Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-08-21 12:07 -0400 (Thu, 21 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4819
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4597
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4539
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4536
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 1147/2318HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maaslin3 1.1.0  (landing page)
William Nickols
Snapshot Date: 2025-08-20 13:45 -0400 (Wed, 20 Aug 2025)
git_url: https://git.bioconductor.org/packages/maaslin3
git_branch: devel
git_last_commit: ed6ae28
git_last_commit_date: 2025-04-15 13:45:33 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 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: 1.1.0
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_1.1.0.tar.gz
StartedAt: 2025-08-19 09:27:33 -0000 (Tue, 19 Aug 2025)
EndedAt: 2025-08-19 09:42:57 -0000 (Tue, 19 Aug 2025)
EllapsedTime: 923.3 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_1.1.0.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 ‘1.1.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘maaslin3’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                     user system elapsed
maaslin_plot_results_from_output   53.044  0.275  53.480
maaslin_plot_results               52.690  0.227  53.075
maaslin_contrast_test              28.627  0.259  28.949
maaslin3                           27.880  0.292  28.225
maaslin_write_results_lefse_format 24.574  0.079  24.734
maaslin_write_results              23.519  0.339  23.938
maaslin_fit                        20.988  0.064  21.112
* 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 ‘1.1.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (maaslin3)

Tests output

maaslin3.Rcheck/tests/testthat.Rout


R version 4.5.0 (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")
2025-08-19 09:35:34.924701 WARNING::Fitting problem for feature 50 returning NA
2025-08-19 09:35:35.050915 WARNING::Fitting problem for feature 62 returning NA
2025-08-19 09:35:35.188128 WARNING::Fitting problem for feature 74 returning NA
2025-08-19 09:35:35.225853 WARNING::Fitting problem for feature 78 returning NA
2025-08-19 09:35:35.29903 WARNING::Fitting problem for feature 84 returning NA
2025-08-19 09:35:35.428253 WARNING::Fitting problem for feature 96 returning NA
2025-08-19 09:35:35.437248 WARNING::Fitting problem for feature 97 returning NA
2025-08-19 09:35:35.457247 WARNING::Fitting problem for feature 99 returning NA
2025-08-19 09:35:35.626895 WARNING::Fitting problem for feature 114 returning NA
2025-08-19 09:35:35.635507 WARNING::Fitting problem for feature 115 returning NA
2025-08-19 09:35:35.715275 WARNING::Fitting problem for feature 123 returning NA
2025-08-19 09:35:35.778612 WARNING::Fitting problem for feature 130 returning NA
2025-08-19 09:35:35.796953 WARNING::Fitting problem for feature 132 returning NA
2025-08-19 09:35:35.860366 WARNING::Fitting problem for feature 139 returning NA
2025-08-19 09:35:35.987628 WARNING::Fitting problem for feature 150 returning NA
2025-08-19 09:35:58.25292 WARNING::Fitting problem for feature 50 returning NA
2025-08-19 09:35:58.38575 WARNING::Fitting problem for feature 62 returning NA
2025-08-19 09:35:58.527493 WARNING::Fitting problem for feature 74 returning NA
2025-08-19 09:35:58.566441 WARNING::Fitting problem for feature 78 returning NA
2025-08-19 09:35:58.627042 WARNING::Fitting problem for feature 84 returning NA
2025-08-19 09:35:58.774698 WARNING::Fitting problem for feature 96 returning NA
2025-08-19 09:35:58.782994 WARNING::Fitting problem for feature 97 returning NA
2025-08-19 09:35:58.802074 WARNING::Fitting problem for feature 99 returning NA
2025-08-19 09:35:58.959459 WARNING::Fitting problem for feature 114 returning NA
2025-08-19 09:35:58.968029 WARNING::Fitting problem for feature 115 returning NA
2025-08-19 09:35:59.047229 WARNING::Fitting problem for feature 123 returning NA
2025-08-19 09:35:59.110753 WARNING::Fitting problem for feature 130 returning NA
2025-08-19 09:35:59.129869 WARNING::Fitting problem for feature 132 returning NA
2025-08-19 09:35:59.194229 WARNING::Fitting problem for feature 139 returning NA
