Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-10-16 11:40 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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 1155/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maaslin3 1.0.2  (landing page)
William Nickols
Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/maaslin3
git_branch: RELEASE_3_21
git_last_commit: d86be18
git_last_commit_date: 2025-10-12 11:15:12 -0400 (Sun, 12 Oct 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  YES
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    OK    OK  YES
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for maaslin3 on kjohnson1

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: 1.0.2
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings maaslin3_1.0.2.tar.gz
StartedAt: 2025-10-15 02:07:40 -0400 (Wed, 15 Oct 2025)
EndedAt: 2025-10-15 02:22:30 -0400 (Wed, 15 Oct 2025)
EllapsedTime: 889.8 seconds
RetCode: 0
Status:   OK  
CheckDir: maaslin3.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings maaslin3_1.0.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/maaslin3.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘1.0.2’
* 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 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               52.197  2.183  54.902
maaslin_plot_results_from_output   52.655  1.551  54.706
maaslin3                           24.777  1.244  26.112
maaslin_contrast_test              22.360  1.621  24.081
maaslin_write_results_lefse_format 18.135  1.102  19.396
maaslin_write_results              17.031  1.087  18.272
maaslin_fit                        14.757  0.818  15.606
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

maaslin3.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL maaslin3
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘maaslin3’ ...
** this is package ‘maaslin3’ version ‘1.0.2’
** 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 (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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")
2025-10-15 02:15:01.860392 WARNING::Fitting problem for feature 50 returning NA
2025-10-15 02:15:01.974421 WARNING::Fitting problem for feature 62 returning NA
2025-10-15 02:15:02.05777 WARNING::Fitting problem for feature 74 returning NA
2025-10-15 02:15:02.088848 WARNING::Fitting problem for feature 78 returning NA
2025-10-15 02:15:02.12557 WARNING::Fitting problem for feature 84 returning NA
2025-10-15 02:15:02.21658 WARNING::Fitting problem for feature 96 returning NA
2025-10-15 02:15:02.223655 WARNING::Fitting problem for feature 97 returning NA
2025-10-15 02:15:02.237115 WARNING::Fitting problem for feature 99 returning NA
2025-10-15 02:15:02.369083 WARNING::Fitting problem for feature 114 returning NA
2025-10-15 02:15:02.375498 WARNING::Fitting problem for feature 115 returning NA
2025-10-15 02:15:02.433212 WARNING::Fitting problem for feature 123 returning NA
2025-10-15 02:15:02.512353 WARNING::Fitting problem for feature 130 returning NA
2025-10-15 02:15:02.52819 WARNING::Fitting problem for feature 132 returning NA
2025-10-15 02:15:02.58384 WARNING::Fitting problem for feature 139 returning NA
2025-10-15 02:15:02.66693 WARNING::Fitting problem for feature 150 returning NA
2025-10-15 02:15:22.57811 WARNING::Fitting problem for feature 50 returning NA
2025-10-15 02:15:22.678648 WARNING::Fitting problem for feature 62 returning NA
2025-10-15 02:15:22.771309 WARNING::Fitting problem for feature 74 returning NA
2025-10-15 02:15:22.800136 WARNING::Fitting problem for feature 78 returning NA
2025-10-15 02:15:22.843264 WARNING::Fitting problem for feature 84 returning NA
2025-10-15 02:15:22.959101 WARNING::Fitting problem for feature 96 returning NA
2025-10-15 02:15:22.96707 WARNING::Fitting problem for feature 97 returning NA
2025-10-15 02:15:22.987505 WARNING::Fitting problem for feature 99 returning NA
2025-10-15 02:15:23.134479 WARNING::Fitting problem for feature 114 returning NA
2025-10-15 02:15:23.143162 WARNING::Fitting problem for feature 115 returning NA
2025-10-15 02:15:23.210965 WARNING::Fitting problem for feature 123 returning NA
2025-10-15 02:15:23.261502 WARNING::Fitting problem for feature 130 returning NA
2025-10-15 02:15:23.275363 WARNING::Fitting problem for feature 132 returning NA
2025-10-15 02:15:23.326269 WARNING::Fitting problem for feature 139 returning NA
2025-10-15 02:15:23.413024 WARNING::Fitting problem for feature 150 returning NA
2025-10-15 02:15:29.358 R[5823:458002370] XType: Using static font registry.
