WARNING::Fitting problem for feature 124 returning NA
2025-10-20 01:36:47.158463 WARNING::Deleting existing residuals file: /tmp/Rtmpe3IAd8/file3438e73909c74e/fits/residuals_linear.rds
2025-10-20 01:36:47.22055 WARNING::Deleting existing fitted file: /tmp/Rtmpe3IAd8/file3438e73909c74e/fits/fitted_linear.rds
2025-10-20 01:36:47.259264 WARNING::Deleting existing residuals file: /tmp/Rtmpe3IAd8/file3438e73909c74e/fits/residuals_logistic.rds
2025-10-20 01:36:47.32965 WARNING::Deleting existing fitted file: /tmp/Rtmpe3IAd8/file3438e73909c74e/fits/fitted_logistic.rds
2025-10-20 01:37:05.2082 WARNING::Fitting problem for feature 50 returning NA
2025-10-20 01:37:05.311925 WARNING::Fitting problem for feature 62 returning NA
2025-10-20 01:37:05.387456 WARNING::Fitting problem for feature 74 returning NA
2025-10-20 01:37:05.410055 WARNING::Fitting problem for feature 78 returning NA
2025-10-20 01:37:05.446165 WARNING::Fitting problem for feature 84 returning NA
2025-10-20 01:37:05.522928 WARNING::Fitting problem for feature 96 returning NA
2025-10-20 01:37:05.528395 WARNING::Fitting problem for feature 97 returning NA
2025-10-20 01:37:05.540565 WARNING::Fitting problem for feature 99 returning NA
2025-10-20 01:37:05.638804 WARNING::Fitting problem for feature 114 returning NA
2025-10-20 01:37:05.644295 WARNING::Fitting problem for feature 115 returning NA
2025-10-20 01:37:05.693233 WARNING::Fitting problem for feature 123 returning NA
2025-10-20 01:37:05.732697 WARNING::Fitting problem for feature 130 returning NA
2025-10-20 01:37:05.744676 WARNING::Fitting problem for feature 132 returning NA
2025-10-20 01:37:05.784509 WARNING::Fitting problem for feature 139 returning NA
2025-10-20 01:37:05.852492 WARNING::Fitting problem for feature 150 returning NA
2025-10-20 01:37:17.569261 WARNING::Fitting problem for feature 50 returning NA
2025-10-20 01:37:17.64421 WARNING::Fitting problem for feature 62 returning NA
2025-10-20 01:37:17.74896 WARNING::Fitting problem for feature 74 returning NA
2025-10-20 01:37:17.771144 WARNING::Fitting problem for feature 78 returning NA
2025-10-20 01:37:17.806296 WARNING::Fitting problem for feature 84 returning NA
2025-10-20 01:37:17.884575 WARNING::Fitting problem for feature 96 returning NA
2025-10-20 01:37:17.890043 WARNING::Fitting problem for feature 97 returning NA
2025-10-20 01:37:17.901856 WARNING::Fitting problem for feature 99 returning NA
2025-10-20 01:37:17.996019 WARNING::Fitting problem for feature 114 returning NA
2025-10-20 01:37:18.001439 WARNING::Fitting problem for feature 115 returning NA
2025-10-20 01:37:18.050776 WARNING::Fitting problem for feature 123 returning NA
2025-10-20 01:37:18.090037 WARNING::Fitting problem for feature 130 returning NA
2025-10-20 01:37:18.101703 WARNING::Fitting problem for feature 132 returning NA
2025-10-20 01:37:18.141525 WARNING::Fitting problem for feature 139 returning NA
2025-10-20 01:37:18.210188 WARNING::Fitting problem for feature 150 returning NA
2025-10-20 01:37:18.460202 WARNING::Deleting existing residuals file: /tmp/Rtmpe3IAd8/file3438e73909c74e/fits/residuals_linear.rds
2025-10-20 01:37:18.52048 WARNING::Deleting existing fitted file: /tmp/Rtmpe3IAd8/file3438e73909c74e/fits/fitted_linear.rds
2025-10-20 01:37:18.583133 WARNING::Deleting existing residuals file: /tmp/Rtmpe3IAd8/file3438e73909c74e/fits/residuals_logistic.rds
2025-10-20 01:37:18.880235 WARNING::Deleting existing fitted file: /tmp/Rtmpe3IAd8/file3438e73909c74e/fits/fitted_logistic.rds
2025-10-20 01:37:38.979355 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-10-20 01:37:38.995931 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-10-20 01:37:39.007042 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-10-20 01:37:39.056494 ERROR::No fixed, group, or
                        ordered effects included in formula.