2025-08-19 09:35:59.313241 WARNING::Fitting problem for feature 150 returning NA
2025-08-19 09:36:23.223713 WARNING::Fitting problem for feature 50 returning NA
2025-08-19 09:36:23.37853 WARNING::Fitting problem for feature 62 returning NA
2025-08-19 09:36:23.506401 WARNING::Fitting problem for feature 74 returning NA
2025-08-19 09:36:23.542282 WARNING::Fitting problem for feature 78 returning NA
2025-08-19 09:36:23.59982 WARNING::Fitting problem for feature 84 returning NA
2025-08-19 09:36:23.727388 WARNING::Fitting problem for feature 96 returning NA
2025-08-19 09:36:23.736397 WARNING::Fitting problem for feature 97 returning NA
2025-08-19 09:36:23.756799 WARNING::Fitting problem for feature 99 returning NA
2025-08-19 09:36:23.923373 WARNING::Fitting problem for feature 114 returning NA
2025-08-19 09:36:23.932394 WARNING::Fitting problem for feature 115 returning NA
2025-08-19 09:36:24.05339 WARNING::Fitting problem for feature 123 returning NA
2025-08-19 09:36:24.12521 WARNING::Fitting problem for feature 130 returning NA
2025-08-19 09:36:24.145326 WARNING::Fitting problem for feature 132 returning NA
2025-08-19 09:36:24.215994 WARNING::Fitting problem for feature 139 returning NA
2025-08-19 09:36:24.337514 WARNING::Fitting problem for feature 150 returning NA
2025-08-19 09:36:46.099671 WARNING::Fitting problem for feature 50 returning NA
2025-08-19 09:36:46.258007 WARNING::Fitting problem for feature 62 returning NA
2025-08-19 09:36:46.386126 WARNING::Fitting problem for feature 74 returning NA
2025-08-19 09:36:46.423381 WARNING::Fitting problem for feature 78 returning NA
2025-08-19 09:36:46.482742 WARNING::Fitting problem for feature 84 returning NA
2025-08-19 09:36:46.61523 WARNING::Fitting problem for feature 96 returning NA
2025-08-19 09:36:46.623876 WARNING::Fitting problem for feature 97 returning NA
2025-08-19 09:36:46.643421 WARNING::Fitting problem for feature 99 returning NA
2025-08-19 09:36:46.8125 WARNING::Fitting problem for feature 114 returning NA
2025-08-19 09:36:46.821171 WARNING::Fitting problem for feature 115 returning NA
2025-08-19 09:36:46.899935 WARNING::Fitting problem for feature 123 returning NA
2025-08-19 09:36:46.964992 WARNING::Fitting problem for feature 130 returning NA
2025-08-19 09:36:46.983624 WARNING::Fitting problem for feature 132 returning NA
2025-08-19 09:36:47.048634 WARNING::Fitting problem for feature 139 returning NA
2025-08-19 09:36:47.160312 WARNING::Fitting problem for feature 150 returning NA
2025-08-19 09:36:47.457142 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpRew2ya/file2d1d352462f7d4/fits/residuals_linear.rds
2025-08-19 09:36:47.525572 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpRew2ya/file2d1d352462f7d4/fits/fitted_linear.rds
2025-08-19 09:36:47.595912 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpRew2ya/file2d1d352462f7d4/fits/residuals_logistic.rds
2025-08-19 09:36:47.939305 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpRew2ya/file2d1d352462f7d4/fits/fitted_logistic.rds
2025-08-19 09:37:09.731833 WARNING::Fitting problem for feature 50 returning NA
2025-08-19 09:37:09.860158 WARNING::Fitting problem for feature 62 returning NA
2025-08-19 09:37:09.990477 WARNING::Fitting problem for feature 74 returning NA
2025-08-19 09:37:10.027415 WARNING::Fitting problem for feature 78 returning NA
2025-08-19 09:37:10.087361 WARNING::Fitting problem for feature 84 returning NA
2025-08-19 09:37:10.220181 WARNING::Fitting problem for feature 96 returning NA
2025-08-19 09:37:10.229389 WARNING::Fitting problem for feature 97 returning NA
2025-08-19 09:37:10.250306 WARNING::Fitting problem for feature 99 returning NA
2025-08-19 09:37:10.427129 WARNING::Fitting problem for feature 114 returning NA
2025-08-19 09:37:10.436598 WARNING::Fitting problem for feature 115 returning NA
2025-08-19 09:37:10.52634 WARNING::Fitting problem for feature 123 returning NA
2025-08-19 09:37:10.597452 WARNING::Fitting problem for feature 130 returning NA
2025-08-19 09:37:10.619198 WARNING::Fitting problem for feature 132 returning NA
2025-08-19 09:37:10.722458 WARNING::Fitting problem for feature 139 returning NA