2025-10-15 02:15:52.270794 WARNING::Fitting problem for feature 50 returning NA
2025-10-15 02:15:52.369411 WARNING::Fitting problem for feature 62 returning NA
2025-10-15 02:15:52.465829 WARNING::Fitting problem for feature 74 returning NA
2025-10-15 02:15:52.502709 WARNING::Fitting problem for feature 78 returning NA
2025-10-15 02:15:52.549565 WARNING::Fitting problem for feature 84 returning NA
2025-10-15 02:15:52.646006 WARNING::Fitting problem for feature 96 returning NA
2025-10-15 02:15:52.652751 WARNING::Fitting problem for feature 97 returning NA
2025-10-15 02:15:52.666031 WARNING::Fitting problem for feature 99 returning NA
2025-10-15 02:15:52.784334 WARNING::Fitting problem for feature 114 returning NA
2025-10-15 02:15:52.791888 WARNING::Fitting problem for feature 115 returning NA
2025-10-15 02:15:52.857212 WARNING::Fitting problem for feature 123 returning NA
2025-10-15 02:15:52.910724 WARNING::Fitting problem for feature 130 returning NA
2025-10-15 02:15:52.92541 WARNING::Fitting problem for feature 132 returning NA
2025-10-15 02:15:52.974208 WARNING::Fitting problem for feature 139 returning NA
2025-10-15 02:15:53.060409 WARNING::Fitting problem for feature 150 returning NA
2025-10-15 02:16:09.667573 WARNING::Fitting problem for feature 50 returning NA
2025-10-15 02:16:09.765287 WARNING::Fitting problem for feature 62 returning NA
2025-10-15 02:16:09.861331 WARNING::Fitting problem for feature 74 returning NA
2025-10-15 02:16:09.895359 WARNING::Fitting problem for feature 78 returning NA
2025-10-15 02:16:09.946894 WARNING::Fitting problem for feature 84 returning NA
2025-10-15 02:16:10.0355 WARNING::Fitting problem for feature 96 returning NA
2025-10-15 02:16:10.04197 WARNING::Fitting problem for feature 97 returning NA
2025-10-15 02:16:10.055712 WARNING::Fitting problem for feature 99 returning NA
2025-10-15 02:16:10.163873 WARNING::Fitting problem for feature 114 returning NA
2025-10-15 02:16:10.170363 WARNING::Fitting problem for feature 115 returning NA
2025-10-15 02:16:10.231596 WARNING::Fitting problem for feature 123 returning NA
2025-10-15 02:16:10.282823 WARNING::Fitting problem for feature 130 returning NA
2025-10-15 02:16:10.2973 WARNING::Fitting problem for feature 132 returning NA
2025-10-15 02:16:10.380375 WARNING::Fitting problem for feature 139 returning NA
2025-10-15 02:16:10.457986 WARNING::Fitting problem for feature 150 returning NA
2025-10-15 02:16:10.68677 WARNING::Deleting existing residuals file: /tmp/RtmpEiOpl0/file16bf294b12a2/fits/residuals_linear.rds
2025-10-15 02:16:10.788673 WARNING::Deleting existing fitted file: /tmp/RtmpEiOpl0/file16bf294b12a2/fits/fitted_linear.rds
2025-10-15 02:16:10.893318 WARNING::Deleting existing residuals file: /tmp/RtmpEiOpl0/file16bf294b12a2/fits/residuals_logistic.rds
2025-10-15 02:16:11.409867 WARNING::Deleting existing fitted file: /tmp/RtmpEiOpl0/file16bf294b12a2/fits/fitted_logistic.rds
2025-10-15 02:16:38.98905 WARNING::Fitting problem for feature 50 returning NA
2025-10-15 02:16:39.082299 WARNING::Fitting problem for feature 62 returning NA
2025-10-15 02:16:39.175242 WARNING::Fitting problem for feature 74 returning NA
2025-10-15 02:16:39.202998 WARNING::Fitting problem for feature 78 returning NA
2025-10-15 02:16:39.249388 WARNING::Fitting problem for feature 84 returning NA
2025-10-15 02:16:39.335154 WARNING::Fitting problem for feature 96 returning NA
2025-10-15 02:16:39.342192 WARNING::Fitting problem for feature 97 returning NA
2025-10-15 02:16:39.356689 WARNING::Fitting problem for feature 99 returning NA
2025-10-15 02:16:39.467395 WARNING::Fitting problem for feature 114 returning NA
2025-10-15 02:16:39.474589 WARNING::Fitting problem for feature 115 returning NA
2025-10-15 02:16:39.535638 WARNING::Fitting problem for feature 123 returning NA
2025-10-15 02:16:39.586323 WARNING::Fitting problem for feature 130 returning NA
2025-10-15 02:16:39.60127 WARNING::Fitting problem for feature 132 returning NA
2025-10-15 02:16:39.649161 WARNING::Fitting problem for feature 139 returning NA
2025-10-15 02:16:39.727185 WARNING::Fitting problem for feature 150 returning NA