2025-10-20 01:37:39.072471 ERROR::Effect name not found in metadata: d
2025-10-20 01:37:39.083082 ERROR::No user formula provided
2025-10-20 01:37:39.111489 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-10-20 01:37:39.122696 ERROR::No fixed/group/ordered/
                        feature-specific effects provided.
2025-10-20 01:37:42.197301 INFO::Writing function arguments to log file
2025-10-20 01:37:42.211612 INFO::Verifying options selected are valid
2025-10-20 01:37:44.563905 INFO::Writing function arguments to log file
2025-10-20 01:37:44.575976 INFO::Verifying options selected are valid
2025-10-20 01:37:44.577061 INFO::Determining format of input files
2025-10-20 01:37:44.578053 INFO::Input format is data samples as rows and metadata samples as rows
2025-10-20 01:37:44.5804 INFO::Running selected normalization method: TSS
2025-10-20 01:37:44.581866 INFO::Creating output feature tables folder
2025-10-20 01:37:44.582813 INFO::Writing normalized data to file /tmp/Rtmpe3IAd8/file3438e717553d8b/features/data_norm.tsv
2025-10-20 01:37:44.58427 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-10-20 01:37:44.585157 INFO::Total samples in data: 16
2025-10-20 01:37:44.586003 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-10-20 01:37:44.586848 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-10-20 01:37:44.588731 INFO::Total filtered features: 0
2025-10-20 01:37:44.589664 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-10-20 01:37:44.59078 INFO::Total features filtered by non-zero variance filtering: 0
2025-10-20 01:37:44.5917 INFO::Filtered feature names from variance filtering:
2025-10-20 01:37:44.592556 INFO::Writing filtered data to file /tmp/Rtmpe3IAd8/file3438e717553d8b/features/filtered_data.tsv
2025-10-20 01:37:44.594002 INFO::Running selected transform method: LOG
2025-10-20 01:37:44.595191 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmpe3IAd8/file3438e717553d8b/features/data_transformed.tsv
2025-10-20 01:37:44.596806 INFO::Applying z-score to standardize continuous metadata
2025-10-20 01:37:44.602029 INFO::Running the linear model component
2025-10-20 01:37:44.615996 INFO::Fitting model to feature number 1, a
2025-10-20 01:37:44.620716 INFO::Fitting model to feature number 2, b
2025-10-20 01:37:44.625161 INFO::Fitting model to feature number 3, c
2025-10-20 01:37:44.632876 INFO::Counting total values for each feature
2025-10-20 01:37:44.634863 INFO::Running the logistic model component
2025-10-20 01:37:44.649488 INFO::Fitting model to feature number 1, a
2025-10-20 01:37:44.656552 INFO::Fitting model to feature number 2, b
2025-10-20 01:37:44.663239 INFO::Fitting model to feature number 3, c
2025-10-20 01:37:44.672436 INFO::Counting total values for each feature
2025-10-20 01:37:44.674657 INFO::Re-running abundances for warn_prevalence
2025-10-20 01:37:44.675601 INFO::Running selected normalization method: TSS
2025-10-20 01:37:44.677149 INFO::Running selected transform method: LOG
2025-10-20 01:37:44.691475 INFO::Fitting model to feature number 1, a
2025-10-20 01:37:44.695939 INFO::Fitting model to feature number 2, b
2025-10-20 01:37:44.700265 INFO::Fitting model to feature number 3, c
2025-10-20 01:37:44.787494 INFO::Creating fits folder
2025-10-20 01:37:44.788702 INFO::Writing residuals to file /tmp/Rtmpe3IAd8/file3438e717553d8b/fits/residuals_linear.rds
2025-10-20 01:37:44.789864 INFO::Writing fitted values to file /tmp/Rtmpe3IAd8/file3438e717553d8b/fits/fitted_linear.rds
2025-10-20 01:37:44.791079 INFO::Writing residuals to file /tmp/Rtmpe3IAd8/file3438e717553d8b/fits/residuals_logistic.rds
2025-10-20 01:37:44.792262 INFO::Writing fitted values to file /tmp/Rtmpe3IAd8/file3438e717553d8b/fits/fitted_logistic.rds
2025-10-20 01:37:44.794925 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /tmp/Rtmpe3IAd8/file3438e717553d8b/all_results.tsv
2025-10-20 01:37:44.796557 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/Rtmpe3IAd8/file3438e717553d8b/significant_results.tsv
