Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-08-15 12:07 -0400 (Fri, 15 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4554
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4535
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 1147/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maaslin3 1.1.0  (landing page)
William Nickols
Snapshot Date: 2025-08-14 13:45 -0400 (Thu, 14 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
palomino8Windows Server 2022 Datacenter / x64  OK    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 palomino8

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

raw results


Summary

Package: maaslin3
Version: 1.1.0
Command: F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:maaslin3.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings maaslin3_1.1.0.tar.gz
StartedAt: 2025-08-15 04:41:56 -0400 (Fri, 15 Aug 2025)
EndedAt: 2025-08-15 04:56:59 -0400 (Fri, 15 Aug 2025)
EllapsedTime: 902.4 seconds
RetCode: 0
Status:   OK  
CheckDir: maaslin3.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:maaslin3.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings maaslin3_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/maaslin3.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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               48.68   2.73   52.44
maaslin_plot_results_from_output   45.57   2.27   47.84
maaslin_contrast_test              27.52   1.97   29.50
maaslin3                           25.14   1.42   29.42
maaslin_write_results_lefse_format 21.75   2.15   23.94
maaslin_write_results              21.34   1.77   23.14
maaslin_fit                        20.02   1.13   21.11
* 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:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL maaslin3
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.22-bioc/R/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 4.5.1 (2025-06-13 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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")
2025-08-15 04:49:48.486131 WARNING::Fitting problem for feature 50 returning NA
2025-08-15 04:49:48.622319 WARNING::Fitting problem for feature 62 returning NA
2025-08-15 04:49:48.768119 WARNING::Fitting problem for feature 74 returning NA
2025-08-15 04:49:48.795267 WARNING::Fitting problem for feature 78 returning NA
2025-08-15 04:49:48.841819 WARNING::Fitting problem for feature 84 returning NA
2025-08-15 04:49:48.975311 WARNING::Fitting problem for feature 96 returning NA
2025-08-15 04:49:48.982378 WARNING::Fitting problem for feature 97 returning NA
2025-08-15 04:49:48.997468 WARNING::Fitting problem for feature 99 returning NA
2025-08-15 04:49:49.116565 WARNING::Fitting problem for feature 114 returning NA
2025-08-15 04:49:49.128373 WARNING::Fitting problem for feature 115 returning NA
2025-08-15 04:49:49.222786 WARNING::Fitting problem for feature 123 returning NA
2025-08-15 04:49:49.272044 WARNING::Fitting problem for feature 130 returning NA
2025-08-15 04:49:49.286719 WARNING::Fitting problem for feature 132 returning NA
2025-08-15 04:49:49.33558 WARNING::Fitting problem for feature 139 returning NA
2025-08-15 04:49:49.419953 WARNING::Fitting problem for feature 150 returning NA
2025-08-15 04:50:10.959942 WARNING::Fitting problem for feature 50 returning NA
2025-08-15 04:50:11.108031 WARNING::Fitting problem for feature 62 returning NA
2025-08-15 04:50:11.251058 WARNING::Fitting problem for feature 74 returning NA
2025-08-15 04:50:11.28926 WARNING::Fitting problem for feature 78 returning NA
2025-08-15 04:50:11.331013 WARNING::Fitting problem for feature 84 returning NA
2025-08-15 04:50:11.425949 WARNING::Fitting problem for feature 96 returning NA