2025-10-15 02:16:54.81716 WARNING::Fitting problem for feature 50 returning NA
2025-10-15 02:16:54.909988 WARNING::Fitting problem for feature 62 returning NA
2025-10-15 02:16:55.004322 WARNING::Fitting problem for feature 74 returning NA
2025-10-15 02:16:55.032059 WARNING::Fitting problem for feature 78 returning NA
2025-10-15 02:16:55.076029 WARNING::Fitting problem for feature 84 returning NA
2025-10-15 02:16:55.168637 WARNING::Fitting problem for feature 96 returning NA
2025-10-15 02:16:55.175679 WARNING::Fitting problem for feature 97 returning NA
2025-10-15 02:16:55.19271 WARNING::Fitting problem for feature 99 returning NA
2025-10-15 02:16:55.310878 WARNING::Fitting problem for feature 114 returning NA
2025-10-15 02:16:55.317977 WARNING::Fitting problem for feature 115 returning NA
2025-10-15 02:16:55.386528 WARNING::Fitting problem for feature 123 returning NA
2025-10-15 02:16:55.441783 WARNING::Fitting problem for feature 130 returning NA
2025-10-15 02:16:55.458711 WARNING::Fitting problem for feature 132 returning NA
2025-10-15 02:16:55.523663 WARNING::Fitting problem for feature 139 returning NA
2025-10-15 02:16:55.619038 WARNING::Fitting problem for feature 150 returning NA
2025-10-15 02:16:55.916666 WARNING::Deleting existing residuals file: /tmp/RtmpEiOpl0/file16bf294b12a2/fits/residuals_linear.rds
2025-10-15 02:16:56.012998 WARNING::Deleting existing fitted file: /tmp/RtmpEiOpl0/file16bf294b12a2/fits/fitted_linear.rds
2025-10-15 02:16:56.119333 WARNING::Deleting existing residuals file: /tmp/RtmpEiOpl0/file16bf294b12a2/fits/residuals_logistic.rds
2025-10-15 02:16:56.640695 WARNING::Deleting existing fitted file: /tmp/RtmpEiOpl0/file16bf294b12a2/fits/fitted_logistic.rds
2025-10-15 02:17:23.589227 WARNING::Fitting problem for feature 50 returning NA
2025-10-15 02:17:23.685852 WARNING::Fitting problem for feature 62 returning NA
2025-10-15 02:17:23.783373 WARNING::Fitting problem for feature 74 returning NA
2025-10-15 02:17:23.808769 WARNING::Fitting problem for feature 78 returning NA
2025-10-15 02:17:23.851865 WARNING::Fitting problem for feature 84 returning NA
2025-10-15 02:17:23.950808 WARNING::Fitting problem for feature 96 returning NA
2025-10-15 02:17:23.957617 WARNING::Fitting problem for feature 97 returning NA
2025-10-15 02:17:23.972279 WARNING::Fitting problem for feature 99 returning NA
2025-10-15 02:17:24.092913 WARNING::Fitting problem for feature 114 returning NA
2025-10-15 02:17:24.102947 WARNING::Fitting problem for feature 115 returning NA
2025-10-15 02:17:24.165419 WARNING::Fitting problem for feature 123 returning NA
2025-10-15 02:17:24.216092 WARNING::Fitting problem for feature 130 returning NA
2025-10-15 02:17:24.231376 WARNING::Fitting problem for feature 132 returning NA
2025-10-15 02:17:24.280836 WARNING::Fitting problem for feature 139 returning NA
2025-10-15 02:17:24.425601 WARNING::Fitting problem for feature 150 returning NA
2025-10-15 02:17:38.14498 WARNING::Fitting problem for feature 50 returning NA
2025-10-15 02:17:38.237467 WARNING::Fitting problem for feature 62 returning NA
2025-10-15 02:17:38.329595 WARNING::Fitting problem for feature 74 returning NA
2025-10-15 02:17:38.356376 WARNING::Fitting problem for feature 78 returning NA
2025-10-15 02:17:38.399327 WARNING::Fitting problem for feature 84 returning NA
2025-10-15 02:17:38.492051 WARNING::Fitting problem for feature 96 returning NA
2025-10-15 02:17:38.498802 WARNING::Fitting problem for feature 97 returning NA
2025-10-15 02:17:38.515186 WARNING::Fitting problem for feature 99 returning NA
2025-10-15 02:17:38.634762 WARNING::Fitting problem for feature 114 returning NA
2025-10-15 02:17:38.642193 WARNING::Fitting problem for feature 115 returning NA
2025-10-15 02:17:38.705628 WARNING::Fitting problem for feature 123 returning NA
2025-10-15 02:17:38.761305 WARNING::Fitting problem for feature 130 returning NA
2025-10-15 02:17:38.776846 WARNING::Fitting problem for feature 132 returning NA
2025-10-15 02:17:38.82787 WARNING::Fitting problem for feature 139 returning NA
2025-10-15 02:17:38.903843 WARNING::Fitting problem for feature 150 returning NA