2025-10-20 01:37:44.79789 INFO::Creating output figures folder
2025-10-20 01:37:44.799245 INFO::Writing summary plot of significant
                        results to file: /tmp/Rtmpe3IAd8/file3438e717553d8b/figures/summary_plot.pdf
2025-10-20 01:37:46.417501 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmpe3IAd8/file3438e717553d8b/figures
2025-10-20 01:37:46.419589 INFO::Plotting associations from most to least significant, grouped by metadata
2025-10-20 01:37:46.424637 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-10-20 01:37:46.944397 INFO::Writing summary plot of
                        significant results to file: /tmp/Rtmpe3IAd8/file3438e717553d8b/figures/summary_plot.pdf
2025-10-20 01:37:48.543654 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmpe3IAd8/file3438e717553d8b/figures
2025-10-20 01:37:48.545156 INFO::Plotting associations from most to least significant, grouped by metadata
2025-10-20 01:37:48.561311 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-10-20 01:37:49.087001 INFO::Running the linear model component
2025-10-20 01:37:49.095663 INFO::Fitting model to feature number 1, a
2025-10-20 01:37:49.099825 INFO::Fitting model to feature number 2, b
2025-10-20 01:37:49.10368 INFO::Fitting model to feature number 3, c
2025-10-20 01:37:49.110326 INFO::Counting total values for each feature
2025-10-20 01:37:49.111915 INFO::Running the logistic model component
2025-10-20 01:37:49.12 INFO::Fitting model to feature number 1, a
2025-10-20 01:37:49.125921 INFO::Fitting model to feature number 2, b
2025-10-20 01:37:49.131525 INFO::Fitting model to feature number 3, c
2025-10-20 01:37:49.139916 INFO::Counting total values for each feature
2025-10-20 01:37:49.14188 INFO::Re-running abundances for warn_prevalence
2025-10-20 01:37:49.142646 INFO::Running selected normalization method: TSS
2025-10-20 01:37:49.143925 INFO::Running selected transform method: LOG
2025-10-20 01:37:49.152299 INFO::Fitting model to feature number 1, a
2025-10-20 01:37:49.156779 INFO::Fitting model to feature number 2, b
2025-10-20 01:37:49.160817 INFO::Fitting model to feature number 3, c
2025-10-20 01:37:49.245142 INFO::Creating output folder
2025-10-20 01:37:49.246053 INFO::Creating output figures folder
2025-10-20 01:37:49.247234 INFO::Writing summary plot of significant
                        results to file: /tmp/Rtmpe3IAd8/file3438e76a05dfdb/figures/summary_plot.pdf
2025-10-20 01:37:50.878258 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmpe3IAd8/file3438e76a05dfdb/figures
2025-10-20 01:37:50.880034 INFO::Plotting associations from most to least significant, grouped by metadata
2025-10-20 01:37:50.885045 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-10-20 01:37:51.846184 INFO::Applying z-score to standardize continuous metadata
2025-10-20 01:37:51.853654 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-10-20 01:37:51.854504 INFO::Bypass z-score application to metadata
2025-10-20 01:37:51.85682 INFO::Bypass z-score application to metadata
2025-10-20 01:37:51.873594 INFO::Determining format of input files
2025-10-20 01:37:51.874546 INFO::Input format is data samples as rows and metadata samples as rows
2025-10-20 01:37:51.875388 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-10-20 01:37:51.882316 INFO::Determining format of input files
2025-10-20 01:37:51.883291 INFO::Input format is data samples as columns and metadata samples as rows
2025-10-20 01:37:51.884577 INFO::Input format is feature_specific_covariate samples as columns
2025-10-20 01:37:51.892147 INFO::Determining format of input files
2025-10-20 01:37:51.89306 INFO::Input format is data samples as rows and metadata samples as rows
2025-10-20 01:37:51.894068 INFO::Input format is feature_specific_covariate samples as columns