2025-08-19 09:37:10.836174 WARNING::Fitting problem for feature 150 returning NA
2025-08-19 09:37:30.646379 WARNING::Fitting problem for feature 50 returning NA
2025-08-19 09:37:30.772194 WARNING::Fitting problem for feature 62 returning NA
2025-08-19 09:37:30.892851 WARNING::Fitting problem for feature 74 returning NA
2025-08-19 09:37:30.92762 WARNING::Fitting problem for feature 78 returning NA
2025-08-19 09:37:30.982814 WARNING::Fitting problem for feature 84 returning NA
2025-08-19 09:37:31.106658 WARNING::Fitting problem for feature 96 returning NA
2025-08-19 09:37:31.114999 WARNING::Fitting problem for feature 97 returning NA
2025-08-19 09:37:31.133787 WARNING::Fitting problem for feature 99 returning NA
2025-08-19 09:37:31.290738 WARNING::Fitting problem for feature 114 returning NA
2025-08-19 09:37:31.300053 WARNING::Fitting problem for feature 115 returning NA
2025-08-19 09:37:31.381401 WARNING::Fitting problem for feature 123 returning NA
2025-08-19 09:37:31.446726 WARNING::Fitting problem for feature 130 returning NA
2025-08-19 09:37:31.465966 WARNING::Fitting problem for feature 132 returning NA
2025-08-19 09:37:31.531966 WARNING::Fitting problem for feature 139 returning NA
2025-08-19 09:37:31.641806 WARNING::Fitting problem for feature 150 returning NA
2025-08-19 09:37:31.922741 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpRew2ya/file2d1d352462f7d4/fits/residuals_linear.rds
2025-08-19 09:37:31.99015 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpRew2ya/file2d1d352462f7d4/fits/fitted_linear.rds
2025-08-19 09:37:32.05925 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpRew2ya/file2d1d352462f7d4/fits/residuals_logistic.rds
2025-08-19 09:37:32.404971 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpRew2ya/file2d1d352462f7d4/fits/fitted_logistic.rds
2025-08-19 09:37:53.691622 WARNING::Fitting problem for feature 50 returning NA
2025-08-19 09:37:53.81601 WARNING::Fitting problem for feature 62 returning NA
2025-08-19 09:37:53.943914 WARNING::Fitting problem for feature 74 returning NA
2025-08-19 09:37:53.98092 WARNING::Fitting problem for feature 78 returning NA
2025-08-19 09:37:54.037547 WARNING::Fitting problem for feature 84 returning NA
2025-08-19 09:37:54.163158 WARNING::Fitting problem for feature 96 returning NA
2025-08-19 09:37:54.172212 WARNING::Fitting problem for feature 97 returning NA
2025-08-19 09:37:54.193562 WARNING::Fitting problem for feature 99 returning NA
2025-08-19 09:37:54.366241 WARNING::Fitting problem for feature 114 returning NA
2025-08-19 09:37:54.375775 WARNING::Fitting problem for feature 115 returning NA
2025-08-19 09:37:54.464982 WARNING::Fitting problem for feature 123 returning NA
2025-08-19 09:37:54.541108 WARNING::Fitting problem for feature 130 returning NA
2025-08-19 09:37:54.56285 WARNING::Fitting problem for feature 132 returning NA
2025-08-19 09:37:54.673083 WARNING::Fitting problem for feature 139 returning NA
2025-08-19 09:37:54.790065 WARNING::Fitting problem for feature 150 returning NA
2025-08-19 09:38:14.091791 WARNING::Fitting problem for feature 50 returning NA
2025-08-19 09:38:14.223087 WARNING::Fitting problem for feature 62 returning NA
2025-08-19 09:38:14.395684 WARNING::Fitting problem for feature 74 returning NA
2025-08-19 09:38:14.434412 WARNING::Fitting problem for feature 78 returning NA
2025-08-19 09:38:14.498355 WARNING::Fitting problem for feature 84 returning NA
2025-08-19 09:38:14.639646 WARNING::Fitting problem for feature 96 returning NA
2025-08-19 09:38:14.649345 WARNING::Fitting problem for feature 97 returning NA
2025-08-19 09:38:14.671202 WARNING::Fitting problem for feature 99 returning NA
2025-08-19 09:38:14.832674 WARNING::Fitting problem for feature 114 returning NA
2025-08-19 09:38:14.841147 WARNING::Fitting problem for feature 115 returning NA
2025-08-19 09:38:14.924998 WARNING::Fitting problem for feature 123 returning NA
2025-08-19 09:38:14.990753 WARNING::Fitting problem for feature 130 returning NA
2025-08-19 09:38:15.010195 WARNING::Fitting problem for feature 132 returning NA
2025-08-19 09:38:15.07832 WARNING::Fitting problem for feature 139 returning NA
2025-08-19 09:38:15.192529 WARNING::Fitting problem for feature 150 returning NA