2025-10-15 02:17:39.174884 WARNING::Deleting existing residuals file: /tmp/RtmpEiOpl0/file16bf294b12a2/fits/residuals_linear.rds
2025-10-15 02:17:39.27583 WARNING::Deleting existing fitted file: /tmp/RtmpEiOpl0/file16bf294b12a2/fits/fitted_linear.rds
2025-10-15 02:17:39.381037 WARNING::Deleting existing residuals file: /tmp/RtmpEiOpl0/file16bf294b12a2/fits/residuals_logistic.rds
2025-10-15 02:17:39.609521 WARNING::Deleting existing fitted file: /tmp/RtmpEiOpl0/file16bf294b12a2/fits/fitted_logistic.rds
2025-10-15 02:18:06.69441 WARNING::Fitting problem for feature 50 returning NA
2025-10-15 02:18:06.791733 WARNING::Fitting problem for feature 62 returning NA
2025-10-15 02:18:06.886944 WARNING::Fitting problem for feature 74 returning NA
2025-10-15 02:18:06.916013 WARNING::Fitting problem for feature 78 returning NA
2025-10-15 02:18:06.959287 WARNING::Fitting problem for feature 84 returning NA
2025-10-15 02:18:07.047942 WARNING::Fitting problem for feature 96 returning NA
2025-10-15 02:18:07.05481 WARNING::Fitting problem for feature 97 returning NA
2025-10-15 02:18:07.069107 WARNING::Fitting problem for feature 99 returning NA
2025-10-15 02:18:07.186908 WARNING::Fitting problem for feature 114 returning NA
2025-10-15 02:18:07.193716 WARNING::Fitting problem for feature 115 returning NA
2025-10-15 02:18:07.248641 WARNING::Fitting problem for feature 123 returning NA
2025-10-15 02:18:07.294281 WARNING::Fitting problem for feature 130 returning NA
2025-10-15 02:18:07.308446 WARNING::Fitting problem for feature 132 returning NA
2025-10-15 02:18:07.357553 WARNING::Fitting problem for feature 139 returning NA
2025-10-15 02:18:07.481507 WARNING::Fitting problem for feature 150 returning NA
2025-10-15 02:18:21.058695 WARNING::Fitting problem for feature 50 returning NA
2025-10-15 02:18:21.15486 WARNING::Fitting problem for feature 62 returning NA
2025-10-15 02:18:21.245576 WARNING::Fitting problem for feature 74 returning NA
2025-10-15 02:18:21.271241 WARNING::Fitting problem for feature 78 returning NA
2025-10-15 02:18:21.309056 WARNING::Fitting problem for feature 84 returning NA
2025-10-15 02:18:21.405654 WARNING::Fitting problem for feature 96 returning NA
2025-10-15 02:18:21.413302 WARNING::Fitting problem for feature 97 returning NA
2025-10-15 02:18:21.426446 WARNING::Fitting problem for feature 99 returning NA
2025-10-15 02:18:21.542806 WARNING::Fitting problem for feature 114 returning NA
2025-10-15 02:18:21.549875 WARNING::Fitting problem for feature 115 returning NA
2025-10-15 02:18:21.612867 WARNING::Fitting problem for feature 123 returning NA
2025-10-15 02:18:21.679806 WARNING::Fitting problem for feature 130 returning NA
2025-10-15 02:18:21.696629 WARNING::Fitting problem for feature 132 returning NA
2025-10-15 02:18:21.747743 WARNING::Fitting problem for feature 139 returning NA
2025-10-15 02:18:21.828553 WARNING::Fitting problem for feature 150 returning NA
2025-10-15 02:18:53.430044 WARNING::Fitting problem for feature 124 returning NA
2025-10-15 02:19:03.116117 WARNING::Fitting problem for feature 124 returning NA
2025-10-15 02:19:33.545608 WARNING::Fitting problem for feature 124 returning NA
2025-10-15 02:19:45.456105 WARNING::Fitting problem for feature 124 returning NA
2025-10-15 02:19:46.095686 WARNING::Deleting existing residuals file: /tmp/RtmpEiOpl0/file16bf26c8e493/fits/residuals_linear.rds
2025-10-15 02:19:46.196052 WARNING::Deleting existing fitted file: /tmp/RtmpEiOpl0/file16bf26c8e493/fits/fitted_linear.rds
2025-10-15 02:19:46.264297 WARNING::Deleting existing residuals file: /tmp/RtmpEiOpl0/file16bf26c8e493/fits/residuals_logistic.rds
2025-10-15 02:19:46.387804 WARNING::Deleting existing fitted file: /tmp/RtmpEiOpl0/file16bf26c8e493/fits/fitted_logistic.rds
2025-10-15 02:20:14.613395 WARNING::Fitting problem for feature 124 returning NA
2025-10-15 02:20:21.252251 WARNING::Fitting problem for feature 124 returning NA
2025-10-15 02:20:21.60005 WARNING::Deleting existing residuals file: /tmp/RtmpEiOpl0/file16bf26c8e493/fits/residuals_linear.rds
2025-10-15 02:20:21.700369 WARNING::Deleting existing fitted file: /tmp/RtmpEiOpl0/file16bf26c8e493/fits/fitted_linear.rds