2025-08-15 04:50:11.433364 WARNING::Fitting problem for feature 97 returning NA
2025-08-15 04:50:11.448565 WARNING::Fitting problem for feature 99 returning NA
2025-08-15 04:50:11.568433 WARNING::Fitting problem for feature 114 returning NA
2025-08-15 04:50:11.575815 WARNING::Fitting problem for feature 115 returning NA
2025-08-15 04:50:11.663647 WARNING::Fitting problem for feature 123 returning NA
2025-08-15 04:50:11.742037 WARNING::Fitting problem for feature 130 returning NA
2025-08-15 04:50:11.76724 WARNING::Fitting problem for feature 132 returning NA
2025-08-15 04:50:11.86507 WARNING::Fitting problem for feature 139 returning NA
2025-08-15 04:50:12.019594 WARNING::Fitting problem for feature 150 returning NA
2025-08-15 04:50:35.913068 WARNING::Fitting problem for feature 50 returning NA
2025-08-15 04:50:36.011884 WARNING::Fitting problem for feature 62 returning NA
2025-08-15 04:50:36.115425 WARNING::Fitting problem for feature 74 returning NA
2025-08-15 04:50:36.158096 WARNING::Fitting problem for feature 78 returning NA
2025-08-15 04:50:36.205405 WARNING::Fitting problem for feature 84 returning NA
2025-08-15 04:50:36.34486 WARNING::Fitting problem for feature 96 returning NA
2025-08-15 04:50:36.357638 WARNING::Fitting problem for feature 97 returning NA
2025-08-15 04:50:36.383971 WARNING::Fitting problem for feature 99 returning NA
2025-08-15 04:50:36.626554 WARNING::Fitting problem for feature 114 returning NA
2025-08-15 04:50:36.640494 WARNING::Fitting problem for feature 115 returning NA
2025-08-15 04:50:36.731415 WARNING::Fitting problem for feature 123 returning NA
2025-08-15 04:50:36.789423 WARNING::Fitting problem for feature 130 returning NA
2025-08-15 04:50:36.805922 WARNING::Fitting problem for feature 132 returning NA
2025-08-15 04:50:36.856747 WARNING::Fitting problem for feature 139 returning NA
2025-08-15 04:50:36.982384 WARNING::Fitting problem for feature 150 returning NA
2025-08-15 04:50:55.098407 WARNING::Fitting problem for feature 50 returning NA
2025-08-15 04:50:55.199525 WARNING::Fitting problem for feature 62 returning NA
2025-08-15 04:50:55.314672 WARNING::Fitting problem for feature 74 returning NA
2025-08-15 04:50:55.357068 WARNING::Fitting problem for feature 78 returning NA
2025-08-15 04:50:55.420709 WARNING::Fitting problem for feature 84 returning NA
2025-08-15 04:50:55.554806 WARNING::Fitting problem for feature 96 returning NA
2025-08-15 04:50:55.566574 WARNING::Fitting problem for feature 97 returning NA
2025-08-15 04:50:55.593096 WARNING::Fitting problem for feature 99 returning NA
2025-08-15 04:50:55.789025 WARNING::Fitting problem for feature 114 returning NA
2025-08-15 04:50:55.797512 WARNING::Fitting problem for feature 115 returning NA
2025-08-15 04:50:55.877412 WARNING::Fitting problem for feature 123 returning NA
2025-08-15 04:50:55.973188 WARNING::Fitting problem for feature 130 returning NA
2025-08-15 04:50:56.002495 WARNING::Fitting problem for feature 132 returning NA
2025-08-15 04:50:56.1365 WARNING::Fitting problem for feature 139 returning NA
2025-08-15 04:50:56.271316 WARNING::Fitting problem for feature 150 returning NA
2025-08-15 04:50:56.610023 WARNING::Deleting existing residuals file: F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file827823315fc0/fits/residuals_linear.rds
2025-08-15 04:50:56.685222 WARNING::Deleting existing fitted file: F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file827823315fc0/fits/fitted_linear.rds
2025-08-15 04:50:56.762591 WARNING::Deleting existing residuals file: F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file827823315fc0/fits/residuals_logistic.rds
2025-08-15 04:50:57.131569 WARNING::Deleting existing fitted file: F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file827823315fc0/fits/fitted_logistic.rds