2025-08-19 09:38:15.490912 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpRew2ya/file2d1d352462f7d4/fits/residuals_linear.rds
2025-08-19 09:38:15.551455 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpRew2ya/file2d1d352462f7d4/fits/fitted_linear.rds
2025-08-19 09:38:15.622146 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpRew2ya/file2d1d352462f7d4/fits/residuals_logistic.rds
2025-08-19 09:38:15.914929 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpRew2ya/file2d1d352462f7d4/fits/fitted_logistic.rds
2025-08-19 09:38:37.209193 WARNING::Fitting problem for feature 50 returning NA
2025-08-19 09:38:37.338231 WARNING::Fitting problem for feature 62 returning NA
2025-08-19 09:38:37.467597 WARNING::Fitting problem for feature 74 returning NA
2025-08-19 09:38:37.50463 WARNING::Fitting problem for feature 78 returning NA
2025-08-19 09:38:37.565597 WARNING::Fitting problem for feature 84 returning NA
2025-08-19 09:38:37.703206 WARNING::Fitting problem for feature 96 returning NA
2025-08-19 09:38:37.711913 WARNING::Fitting problem for feature 97 returning NA
2025-08-19 09:38:37.730909 WARNING::Fitting problem for feature 99 returning NA
2025-08-19 09:38:37.901969 WARNING::Fitting problem for feature 114 returning NA
2025-08-19 09:38:37.910931 WARNING::Fitting problem for feature 115 returning NA
2025-08-19 09:38:38.002265 WARNING::Fitting problem for feature 123 returning NA
2025-08-19 09:38:38.076845 WARNING::Fitting problem for feature 130 returning NA
2025-08-19 09:38:38.099145 WARNING::Fitting problem for feature 132 returning NA
2025-08-19 09:38:38.174903 WARNING::Fitting problem for feature 139 returning NA
2025-08-19 09:38:38.295428 WARNING::Fitting problem for feature 150 returning NA
2025-08-19 09:38:57.963396 WARNING::Fitting problem for feature 50 returning NA
2025-08-19 09:38:58.126957 WARNING::Fitting problem for feature 62 returning NA
2025-08-19 09:38:58.253712 WARNING::Fitting problem for feature 74 returning NA
2025-08-19 09:38:58.290528 WARNING::Fitting problem for feature 78 returning NA
2025-08-19 09:38:58.349326 WARNING::Fitting problem for feature 84 returning NA
2025-08-19 09:38:58.477978 WARNING::Fitting problem for feature 96 returning NA
2025-08-19 09:38:58.486923 WARNING::Fitting problem for feature 97 returning NA
2025-08-19 09:38:58.507442 WARNING::Fitting problem for feature 99 returning NA
2025-08-19 09:38:58.674972 WARNING::Fitting problem for feature 114 returning NA
2025-08-19 09:38:58.684256 WARNING::Fitting problem for feature 115 returning NA
2025-08-19 09:38:58.769628 WARNING::Fitting problem for feature 123 returning NA
2025-08-19 09:38:58.835863 WARNING::Fitting problem for feature 130 returning NA
2025-08-19 09:38:58.854853 WARNING::Fitting problem for feature 132 returning NA
2025-08-19 09:38:58.920506 WARNING::Fitting problem for feature 139 returning NA
2025-08-19 09:38:59.03203 WARNING::Fitting problem for feature 150 returning NA
2025-08-19 09:39:25.281888 WARNING::Fitting problem for feature 124 returning NA
2025-08-19 09:39:40.601715 WARNING::Fitting problem for feature 124 returning NA
2025-08-19 09:40:10.146671 WARNING::Fitting problem for feature 124 returning NA
2025-08-19 09:40:27.573055 WARNING::Fitting problem for feature 124 returning NA
2025-08-19 09:40:28.575552 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpRew2ya/file2d1d356f79a5b6/fits/residuals_linear.rds
2025-08-19 09:40:28.63962 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpRew2ya/file2d1d356f79a5b6/fits/fitted_linear.rds
2025-08-19 09:40:28.681509 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpRew2ya/file2d1d356f79a5b6/fits/residuals_logistic.rds
2025-08-19 09:40:28.757387 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpRew2ya/file2d1d356f79a5b6/fits/fitted_logistic.rds
2025-08-19 09:40:52.3231 WARNING::Fitting problem for feature 124 returning NA
2025-08-19 09:41:00.59698 WARNING::Fitting problem for feature 124 returning NA
2025-08-19 09:41:01.092232 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpRew2ya/file2d1d356f79a5b6/fits/residuals_linear.rds
2025-08-19 09:41:01.160529 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpRew2ya/file2d1d356f79a5b6/fits/fitted_linear.rds
