Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-10-16 12:07 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4867
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4655
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4600
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4610
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 1161/2346HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maaslin3 1.1.2  (landing page)
William Nickols
Snapshot Date: 2025-10-15 13:45 -0400 (Wed, 15 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 taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: maaslin3
Version: 1.1.2
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings maaslin3_1.1.2.tar.gz
StartedAt: 2025-10-14 09:45:17 -0000 (Tue, 14 Oct 2025)
EndedAt: 2025-10-14 10:02:21 -0000 (Tue, 14 Oct 2025)
EllapsedTime: 1023.9 seconds
RetCode: 0
Status:   OK  
CheckDir: maaslin3.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings maaslin3_1.1.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/maaslin3.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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               64.679  0.218  65.109
maaslin_plot_results_from_output   63.309  0.311  63.769
maaslin3                           30.097  1.407  31.621
maaslin_contrast_test              28.105  0.806  29.031
maaslin_write_results_lefse_format 24.479  0.148  24.673
maaslin_write_results              21.317  0.147  21.507
maaslin_fit                        20.934  0.166  21.171
* 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:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL maaslin3
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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")
2025-10-14 09:53:48.297085 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 09:53:48.424959 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 09:53:48.585802 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 09:53:48.620207 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 09:53:48.674399 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 09:53:48.79429 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 09:53:48.802334 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 09:53:48.820374 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 09:53:48.983509 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 09:53:48.991772 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 09:53:49.069968 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 09:53:49.132951 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 09:53:49.151603 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 09:53:49.226261 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 09:53:49.337507 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 09:54:12.88805 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 09:54:13.013297 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 09:54:13.156977 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 09:54:13.192475 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 09:54:13.248775 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 09:54:13.386393 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 09:54:13.395186 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 09:54:13.414061 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 09:54:13.568444 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 09:54:13.576724 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 09:54:13.656493 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 09:54:13.72243 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 09:54:13.741549 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 09:54:13.805711 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 09:54:13.919706 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 09:54:46.333664 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 09:54:46.479977 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 09:54:46.617046 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 09:54:46.65536 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 09:54:46.716466 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 09:54:46.85537 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 09:54:46.870664 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 09:54:46.893278 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 09:54:47.078006 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 09:54:47.088839 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 09:54:47.19061 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 09:54:47.276253 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 09:54:47.301285 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 09:54:47.384802 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 09:54:47.519313 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 09:55:08.718434 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 09:55:08.869421 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 09:55:08.99246 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 09:55:09.02753 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 09:55:09.083964 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 09:55:09.209343 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 09:55:09.217748 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 09:55:09.236501 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 09:55:09.407585 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 09:55:09.416338 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 09:55:09.498194 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 09:55:09.563775 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 09:55:09.582569 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 09:55:09.649014 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 09:55:09.762383 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 09:55:10.069611 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7365c90b8/fits/residuals_linear.rds
2025-10-14 09:55:10.138572 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7365c90b8/fits/fitted_linear.rds
2025-10-14 09:55:10.209023 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7365c90b8/fits/residuals_logistic.rds
2025-10-14 09:55:10.556324 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7365c90b8/fits/fitted_logistic.rds
2025-10-14 09:55:39.629239 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 09:55:39.761089 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 09:55:39.88938 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 09:55:39.928332 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 09:55:39.988298 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 09:55:40.119736 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 09:55:40.128604 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 09:55:40.14881 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 09:55:40.306417 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 09:55:40.31494 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 09:55:40.395253 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 09:55:40.460352 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 09:55:40.479476 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 09:55:40.543883 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 09:55:41.65153 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 09:56:02.175 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 09:56:02.302835 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 09:56:02.42597 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 09:56:02.461846 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 09:56:02.519103 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 09:56:02.649408 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 09:56:02.658679 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 09:56:02.679338 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 09:56:02.837207 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 09:56:02.845752 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 09:56:02.926301 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 09:56:02.992115 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 09:56:03.014222 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 09:56:03.089232 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 09:56:03.216391 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 09:56:03.588884 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7365c90b8/fits/residuals_linear.rds
2025-10-14 09:56:03.65829 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7365c90b8/fits/fitted_linear.rds
2025-10-14 09:56:03.729579 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7365c90b8/fits/residuals_logistic.rds
2025-10-14 09:56:04.079816 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7365c90b8/fits/fitted_logistic.rds