2025-10-15 02:20:21.767839 WARNING::Deleting existing residuals file: /tmp/RtmpEiOpl0/file16bf26c8e493/fits/residuals_logistic.rds
2025-10-15 02:20:21.890054 WARNING::Deleting existing fitted file: /tmp/RtmpEiOpl0/file16bf26c8e493/fits/fitted_logistic.rds
2025-10-15 02:20:46.471651 WARNING::Fitting problem for feature 124 returning NA
2025-10-15 02:20:54.808981 WARNING::Fitting problem for feature 124 returning NA
2025-10-15 02:20:55.149737 WARNING::Deleting existing residuals file: /tmp/RtmpEiOpl0/file16bf26c8e493/fits/residuals_linear.rds
2025-10-15 02:20:55.251462 WARNING::Deleting existing fitted file: /tmp/RtmpEiOpl0/file16bf26c8e493/fits/fitted_linear.rds
2025-10-15 02:20:55.318779 WARNING::Deleting existing residuals file: /tmp/RtmpEiOpl0/file16bf26c8e493/fits/residuals_logistic.rds
2025-10-15 02:20:55.438844 WARNING::Deleting existing fitted file: /tmp/RtmpEiOpl0/file16bf26c8e493/fits/fitted_logistic.rds
2025-10-15 02:21:20.024308 WARNING::Fitting problem for feature 50 returning NA
2025-10-15 02:21:20.116582 WARNING::Fitting problem for feature 62 returning NA
2025-10-15 02:21:20.228964 WARNING::Fitting problem for feature 74 returning NA
2025-10-15 02:21:20.265136 WARNING::Fitting problem for feature 78 returning NA
2025-10-15 02:21:20.33123 WARNING::Fitting problem for feature 84 returning NA
2025-10-15 02:21:20.439205 WARNING::Fitting problem for feature 96 returning NA
2025-10-15 02:21:20.452191 WARNING::Fitting problem for feature 97 returning NA
2025-10-15 02:21:20.468897 WARNING::Fitting problem for feature 99 returning NA
2025-10-15 02:21:20.625867 WARNING::Fitting problem for feature 114 returning NA
2025-10-15 02:21:20.637233 WARNING::Fitting problem for feature 115 returning NA
2025-10-15 02:21:20.720655 WARNING::Fitting problem for feature 123 returning NA
2025-10-15 02:21:20.784663 WARNING::Fitting problem for feature 130 returning NA
2025-10-15 02:21:20.801371 WARNING::Fitting problem for feature 132 returning NA
2025-10-15 02:21:20.865293 WARNING::Fitting problem for feature 139 returning NA
2025-10-15 02:21:21.019168 WARNING::Fitting problem for feature 150 returning NA
2025-10-15 02:21:34.69688 WARNING::Fitting problem for feature 50 returning NA
2025-10-15 02:21:34.790264 WARNING::Fitting problem for feature 62 returning NA
2025-10-15 02:21:34.886184 WARNING::Fitting problem for feature 74 returning NA
2025-10-15 02:21:34.914368 WARNING::Fitting problem for feature 78 returning NA
2025-10-15 02:21:34.95605 WARNING::Fitting problem for feature 84 returning NA
2025-10-15 02:21:35.054067 WARNING::Fitting problem for feature 96 returning NA
2025-10-15 02:21:35.062807 WARNING::Fitting problem for feature 97 returning NA
2025-10-15 02:21:35.07778 WARNING::Fitting problem for feature 99 returning NA
2025-10-15 02:21:35.199641 WARNING::Fitting problem for feature 114 returning NA
2025-10-15 02:21:35.2072 WARNING::Fitting problem for feature 115 returning NA
2025-10-15 02:21:35.274269 WARNING::Fitting problem for feature 123 returning NA
2025-10-15 02:21:35.325892 WARNING::Fitting problem for feature 130 returning NA
2025-10-15 02:21:35.340662 WARNING::Fitting problem for feature 132 returning NA
2025-10-15 02:21:35.394664 WARNING::Fitting problem for feature 139 returning NA
2025-10-15 02:21:35.489187 WARNING::Fitting problem for feature 150 returning NA
2025-10-15 02:21:35.833885 WARNING::Deleting existing residuals file: /tmp/RtmpEiOpl0/file16bf26c8e493/fits/residuals_linear.rds
2025-10-15 02:21:35.932743 WARNING::Deleting existing fitted file: /tmp/RtmpEiOpl0/file16bf26c8e493/fits/fitted_linear.rds
2025-10-15 02:21:36.036603 WARNING::Deleting existing residuals file: /tmp/RtmpEiOpl0/file16bf26c8e493/fits/residuals_logistic.rds
2025-10-15 02:21:36.548628 WARNING::Deleting existing fitted file: /tmp/RtmpEiOpl0/file16bf26c8e493/fits/fitted_logistic.rds
2025-10-15 02:22:02.300837 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-10-15 02:22:02.320307 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-10-15 02:22:02.334138 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-10-15 02:22:02.413615 ERROR::No fixed, group, or
                        ordered effects included in formula.