2025-08-19 09:41:01.203761 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpRew2ya/file2d1d356f79a5b6/fits/residuals_logistic.rds
2025-08-19 09:41:01.28162 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpRew2ya/file2d1d356f79a5b6/fits/fitted_logistic.rds
2025-08-19 09:41:22.114391 WARNING::Fitting problem for feature 124 returning NA
2025-08-19 09:41:30.2068 WARNING::Fitting problem for feature 124 returning NA
2025-08-19 09:41:30.727937 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpRew2ya/file2d1d356f79a5b6/fits/residuals_linear.rds
2025-08-19 09:41:30.797056 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpRew2ya/file2d1d356f79a5b6/fits/fitted_linear.rds
2025-08-19 09:41:30.840255 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpRew2ya/file2d1d356f79a5b6/fits/residuals_logistic.rds
2025-08-19 09:41:30.920188 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpRew2ya/file2d1d356f79a5b6/fits/fitted_logistic.rds
2025-08-19 09:41:51.522135 WARNING::Fitting problem for feature 50 returning NA
2025-08-19 09:41:51.655324 WARNING::Fitting problem for feature 62 returning NA
2025-08-19 09:41:51.792295 WARNING::Fitting problem for feature 74 returning NA
2025-08-19 09:41:51.833066 WARNING::Fitting problem for feature 78 returning NA
2025-08-19 09:41:51.897368 WARNING::Fitting problem for feature 84 returning NA
2025-08-19 09:41:52.037655 WARNING::Fitting problem for feature 96 returning NA
2025-08-19 09:41:52.04722 WARNING::Fitting problem for feature 97 returning NA
2025-08-19 09:41:52.068948 WARNING::Fitting problem for feature 99 returning NA
2025-08-19 09:41:52.234746 WARNING::Fitting problem for feature 114 returning NA
2025-08-19 09:41:52.243462 WARNING::Fitting problem for feature 115 returning NA
2025-08-19 09:41:52.329626 WARNING::Fitting problem for feature 123 returning NA
2025-08-19 09:41:52.402358 WARNING::Fitting problem for feature 130 returning NA
2025-08-19 09:41:52.422291 WARNING::Fitting problem for feature 132 returning NA
2025-08-19 09:41:52.493923 WARNING::Fitting problem for feature 139 returning NA
2025-08-19 09:41:52.617666 WARNING::Fitting problem for feature 150 returning NA
2025-08-19 09:42:11.473683 WARNING::Fitting problem for feature 50 returning NA
2025-08-19 09:42:11.606153 WARNING::Fitting problem for feature 62 returning NA
2025-08-19 09:42:11.734553 WARNING::Fitting problem for feature 74 returning NA
2025-08-19 09:42:11.774623 WARNING::Fitting problem for feature 78 returning NA
2025-08-19 09:42:11.837474 WARNING::Fitting problem for feature 84 returning NA
2025-08-19 09:42:11.965173 WARNING::Fitting problem for feature 96 returning NA
2025-08-19 09:42:11.973764 WARNING::Fitting problem for feature 97 returning NA
2025-08-19 09:42:11.993223 WARNING::Fitting problem for feature 99 returning NA
2025-08-19 09:42:12.152555 WARNING::Fitting problem for feature 114 returning NA
2025-08-19 09:42:12.16153 WARNING::Fitting problem for feature 115 returning NA
2025-08-19 09:42:12.246101 WARNING::Fitting problem for feature 123 returning NA
2025-08-19 09:42:12.313018 WARNING::Fitting problem for feature 130 returning NA
2025-08-19 09:42:12.331966 WARNING::Fitting problem for feature 132 returning NA
2025-08-19 09:42:12.399862 WARNING::Fitting problem for feature 139 returning NA
2025-08-19 09:42:12.517786 WARNING::Fitting problem for feature 150 returning NA
2025-08-19 09:42:13.902882 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpRew2ya/file2d1d356f79a5b6/fits/residuals_linear.rds
2025-08-19 09:42:13.96784 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpRew2ya/file2d1d356f79a5b6/fits/fitted_linear.rds
2025-08-19 09:42:14.03437 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpRew2ya/file2d1d356f79a5b6/fits/residuals_logistic.rds
2025-08-19 09:42:14.350554 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpRew2ya/file2d1d356f79a5b6/fits/fitted_logistic.rds
2025-08-19 09:42:34.960179 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-08-19 09:42:34.986741 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-08-19 09:42:35.005682 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-08-19 09:42:35.08782 ERROR::No fixed, group, or
                        ordered effects included in formula.