2025-08-15 04:51:19.156188 WARNING::Fitting problem for feature 50 returning NA
2025-08-15 04:51:19.304905 WARNING::Fitting problem for feature 62 returning NA
2025-08-15 04:51:19.452591 WARNING::Fitting problem for feature 74 returning NA
2025-08-15 04:51:19.498439 WARNING::Fitting problem for feature 78 returning NA
2025-08-15 04:51:19.562754 WARNING::Fitting problem for feature 84 returning NA
2025-08-15 04:51:19.693335 WARNING::Fitting problem for feature 96 returning NA
2025-08-15 04:51:19.705457 WARNING::Fitting problem for feature 97 returning NA
2025-08-15 04:51:19.7307 WARNING::Fitting problem for feature 99 returning NA
2025-08-15 04:51:19.921475 WARNING::Fitting problem for feature 114 returning NA
2025-08-15 04:51:19.935163 WARNING::Fitting problem for feature 115 returning NA
2025-08-15 04:51:20.020913 WARNING::Fitting problem for feature 123 returning NA
2025-08-15 04:51:20.079368 WARNING::Fitting problem for feature 130 returning NA
2025-08-15 04:51:20.099975 WARNING::Fitting problem for feature 132 returning NA
2025-08-15 04:51:20.163728 WARNING::Fitting problem for feature 139 returning NA
2025-08-15 04:51:20.416845 WARNING::Fitting problem for feature 150 returning NA
2025-08-15 04:51:39.440404 WARNING::Fitting problem for feature 50 returning NA
2025-08-15 04:51:39.575724 WARNING::Fitting problem for feature 62 returning NA
2025-08-15 04:51:39.740127 WARNING::Fitting problem for feature 74 returning NA
2025-08-15 04:51:39.786661 WARNING::Fitting problem for feature 78 returning NA
2025-08-15 04:51:39.860885 WARNING::Fitting problem for feature 84 returning NA
2025-08-15 04:51:39.99411 WARNING::Fitting problem for feature 96 returning NA
2025-08-15 04:51:40.003013 WARNING::Fitting problem for feature 97 returning NA
2025-08-15 04:51:40.026114 WARNING::Fitting problem for feature 99 returning NA
2025-08-15 04:51:40.300144 WARNING::Fitting problem for feature 114 returning NA
2025-08-15 04:51:40.312176 WARNING::Fitting problem for feature 115 returning NA
2025-08-15 04:51:40.412081 WARNING::Fitting problem for feature 123 returning NA
2025-08-15 04:51:40.487407 WARNING::Fitting problem for feature 130 returning NA
2025-08-15 04:51:40.502895 WARNING::Fitting problem for feature 132 returning NA
2025-08-15 04:51:40.552965 WARNING::Fitting problem for feature 139 returning NA
2025-08-15 04:51:40.651735 WARNING::Fitting problem for feature 150 returning NA
2025-08-15 04:51:40.917179 WARNING::Deleting existing residuals file: F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file827823315fc0/fits/residuals_linear.rds
2025-08-15 04:51:40.988344 WARNING::Deleting existing fitted file: F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file827823315fc0/fits/fitted_linear.rds
2025-08-15 04:51:41.042243 WARNING::Deleting existing residuals file: F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file827823315fc0/fits/residuals_logistic.rds
2025-08-15 04:51:41.388422 WARNING::Deleting existing fitted file: F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file827823315fc0/fits/fitted_logistic.rds
2025-08-15 04:52:03.240544 WARNING::Fitting problem for feature 50 returning NA
2025-08-15 04:52:03.375273 WARNING::Fitting problem for feature 62 returning NA
2025-08-15 04:52:03.515234 WARNING::Fitting problem for feature 74 returning NA
2025-08-15 04:52:03.55553 WARNING::Fitting problem for feature 78 returning NA
2025-08-15 04:52:03.619383 WARNING::Fitting problem for feature 84 returning NA
2025-08-15 04:52:03.749392 WARNING::Fitting problem for feature 96 returning NA
2025-08-15 04:52:03.75683 WARNING::Fitting problem for feature 97 returning NA
2025-08-15 04:52:03.772375 WARNING::Fitting problem for feature 99 returning NA
2025-08-15 04:52:03.951589 WARNING::Fitting problem for feature 114 returning NA