2025-10-14 09:56:33.697616 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 09:56:33.827116 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 09:56:33.954521 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 09:56:33.992677 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 09:56:34.053371 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 09:56:34.185914 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 09:56:34.195143 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 09:56:34.215683 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 09:56:34.382472 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 09:56:34.391449 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 09:56:34.478294 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 09:56:34.554528 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 09:56:34.575792 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 09:56:34.649282 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 09:56:34.782635 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 09:56:53.087259 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 09:56:53.209674 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 09:56:53.330537 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 09:56:53.365752 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 09:56:53.423108 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 09:56:53.55208 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 09:56:53.560529 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 09:56:53.579888 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 09:56:53.744286 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 09:56:53.753075 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 09:56:53.875915 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 09:56:53.944489 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 09:56:53.964252 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 09:56:54.03243 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 09:56:54.147333 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 09:56:54.443198 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7365c90b8/fits/residuals_linear.rds
2025-10-14 09:56:54.51169 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7365c90b8/fits/fitted_linear.rds
2025-10-14 09:56:54.581745 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7365c90b8/fits/residuals_logistic.rds
2025-10-14 09:56:54.928529 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7365c90b8/fits/fitted_logistic.rds
2025-10-14 09:57:23.615538 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 09:57:23.740283 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 09:57:23.862448 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 09:57:23.897909 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 09:57:23.953274 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 09:57:24.076608 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 09:57:24.085098 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 09:57:24.104428 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 09:57:24.264537 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 09:57:24.273528 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 09:57:24.393174 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 09:57:24.460793 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 09:57:24.480629 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 09:57:24.545641 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 09:57:24.655801 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 09:57:44.137084 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 09:57:44.263083 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 09:57:44.386384 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 09:57:44.422069 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 09:57:44.478827 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 09:57:44.605676 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 09:57:44.614208 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 09:57:44.633589 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 09:57:44.789282 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 09:57:44.797781 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 09:57:44.877542 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 09:57:44.94268 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 09:57:44.961549 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 09:57:45.025102 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 09:57:45.137948 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 09:58:18.180562 WARNING::Fitting problem for feature 124 returning NA
2025-10-14 09:58:32.918088 WARNING::Fitting problem for feature 124 returning NA
2025-10-14 09:59:07.352095 WARNING::Fitting problem for feature 124 returning NA
2025-10-14 09:59:21.189008 WARNING::Fitting problem for feature 124 returning NA
2025-10-14 09:59:22.185082 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc742cadf73/fits/residuals_linear.rds
2025-10-14 09:59:22.251775 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc742cadf73/fits/fitted_linear.rds
2025-10-14 09:59:22.294461 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc742cadf73/fits/residuals_logistic.rds
2025-10-14 09:59:22.371411 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc742cadf73/fits/fitted_logistic.rds
2025-10-14 09:59:53.799718 WARNING::Fitting problem for feature 124 returning NA
2025-10-14 10:00:03.258312 WARNING::Fitting problem for feature 124 returning NA
2025-10-14 10:00:03.748904 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc742cadf73/fits/residuals_linear.rds
2025-10-14 10:00:03.81826 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc742cadf73/fits/fitted_linear.rds
2025-10-14 10:00:03.861795 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc742cadf73/fits/residuals_logistic.rds
2025-10-14 10:00:03.940302 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc742cadf73/fits/fitted_logistic.rds
2025-10-14 10:00:30.097598 WARNING::Fitting problem for feature 124 returning NA
2025-10-14 10:00:39.577579 WARNING::Fitting problem for feature 124 returning NA
2025-10-14 10:00:40.074272 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc742cadf73/fits/residuals_linear.rds
2025-10-14 10:00:40.144403 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc742cadf73/fits/fitted_linear.rds
2025-10-14 10:00:40.18807 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc742cadf73/fits/residuals_logistic.rds
2025-10-14 10:00:40.266353 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc742cadf73/fits/fitted_logistic.rds
2025-10-14 10:01:05.529715 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 10:01:05.702811 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 10:01:05.835103 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 10:01:05.872494 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 10:01:05.930542 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 10:01:06.05835 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 10:01:06.067145 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 10:01:06.086759 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 10:01:06.25198 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 10:01:06.261712 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 10:01:06.351758 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 10:01:06.420875 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 10:01:06.440938 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 10:01:06.510011 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 10:01:06.630306 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 10:01:26.676891 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 10:01:26.804905 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 10:01:26.929374 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 10:01:26.964231 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 10:01:27.05984 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 10:01:27.193214 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 10:01:27.202337 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 10:01:27.223058 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 10:01:27.389796 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 10:01:27.398533 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 10:01:27.482452 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 10:01:27.550028 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 10:01:27.57172 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 10:01:27.641235 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 10:01:27.758743 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 10:01:28.117198 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc742cadf73/fits/residuals_linear.rds
2025-10-14 10:01:28.178528 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc742cadf73/fits/fitted_linear.rds
2025-10-14 10:01:28.241173 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc742cadf73/fits/residuals_logistic.rds
2025-10-14 10:01:28.531533 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc742cadf73/fits/fitted_logistic.rds
2025-10-14 10:01:56.736264 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-10-14 10:01:56.762645 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-10-14 10:01:56.780509 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-10-14 10:01:56.864037 ERROR::No fixed, group, or
                        ordered effects included in formula.