2025-08-19 09:42:35.112292 ERROR::Effect name not found in metadata: d
2025-08-19 09:42:35.128987 ERROR::No user formula provided
2025-08-19 09:42:35.173396 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-08-19 09:42:35.190892 ERROR::No fixed/group/ordered/
                        feature-specific effects provided.
2025-08-19 09:42:40.088724 INFO::Writing function arguments to log file
2025-08-19 09:42:40.114177 INFO::Verifying options selected are valid
2025-08-19 09:42:42.640427 INFO::Writing function arguments to log file
2025-08-19 09:42:42.661513 INFO::Verifying options selected are valid
2025-08-19 09:42:42.663196 INFO::Determining format of input files
2025-08-19 09:42:42.664845 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-19 09:42:42.668666 INFO::Running selected normalization method: TSS
2025-08-19 09:42:42.671076 INFO::Creating output feature tables folder
2025-08-19 09:42:42.672771 INFO::Writing normalized data to file /home/biocbuild/tmp/RtmpRew2ya/file2d1d3533380760/features/data_norm.tsv
2025-08-19 09:42:42.675202 INFO::Filter data based on min abundance and min prevalence
2025-08-19 09:42:42.676818 INFO::Total samples in data: 16
2025-08-19 09:42:42.678343 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-08-19 09:42:42.681387 INFO::Total filtered features: 0
2025-08-19 09:42:42.683033 INFO::Filtered feature names from abundance and prevalence filtering:
2025-08-19 09:42:42.68502 INFO::Total features filtered by non-zero variance filtering: 0
2025-08-19 09:42:42.686641 INFO::Filtered feature names from variance filtering:
2025-08-19 09:42:42.68816 INFO::Writing filtered data to file /home/biocbuild/tmp/RtmpRew2ya/file2d1d3533380760/features/filtered_data.tsv
2025-08-19 09:42:42.690628 INFO::Running selected transform method: LOG
2025-08-19 09:42:42.692674 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpRew2ya/file2d1d3533380760/features/data_transformed.tsv
2025-08-19 09:42:42.695535 INFO::Applying z-score to standardize continuous metadata
2025-08-19 09:42:42.703872 INFO::Running the linear model component
2025-08-19 09:42:42.729064 INFO::Fitting model to feature number 1, a
2025-08-19 09:42:42.73622 INFO::Fitting model to feature number 2, b
2025-08-19 09:42:42.743471 INFO::Fitting model to feature number 3, c
2025-08-19 09:42:42.755761 INFO::Counting total values for each feature
2025-08-19 09:42:42.759067 INFO::Running the logistic model component
2025-08-19 09:42:42.786716 INFO::Fitting model to feature number 1, a
2025-08-19 09:42:42.797413 INFO::Fitting model to feature number 2, b
2025-08-19 09:42:42.807263 INFO::Fitting model to feature number 3, c
2025-08-19 09:42:42.821477 INFO::Counting total values for each feature
2025-08-19 09:42:42.824964 INFO::Re-running abundances for warn_prevalence
2025-08-19 09:42:42.826553 INFO::Running selected normalization method: TSS
2025-08-19 09:42:42.828962 INFO::Running selected transform method: LOG
2025-08-19 09:42:42.85205 INFO::Fitting model to feature number 1, a
2025-08-19 09:42:42.859344 INFO::Fitting model to feature number 2, b
2025-08-19 09:42:42.866585 INFO::Fitting model to feature number 3, c
2025-08-19 09:42:43.010747 INFO::Creating fits folder
2025-08-19 09:42:43.012534 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpRew2ya/file2d1d3533380760/fits/residuals_linear.rds
2025-08-19 09:42:43.014347 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpRew2ya/file2d1d3533380760/fits/fitted_linear.rds
2025-08-19 09:42:43.016319 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpRew2ya/file2d1d3533380760/fits/residuals_logistic.rds
2025-08-19 09:42:43.018315 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpRew2ya/file2d1d3533380760/fits/fitted_logistic.rds
2025-08-19 09:42:43.022617 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /home/biocbuild/tmp/RtmpRew2ya/file2d1d3533380760/all_results.tsv