2025-10-15 02:22:02.433307 ERROR::Effect name not found in metadata: d
2025-10-15 02:22:02.446212 ERROR::No user formula provided
2025-10-15 02:22:02.479009 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-10-15 02:22:02.493285 ERROR::No fixed/group/ordered/
                        feature-specific effects provided.
2025-10-15 02:22:05.630802 INFO::Writing function arguments to log file
2025-10-15 02:22:05.647863 INFO::Verifying options selected are valid
2025-10-15 02:22:08.512207 INFO::Writing function arguments to log file
2025-10-15 02:22:08.525372 INFO::Verifying options selected are valid
2025-10-15 02:22:08.526604 INFO::Determining format of input files
2025-10-15 02:22:08.527544 INFO::Input format is data samples as rows and metadata samples as rows
2025-10-15 02:22:08.532056 INFO::Running selected normalization method: TSS
2025-10-15 02:22:08.535143 INFO::Creating output feature tables folder
2025-10-15 02:22:08.536493 INFO::Writing normalized data to file /tmp/RtmpEiOpl0/file16bf7c6c78bf/features/data_norm.tsv
2025-10-15 02:22:08.538387 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-10-15 02:22:08.539382 INFO::Total samples in data: 16
2025-10-15 02:22:08.540265 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-10-15 02:22:08.541121 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-10-15 02:22:08.543109 INFO::Total filtered features: 0
2025-10-15 02:22:08.544198 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-10-15 02:22:08.545383 INFO::Total features filtered by non-zero variance filtering: 0
2025-10-15 02:22:08.546304 INFO::Filtered feature names from variance filtering:
2025-10-15 02:22:08.54717 INFO::Writing filtered data to file /tmp/RtmpEiOpl0/file16bf7c6c78bf/features/filtered_data.tsv
2025-10-15 02:22:08.548889 INFO::Running selected transform method: LOG
2025-10-15 02:22:08.550089 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpEiOpl0/file16bf7c6c78bf/features/data_transformed.tsv
2025-10-15 02:22:08.551918 INFO::Applying z-score to standardize continuous metadata
2025-10-15 02:22:08.557714 INFO::Running the linear model component
2025-10-15 02:22:08.576992 INFO::Fitting model to feature number 1, a
2025-10-15 02:22:08.584097 INFO::Fitting model to feature number 2, b
2025-10-15 02:22:08.589465 INFO::Fitting model to feature number 3, c
2025-10-15 02:22:08.598177 INFO::Counting total values for each feature
2025-10-15 02:22:08.600747 INFO::Running the logistic model component
2025-10-15 02:22:08.61867 INFO::Fitting model to feature number 1, a
2025-10-15 02:22:08.625997 INFO::Fitting model to feature number 2, b
2025-10-15 02:22:08.63386 INFO::Fitting model to feature number 3, c
2025-10-15 02:22:08.647107 INFO::Counting total values for each feature
2025-10-15 02:22:08.65003 INFO::Re-running abundances for warn_prevalence
2025-10-15 02:22:08.651148 INFO::Running selected normalization method: TSS
2025-10-15 02:22:08.652861 INFO::Running selected transform method: LOG
2025-10-15 02:22:08.668562 INFO::Fitting model to feature number 1, a
2025-10-15 02:22:08.673501 INFO::Fitting model to feature number 2, b
2025-10-15 02:22:08.67774 INFO::Fitting model to feature number 3, c
2025-10-15 02:22:08.778667 INFO::Creating fits folder
2025-10-15 02:22:08.780615 INFO::Writing residuals to file /tmp/RtmpEiOpl0/file16bf7c6c78bf/fits/residuals_linear.rds
2025-10-15 02:22:08.78221 INFO::Writing fitted values to file /tmp/RtmpEiOpl0/file16bf7c6c78bf/fits/fitted_linear.rds
2025-10-15 02:22:08.783579 INFO::Writing residuals to file /tmp/RtmpEiOpl0/file16bf7c6c78bf/fits/residuals_logistic.rds
2025-10-15 02:22:08.784983 INFO::Writing fitted values to file /tmp/RtmpEiOpl0/file16bf7c6c78bf/fits/fitted_logistic.rds
2025-10-15 02:22:08.788947 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /tmp/RtmpEiOpl0/file16bf7c6c78bf/all_results.tsv