2025-10-14 10:01:56.89053 ERROR::Effect name not found in metadata: d
2025-10-14 10:01:56.908221 ERROR::No user formula provided
2025-10-14 10:01:56.95452 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-10-14 10:01:56.972581 ERROR::No fixed/group/ordered/
                        feature-specific effects provided.
2025-10-14 10:02:01.885631 INFO::Writing function arguments to log file
2025-10-14 10:02:01.907919 INFO::Verifying options selected are valid
2025-10-14 10:02:05.284496 INFO::Writing function arguments to log file
2025-10-14 10:02:05.303212 INFO::Verifying options selected are valid
2025-10-14 10:02:05.304849 INFO::Determining format of input files
2025-10-14 10:02:05.306279 INFO::Input format is data samples as rows and metadata samples as rows
2025-10-14 10:02:05.30987 INFO::Running selected normalization method: TSS
2025-10-14 10:02:05.312136 INFO::Creating output feature tables folder
2025-10-14 10:02:05.313661 INFO::Writing normalized data to file /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7645c0547/features/data_norm.tsv
2025-10-14 10:02:05.31585 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-10-14 10:02:05.317282 INFO::Total samples in data: 16
2025-10-14 10:02:05.3186 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-10-14 10:02:05.319921 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-10-14 10:02:05.32286 INFO::Total filtered features: 0
2025-10-14 10:02:05.324429 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-10-14 10:02:05.326158 INFO::Total features filtered by non-zero variance filtering: 0
2025-10-14 10:02:05.32759 INFO::Filtered feature names from variance filtering:
2025-10-14 10:02:05.328895 INFO::Writing filtered data to file /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7645c0547/features/filtered_data.tsv
2025-10-14 10:02:05.331013 INFO::Running selected transform method: LOG
2025-10-14 10:02:05.332767 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7645c0547/features/data_transformed.tsv
2025-10-14 10:02:05.335182 INFO::Applying z-score to standardize continuous metadata
2025-10-14 10:02:05.343103 INFO::Running the linear model component
2025-10-14 10:02:05.365825 INFO::Fitting model to feature number 1, a
2025-10-14 10:02:05.373042 INFO::Fitting model to feature number 2, b
2025-10-14 10:02:05.379718 INFO::Fitting model to feature number 3, c
2025-10-14 10:02:05.390758 INFO::Counting total values for each feature
2025-10-14 10:02:05.393728 INFO::Running the logistic model component
2025-10-14 10:02:05.415276 INFO::Fitting model to feature number 1, a
2025-10-14 10:02:05.425072 INFO::Fitting model to feature number 2, b
2025-10-14 10:02:05.434768 INFO::Fitting model to feature number 3, c
2025-10-14 10:02:05.448476 INFO::Counting total values for each feature
2025-10-14 10:02:05.451855 INFO::Re-running abundances for warn_prevalence
2025-10-14 10:02:05.453251 INFO::Running selected normalization method: TSS
2025-10-14 10:02:05.455514 INFO::Running selected transform method: LOG
2025-10-14 10:02:05.477154 INFO::Fitting model to feature number 1, a
2025-10-14 10:02:05.483813 INFO::Fitting model to feature number 2, b
2025-10-14 10:02:05.490406 INFO::Fitting model to feature number 3, c
2025-10-14 10:02:05.624229 INFO::Creating fits folder
2025-10-14 10:02:05.625926 INFO::Writing residuals to file /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7645c0547/fits/residuals_linear.rds
2025-10-14 10:02:05.627508 INFO::Writing fitted values to file /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7645c0547/fits/fitted_linear.rds
2025-10-14 10:02:05.629241 INFO::Writing residuals to file /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7645c0547/fits/residuals_logistic.rds
2025-10-14 10:02:05.630901 INFO::Writing fitted values to file /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7645c0547/fits/fitted_logistic.rds
2025-10-14 10:02:05.634773 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7645c0547/all_results.tsv