2025-08-19 09:42:43.025383 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/RtmpRew2ya/file2d1d3533380760/significant_results.tsv
2025-08-19 09:42:43.027618 INFO::Creating output figures folder
2025-08-19 09:42:43.029996 INFO::Writing summary plot of significant
                        results to file: /home/biocbuild/tmp/RtmpRew2ya/file2d1d3533380760/figures/summary_plot.pdf
2025-08-19 09:42:44.805616 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/RtmpRew2ya/file2d1d3533380760/figures
2025-08-19 09:42:44.808496 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-19 09:42:44.816312 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-19 09:42:45.341542 INFO::Writing summary plot of
                        significant results to file: /home/biocbuild/tmp/RtmpRew2ya/file2d1d3533380760/figures/summary_plot.pdf
2025-08-19 09:42:47.102647 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/RtmpRew2ya/file2d1d3533380760/figures
2025-08-19 09:42:47.104727 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-19 09:42:47.11255 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-19 09:42:47.620567 INFO::Running the linear model component
2025-08-19 09:42:47.63584 INFO::Fitting model to feature number 1, a
2025-08-19 09:42:47.643092 INFO::Fitting model to feature number 2, b
2025-08-19 09:42:47.649997 INFO::Fitting model to feature number 3, c
2025-08-19 09:42:47.660898 INFO::Counting total values for each feature
2025-08-19 09:42:47.663537 INFO::Running the logistic model component
2025-08-19 09:42:47.67789 INFO::Fitting model to feature number 1, a
2025-08-19 09:42:47.707788 INFO::Fitting model to feature number 2, b
2025-08-19 09:42:47.718616 INFO::Fitting model to feature number 3, c
2025-08-19 09:42:47.733 INFO::Counting total values for each feature
2025-08-19 09:42:47.736211 INFO::Re-running abundances for warn_prevalence
2025-08-19 09:42:47.737635 INFO::Running selected normalization method: TSS
2025-08-19 09:42:47.739893 INFO::Running selected transform method: LOG
2025-08-19 09:42:47.754955 INFO::Fitting model to feature number 1, a
2025-08-19 09:42:47.762138 INFO::Fitting model to feature number 2, b
2025-08-19 09:42:47.769736 INFO::Fitting model to feature number 3, c
2025-08-19 09:42:47.909642 INFO::Creating output folder
2025-08-19 09:42:47.911038 INFO::Creating output figures folder
2025-08-19 09:42:47.912924 INFO::Writing summary plot of significant
                        results to file: /home/biocbuild/tmp/RtmpRew2ya/file2d1d35c8808d/figures/summary_plot.pdf
2025-08-19 09:42:49.681203 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/RtmpRew2ya/file2d1d35c8808d/figures
2025-08-19 09:42:49.68366 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-19 09:42:49.691095 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-19 09:42:50.907927 INFO::Applying z-score to standardize continuous metadata
2025-08-19 09:42:50.919192 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-08-19 09:42:50.920453 INFO::Bypass z-score application to metadata
2025-08-19 09:42:50.924324 INFO::Bypass z-score application to metadata
2025-08-19 09:42:50.950803 INFO::Determining format of input files
2025-08-19 09:42:50.952102 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-19 09:42:50.953429 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-08-19 09:42:50.964119 INFO::Determining format of input files
2025-08-19 09:42:50.965785 INFO::Input format is data samples as columns and metadata samples as rows
2025-08-19 09:42:50.967793 INFO::Input format is feature_specific_covariate samples as columns
2025-08-19 09:42:50.980423 INFO::Determining format of input files
2025-08-19 09:42:50.981993 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-19 09:42:50.98359 INFO::Input format is feature_specific_covariate samples as columns
2025-08-19 09:42:50.986343 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-08-19 09:42:50.987611 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-08-19 09:42:51.004261 INFO::Running selected transform method: LOG