2025-10-20 01:37:51.895714 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-10-20 01:37:51.896488 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-10-20 01:37:51.906932 INFO::Running selected transform method: LOG
2025-10-20 01:37:51.908026 INFO::Creating output feature tables folder
2025-10-20 01:37:51.908876 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmpe3IAd8/file3438e77e195b19/features/data_transformed.tsv
2025-10-20 01:37:51.912631 INFO::Running selected transform method: LOG
2025-10-20 01:37:51.913651 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmpe3IAd8/file3438e77e195b19/features/data_transformed.tsv
2025-10-20 01:37:51.917445 INFO::Running selected transform method: PLOG
2025-10-20 01:37:51.930266 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmpe3IAd8/file3438e77e195b19/features/data_transformed.tsv
2025-10-20 01:37:51.933858 INFO::Running selected transform method: NONE
2025-10-20 01:37:51.934756 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmpe3IAd8/file3438e77e195b19/features/data_transformed.tsv
2025-10-20 01:37:51.942847 INFO::Running the linear model component
2025-10-20 01:37:51.951445 INFO::Fitting model to feature number 1, a
2025-10-20 01:37:51.95574 INFO::Fitting model to feature number 2, b
2025-10-20 01:37:51.959789 INFO::Fitting model to feature number 3, c
2025-10-20 01:37:51.966757 INFO::Counting total values for each feature
2025-10-20 01:37:51.968454 INFO::Running the logistic model component
2025-10-20 01:37:51.976942 INFO::Fitting model to feature number 1, a
2025-10-20 01:37:51.983111 INFO::Fitting model to feature number 2, b
2025-10-20 01:37:51.988902 INFO::Fitting model to feature number 3, c
2025-10-20 01:37:51.99757 INFO::Counting total values for each feature
2025-10-20 01:37:51.999531 INFO::Re-running abundances for warn_prevalence
2025-10-20 01:37:52.00029 INFO::Running selected normalization method: TSS
2025-10-20 01:37:52.001607 INFO::Running selected transform method: LOG
2025-10-20 01:37:52.009917 INFO::Fitting model to feature number 1, a
2025-10-20 01:37:52.013905 INFO::Fitting model to feature number 2, b
2025-10-20 01:37:52.017756 INFO::Fitting model to feature number 3, c
2025-10-20 01:37:52.099399 INFO::Creating output folder
2025-10-20 01:37:52.100311 INFO::Creating fits folder
2025-10-20 01:37:52.101101 INFO::Writing residuals to file /tmp/Rtmpe3IAd8/file3438e72aa34d16/fits/residuals_linear.rds
2025-10-20 01:37:52.102032 INFO::Writing fitted values to file /tmp/Rtmpe3IAd8/file3438e72aa34d16/fits/fitted_linear.rds
2025-10-20 01:37:52.103053 INFO::Writing residuals to file /tmp/Rtmpe3IAd8/file3438e72aa34d16/fits/residuals_logistic.rds
2025-10-20 01:37:52.104032 INFO::Writing fitted values to file /tmp/Rtmpe3IAd8/file3438e72aa34d16/fits/fitted_logistic.rds
2025-10-20 01:37:52.106366 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /tmp/Rtmpe3IAd8/file3438e72aa34d16/all_results.tsv
2025-10-20 01:37:52.107836 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/Rtmpe3IAd8/file3438e72aa34d16/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]

[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
> 
> 
> proc.time()
   user  system elapsed 
351.005   4.607 355.582 

Example timings

maaslin3.Rcheck/maaslin3-Ex.timings

nameusersystemelapsed
maaslin319.803 0.65020.454
maaslin_check_arguments0.1170.0000.118
maaslin_check_formula0.1260.0000.127
maaslin_compute_formula0.1290.0000.131
maaslin_contrast_test16.226 0.43716.665
maaslin_filter0.4390.0140.453
maaslin_fit12.332 0.11512.447
maaslin_log_arguments0.1260.0030.129
maaslin_normalize0.2560.0040.261
maaslin_plot_results42.596 0.23442.809
maaslin_plot_results_from_output43.070 0.27243.346
maaslin_process_metadata0.4260.0090.435
maaslin_read_data0.1430.0000.143
maaslin_reorder_data0.1240.0040.129
maaslin_transform0.5190.0100.529
maaslin_write_results12.498 0.12712.627
maaslin_write_results_lefse_format13.663 0.10013.763
preprocess_dna_mtx0.0140.0010.015
preprocess_taxa_mtx0.0050.0000.005