2025-10-14 10:02:05.637223 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): /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7645c0547/significant_results.tsv
2025-10-14 10:02:05.639103 INFO::Creating output figures folder
2025-10-14 10:02:05.641176 INFO::Writing summary plot of significant
                        results to file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7645c0547/figures/summary_plot.pdf
2025-10-14 10:02:07.956454 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7645c0547/figures
2025-10-14 10:02:07.959217 INFO::Plotting associations from most to least significant, grouped by metadata
2025-10-14 10:02:07.967029 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-10-14 10:02:08.697423 INFO::Writing summary plot of
                        significant results to file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7645c0547/figures/summary_plot.pdf
2025-10-14 10:02:11.029326 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc7645c0547/figures
2025-10-14 10:02:11.031615 INFO::Plotting associations from most to least significant, grouped by metadata
2025-10-14 10:02:11.039185 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-10-14 10:02:11.805944 INFO::Running the linear model component
2025-10-14 10:02:11.820549 INFO::Fitting model to feature number 1, a
2025-10-14 10:02:11.827154 INFO::Fitting model to feature number 2, b
2025-10-14 10:02:11.833642 INFO::Fitting model to feature number 3, c
2025-10-14 10:02:11.844691 INFO::Counting total values for each feature
2025-10-14 10:02:11.847363 INFO::Running the logistic model component
2025-10-14 10:02:11.860875 INFO::Fitting model to feature number 1, a
2025-10-14 10:02:11.870121 INFO::Fitting model to feature number 2, b
2025-10-14 10:02:11.879117 INFO::Fitting model to feature number 3, c
2025-10-14 10:02:11.892144 INFO::Counting total values for each feature
2025-10-14 10:02:11.895255 INFO::Re-running abundances for warn_prevalence
2025-10-14 10:02:11.896409 INFO::Running selected normalization method: TSS
2025-10-14 10:02:11.89841 INFO::Running selected transform method: LOG
2025-10-14 10:02:11.91217 INFO::Fitting model to feature number 1, a
2025-10-14 10:02:11.918413 INFO::Fitting model to feature number 2, b
2025-10-14 10:02:11.924649 INFO::Fitting model to feature number 3, c
2025-10-14 10:02:12.058478 INFO::Creating output folder
2025-10-14 10:02:12.059975 INFO::Creating output figures folder
2025-10-14 10:02:12.061994 INFO::Writing summary plot of significant
                        results to file: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc73e0b5123/figures/summary_plot.pdf
2025-10-14 10:02:14.371514 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/Rtmp80uVj2/file22fcc73e0b5123/figures
2025-10-14 10:02:14.373952 INFO::Plotting associations from most to least significant, grouped by metadata
2025-10-14 10:02:14.381267 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-10-14 10:02:15.791193 INFO::Applying z-score to standardize continuous metadata
2025-10-14 10:02:15.803452 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-10-14 10:02:15.804833 INFO::Bypass z-score application to metadata
2025-10-14 10:02:15.808721 INFO::Bypass z-score application to metadata
2025-10-14 10:02:15.835512 INFO::Determining format of input files
2025-10-14 10:02:15.836896 INFO::Input format is data samples as rows and metadata samples as rows
2025-10-14 10:02:15.838207 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-10-14 10:02:15.849337 INFO::Determining format of input files
2025-10-14 10:02:15.850919 INFO::Input format is data samples as columns and metadata samples as rows
2025-10-14 10:02:15.852904 INFO::Input format is feature_specific_covariate samples as columns
2025-10-14 10:02:15.865185 INFO::Determining format of input files
2025-10-14 10:02:15.866692 INFO::Input format is data samples as rows and metadata samples as rows
2025-10-14 10:02:15.868326 INFO::Input format is feature_specific_covariate samples as columns