2025-08-19 09:42:51.00596 INFO::Creating output feature tables folder
2025-08-19 09:42:51.007208 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpRew2ya/file2d1d3518944041/features/data_transformed.tsv
2025-08-19 09:42:51.013012 INFO::Running selected transform method: LOG
2025-08-19 09:42:51.014664 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpRew2ya/file2d1d3518944041/features/data_transformed.tsv
2025-08-19 09:42:51.020406 INFO::Running selected transform method: PLOG
2025-08-19 09:42:51.022995 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpRew2ya/file2d1d3518944041/features/data_transformed.tsv
2025-08-19 09:42:51.02733 INFO::Running selected transform method: NONE
2025-08-19 09:42:51.028581 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpRew2ya/file2d1d3518944041/features/data_transformed.tsv
2025-08-19 09:42:51.040762 INFO::Running the linear model component
2025-08-19 09:42:51.055578 INFO::Fitting model to feature number 1, a
2025-08-19 09:42:51.06267 INFO::Fitting model to feature number 2, b
2025-08-19 09:42:51.069712 INFO::Fitting model to feature number 3, c
2025-08-19 09:42:51.081554 INFO::Counting total values for each feature
2025-08-19 09:42:51.08433 INFO::Running the logistic model component
2025-08-19 09:42:51.098958 INFO::Fitting model to feature number 1, a
2025-08-19 09:42:51.108646 INFO::Fitting model to feature number 2, b
2025-08-19 09:42:51.118454 INFO::Fitting model to feature number 3, c
2025-08-19 09:42:51.132851 INFO::Counting total values for each feature
2025-08-19 09:42:51.136103 INFO::Re-running abundances for warn_prevalence
2025-08-19 09:42:51.137505 INFO::Running selected normalization method: TSS
2025-08-19 09:42:51.139769 INFO::Running selected transform method: LOG
2025-08-19 09:42:51.154835 INFO::Fitting model to feature number 1, a
2025-08-19 09:42:51.161947 INFO::Fitting model to feature number 2, b
2025-08-19 09:42:51.168941 INFO::Fitting model to feature number 3, c
2025-08-19 09:42:51.312647 INFO::Creating output folder
2025-08-19 09:42:51.314242 INFO::Creating fits folder
2025-08-19 09:42:51.31566 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpRew2ya/file2d1d357ca158d3/fits/residuals_linear.rds
2025-08-19 09:42:51.317273 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpRew2ya/file2d1d357ca158d3/fits/fitted_linear.rds
2025-08-19 09:42:51.319005 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpRew2ya/file2d1d357ca158d3/fits/residuals_logistic.rds
2025-08-19 09:42:51.320673 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpRew2ya/file2d1d357ca158d3/fits/fitted_logistic.rds
2025-08-19 09:42:51.324553 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /home/biocbuild/tmp/RtmpRew2ya/file2d1d357ca158d3/all_results.tsv
2025-08-19 09:42:51.326909 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/RtmpRew2ya/file2d1d357ca158d3/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]

[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
> 
> 
> proc.time()
   user  system elapsed 
444.498   4.778 450.691

Example timings

maaslin3.Rcheck/maaslin3-Ex.timings

nameusersystemelapsed
maaslin327.880 0.29228.225
maaslin_check_arguments0.2030.0000.204
maaslin_check_formula0.2040.0000.204
maaslin_compute_formula0.2070.0000.207
maaslin_contrast_test28.627 0.25928.949
maaslin_filter0.7150.0080.724
maaslin_fit20.988 0.06421.112
maaslin_log_arguments0.1900.0040.195
maaslin_normalize0.3700.0080.379
maaslin_plot_results52.690 0.22753.075
maaslin_plot_results_from_output53.044 0.27553.480
maaslin_process_metadata0.6360.0120.650
maaslin_read_data0.1960.0040.200
maaslin_reorder_data0.2080.0000.208
maaslin_transform0.7920.0160.810
maaslin_write_results23.519 0.33923.938
maaslin_write_results_lefse_format24.574 0.07924.734
preprocess_dna_mtx0.0050.0000.005
preprocess_taxa_mtx0.0060.0000.006