2025-10-15 02:22:08.791853 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/RtmpEiOpl0/file16bf7c6c78bf/significant_results.tsv
2025-10-15 02:22:08.794285 INFO::Creating output figures folder
2025-10-15 02:22:08.796131 INFO::Writing summary plot of significant
                        results to file: /tmp/RtmpEiOpl0/file16bf7c6c78bf/figures/summary_plot.pdf
2025-10-15 02:22:10.816152 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpEiOpl0/file16bf7c6c78bf/figures
2025-10-15 02:22:10.818731 INFO::Plotting associations from most to least significant, grouped by metadata
2025-10-15 02:22:10.824784 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-10-15 02:22:11.473249 INFO::Writing summary plot of
                        significant results to file: /tmp/RtmpEiOpl0/file16bf7c6c78bf/figures/summary_plot.pdf
2025-10-15 02:22:13.633286 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpEiOpl0/file16bf7c6c78bf/figures
2025-10-15 02:22:13.635404 INFO::Plotting associations from most to least significant, grouped by metadata
2025-10-15 02:22:13.642243 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-10-15 02:22:14.319198 INFO::Running the linear model component
2025-10-15 02:22:14.329392 INFO::Fitting model to feature number 1, a
2025-10-15 02:22:14.334327 INFO::Fitting model to feature number 2, b
2025-10-15 02:22:14.338338 INFO::Fitting model to feature number 3, c
2025-10-15 02:22:14.345591 INFO::Counting total values for each feature
2025-10-15 02:22:14.347313 INFO::Running the logistic model component
2025-10-15 02:22:14.35522 INFO::Fitting model to feature number 1, a
2025-10-15 02:22:14.36376 INFO::Fitting model to feature number 2, b
2025-10-15 02:22:14.370328 INFO::Fitting model to feature number 3, c
2025-10-15 02:22:14.380011 INFO::Counting total values for each feature
2025-10-15 02:22:14.382369 INFO::Re-running abundances for warn_prevalence
2025-10-15 02:22:14.383211 INFO::Running selected normalization method: TSS
2025-10-15 02:22:14.384605 INFO::Running selected transform method: LOG
2025-10-15 02:22:14.394581 INFO::Fitting model to feature number 1, a
2025-10-15 02:22:14.399241 INFO::Fitting model to feature number 2, b
2025-10-15 02:22:14.403239 INFO::Fitting model to feature number 3, c
2025-10-15 02:22:14.504783 INFO::Creating output folder
2025-10-15 02:22:14.507062 INFO::Creating output figures folder
2025-10-15 02:22:14.508621 INFO::Writing summary plot of significant
                        results to file: /tmp/RtmpEiOpl0/file16bf279f9390/figures/summary_plot.pdf
2025-10-15 02:22:16.503732 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpEiOpl0/file16bf279f9390/figures
2025-10-15 02:22:16.505913 INFO::Plotting associations from most to least significant, grouped by metadata
2025-10-15 02:22:16.511707 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-10-15 02:22:17.830224 INFO::Applying z-score to standardize continuous metadata
2025-10-15 02:22:17.841835 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-10-15 02:22:17.842891 INFO::Bypass z-score application to metadata
2025-10-15 02:22:17.845479 INFO::Bypass z-score application to metadata
2025-10-15 02:22:17.868014 INFO::Determining format of input files
2025-10-15 02:22:17.869165 INFO::Input format is data samples as rows and metadata samples as rows
2025-10-15 02:22:17.869948 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-10-15 02:22:17.877632 INFO::Determining format of input files
2025-10-15 02:22:17.879096 INFO::Input format is data samples as columns and metadata samples as rows
2025-10-15 02:22:17.88051 INFO::Input format is feature_specific_covariate samples as columns
2025-10-15 02:22:17.891184 INFO::Determining format of input files
2025-10-15 02:22:17.892425 INFO::Input format is data samples as rows and metadata samples as rows
2025-10-15 02:22:17.893456 INFO::Input format is feature_specific_covariate samples as columns