2025-10-14 10:02:15.870905 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-10-14 10:02:15.872149 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-10-14 10:02:15.888927 INFO::Running selected transform method: LOG
2025-10-14 10:02:15.890733 INFO::Creating output feature tables folder
2025-10-14 10:02:15.892142 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/Rtmp80uVj2/file22fcc730a26e51/features/data_transformed.tsv
2025-10-14 10:02:15.898092 INFO::Running selected transform method: LOG
2025-10-14 10:02:15.899848 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/Rtmp80uVj2/file22fcc730a26e51/features/data_transformed.tsv
2025-10-14 10:02:15.905668 INFO::Running selected transform method: PLOG
2025-10-14 10:02:15.908335 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/Rtmp80uVj2/file22fcc730a26e51/features/data_transformed.tsv
2025-10-14 10:02:15.912719 INFO::Running selected transform method: NONE
2025-10-14 10:02:15.914041 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/Rtmp80uVj2/file22fcc730a26e51/features/data_transformed.tsv
2025-10-14 10:02:15.945352 INFO::Running the linear model component
2025-10-14 10:02:15.962193 INFO::Fitting model to feature number 1, a
2025-10-14 10:02:15.969451 INFO::Fitting model to feature number 2, b
2025-10-14 10:02:15.977077 INFO::Fitting model to feature number 3, c
2025-10-14 10:02:15.989004 INFO::Counting total values for each feature
2025-10-14 10:02:15.991767 INFO::Running the logistic model component
2025-10-14 10:02:16.006598 INFO::Fitting model to feature number 1, a
2025-10-14 10:02:16.016795 INFO::Fitting model to feature number 2, b
2025-10-14 10:02:16.026833 INFO::Fitting model to feature number 3, c
2025-10-14 10:02:16.04172 INFO::Counting total values for each feature
2025-10-14 10:02:16.045143 INFO::Re-running abundances for warn_prevalence
2025-10-14 10:02:16.04655 INFO::Running selected normalization method: TSS
2025-10-14 10:02:16.049024 INFO::Running selected transform method: LOG
2025-10-14 10:02:16.064149 INFO::Fitting model to feature number 1, a
2025-10-14 10:02:16.071319 INFO::Fitting model to feature number 2, b
2025-10-14 10:02:16.078565 INFO::Fitting model to feature number 3, c
2025-10-14 10:02:16.225574 INFO::Creating output folder
2025-10-14 10:02:16.22716 INFO::Creating fits folder
2025-10-14 10:02:16.228654 INFO::Writing residuals to file /home/biocbuild/tmp/Rtmp80uVj2/file22fcc74ea7ea8d/fits/residuals_linear.rds
2025-10-14 10:02:16.230343 INFO::Writing fitted values to file /home/biocbuild/tmp/Rtmp80uVj2/file22fcc74ea7ea8d/fits/fitted_linear.rds
2025-10-14 10:02:16.232209 INFO::Writing residuals to file /home/biocbuild/tmp/Rtmp80uVj2/file22fcc74ea7ea8d/fits/residuals_logistic.rds
2025-10-14 10:02:16.234081 INFO::Writing fitted values to file /home/biocbuild/tmp/Rtmp80uVj2/file22fcc74ea7ea8d/fits/fitted_logistic.rds
2025-10-14 10:02:16.238351 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /home/biocbuild/tmp/Rtmp80uVj2/file22fcc74ea7ea8d/all_results.tsv
2025-10-14 10:02:16.241095 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): /home/biocbuild/tmp/Rtmp80uVj2/file22fcc74ea7ea8d/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]

[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
> 
> 
> proc.time()
   user  system elapsed 
513.330   7.416 522.369

Example timings

maaslin3.Rcheck/maaslin3-Ex.timings

nameusersystemelapsed
maaslin330.097 1.40731.621
maaslin_check_arguments0.1830.0040.188
maaslin_check_formula0.2060.0000.207
maaslin_compute_formula0.2100.0040.215
maaslin_contrast_test28.105 0.80629.031
maaslin_filter0.6640.0090.675
maaslin_fit20.934 0.16621.171
maaslin_log_arguments0.1940.0040.199
maaslin_normalize0.3710.0080.381
maaslin_plot_results64.679 0.21865.109
maaslin_plot_results_from_output63.309 0.31163.769
maaslin_process_metadata0.6430.0170.660
maaslin_read_data0.1940.0000.195
maaslin_reorder_data0.1970.0040.203
maaslin_transform0.7690.0040.774
maaslin_write_results21.317 0.14721.507
maaslin_write_results_lefse_format24.479 0.14824.673
preprocess_dna_mtx0.0050.0000.005
preprocess_taxa_mtx0.0030.0030.006