2025-10-15 02:22:17.894974 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-10-15 02:22:17.895663 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-10-15 02:22:17.909386 INFO::Running selected transform method: LOG
2025-10-15 02:22:17.911437 INFO::Creating output feature tables folder
2025-10-15 02:22:17.913044 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpEiOpl0/file16bf67495f62/features/data_transformed.tsv
2025-10-15 02:22:17.918488 INFO::Running selected transform method: LOG
2025-10-15 02:22:17.920005 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpEiOpl0/file16bf67495f62/features/data_transformed.tsv
2025-10-15 02:22:17.926761 INFO::Running selected transform method: PLOG
2025-10-15 02:22:17.930014 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpEiOpl0/file16bf67495f62/features/data_transformed.tsv
2025-10-15 02:22:17.934277 INFO::Running selected transform method: NONE
2025-10-15 02:22:17.935256 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpEiOpl0/file16bf67495f62/features/data_transformed.tsv
2025-10-15 02:22:17.944819 INFO::Running the linear model component
2025-10-15 02:22:17.956212 INFO::Fitting model to feature number 1, a
2025-10-15 02:22:17.961228 INFO::Fitting model to feature number 2, b
2025-10-15 02:22:17.965417 INFO::Fitting model to feature number 3, c
2025-10-15 02:22:17.973262 INFO::Counting total values for each feature
2025-10-15 02:22:17.975138 INFO::Running the logistic model component
2025-10-15 02:22:17.983242 INFO::Fitting model to feature number 1, a
2025-10-15 02:22:17.989678 INFO::Fitting model to feature number 2, b
2025-10-15 02:22:17.995366 INFO::Fitting model to feature number 3, c
2025-10-15 02:22:18.005356 INFO::Counting total values for each feature
2025-10-15 02:22:18.008414 INFO::Re-running abundances for warn_prevalence
2025-10-15 02:22:18.009543 INFO::Running selected normalization method: TSS
2025-10-15 02:22:18.011099 INFO::Running selected transform method: LOG
2025-10-15 02:22:18.01984 INFO::Fitting model to feature number 1, a
2025-10-15 02:22:18.024829 INFO::Fitting model to feature number 2, b
2025-10-15 02:22:18.029164 INFO::Fitting model to feature number 3, c
2025-10-15 02:22:18.152388 INFO::Creating output folder
2025-10-15 02:22:18.154268 INFO::Creating fits folder
2025-10-15 02:22:18.155561 INFO::Writing residuals to file /tmp/RtmpEiOpl0/file16bf2154fe8/fits/residuals_linear.rds
2025-10-15 02:22:18.15732 INFO::Writing fitted values to file /tmp/RtmpEiOpl0/file16bf2154fe8/fits/fitted_linear.rds
2025-10-15 02:22:18.158813 INFO::Writing residuals to file /tmp/RtmpEiOpl0/file16bf2154fe8/fits/residuals_logistic.rds
2025-10-15 02:22:18.16021 INFO::Writing fitted values to file /tmp/RtmpEiOpl0/file16bf2154fe8/fits/fitted_logistic.rds
2025-10-15 02:22:18.163369 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /tmp/RtmpEiOpl0/file16bf2154fe8/all_results.tsv
2025-10-15 02:22:18.168896 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/RtmpEiOpl0/file16bf2154fe8/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]

[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
> 
> 
> proc.time()
   user  system elapsed 
435.779  11.438 450.630 

Example timings

maaslin3.Rcheck/maaslin3-Ex.timings

nameusersystemelapsed
maaslin324.777 1.24426.112
maaslin_check_arguments0.2230.0030.226
maaslin_check_formula0.1950.0080.205
maaslin_compute_formula0.2000.0090.210
maaslin_contrast_test22.360 1.62124.081
maaslin_filter0.6550.0420.697
maaslin_fit14.757 0.81815.606
maaslin_log_arguments0.1820.0070.189
maaslin_normalize0.3970.0200.417
maaslin_plot_results52.197 2.18354.902
maaslin_plot_results_from_output52.655 1.55154.706
maaslin_process_metadata0.6930.0470.749
maaslin_read_data0.1730.0080.184
maaslin_reorder_data0.1820.0110.206
maaslin_transform0.8870.0720.970
maaslin_write_results17.031 1.08718.272
maaslin_write_results_lefse_format18.135 1.10219.396
preprocess_dna_mtx0.0040.0010.005
preprocess_taxa_mtx0.0040.0010.004