2025-08-15 04:52:03.964343 WARNING::Fitting problem for feature 115 returning NA
2025-08-15 04:52:04.062716 WARNING::Fitting problem for feature 123 returning NA
2025-08-15 04:52:04.142822 WARNING::Fitting problem for feature 130 returning NA
2025-08-15 04:52:04.167048 WARNING::Fitting problem for feature 132 returning NA
2025-08-15 04:52:04.248938 WARNING::Fitting problem for feature 139 returning NA
2025-08-15 04:52:04.395649 WARNING::Fitting problem for feature 150 returning NA
2025-08-15 04:52:21.279484 WARNING::Fitting problem for feature 50 returning NA
2025-08-15 04:52:21.431212 WARNING::Fitting problem for feature 62 returning NA
2025-08-15 04:52:21.534897 WARNING::Fitting problem for feature 74 returning NA
2025-08-15 04:52:21.581104 WARNING::Fitting problem for feature 78 returning NA
2025-08-15 04:52:21.652446 WARNING::Fitting problem for feature 84 returning NA
2025-08-15 04:52:21.812364 WARNING::Fitting problem for feature 96 returning NA
2025-08-15 04:52:21.824589 WARNING::Fitting problem for feature 97 returning NA
2025-08-15 04:52:21.85073 WARNING::Fitting problem for feature 99 returning NA
2025-08-15 04:52:22.043847 WARNING::Fitting problem for feature 114 returning NA
2025-08-15 04:52:22.054636 WARNING::Fitting problem for feature 115 returning NA
2025-08-15 04:52:22.148487 WARNING::Fitting problem for feature 123 returning NA
2025-08-15 04:52:22.274411 WARNING::Fitting problem for feature 130 returning NA
2025-08-15 04:52:22.296412 WARNING::Fitting problem for feature 132 returning NA
2025-08-15 04:52:22.373724 WARNING::Fitting problem for feature 139 returning NA
2025-08-15 04:52:22.508419 WARNING::Fitting problem for feature 150 returning NA
2025-08-15 04:52:22.822838 WARNING::Deleting existing residuals file: F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file827823315fc0/fits/residuals_linear.rds
2025-08-15 04:52:22.894622 WARNING::Deleting existing fitted file: F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file827823315fc0/fits/fitted_linear.rds
2025-08-15 04:52:22.970799 WARNING::Deleting existing residuals file: F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file827823315fc0/fits/residuals_logistic.rds
2025-08-15 04:52:23.329763 WARNING::Deleting existing fitted file: F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file827823315fc0/fits/fitted_logistic.rds
2025-08-15 04:52:46.299243 WARNING::Fitting problem for feature 50 returning NA
2025-08-15 04:52:46.45972 WARNING::Fitting problem for feature 62 returning NA
2025-08-15 04:52:46.643413 WARNING::Fitting problem for feature 74 returning NA
2025-08-15 04:52:46.685398 WARNING::Fitting problem for feature 78 returning NA
2025-08-15 04:52:46.745941 WARNING::Fitting problem for feature 84 returning NA
2025-08-15 04:52:46.881972 WARNING::Fitting problem for feature 96 returning NA
2025-08-15 04:52:46.893466 WARNING::Fitting problem for feature 97 returning NA
2025-08-15 04:52:46.915256 WARNING::Fitting problem for feature 99 returning NA
2025-08-15 04:52:47.039669 WARNING::Fitting problem for feature 114 returning NA
2025-08-15 04:52:47.052662 WARNING::Fitting problem for feature 115 returning NA
2025-08-15 04:52:47.139562 WARNING::Fitting problem for feature 123 returning NA
2025-08-15 04:52:47.218218 WARNING::Fitting problem for feature 130 returning NA
2025-08-15 04:52:47.241704 WARNING::Fitting problem for feature 132 returning NA
2025-08-15 04:52:47.317189 WARNING::Fitting problem for feature 139 returning NA
2025-08-15 04:52:47.452766 WARNING::Fitting problem for feature 150 returning NA
2025-08-15 04:53:06.075218 WARNING::Fitting problem for feature 50 returning NA
2025-08-15 04:53:06.225781 WARNING::Fitting problem for feature 62 returning NA
2025-08-15 04:53:06.374954 WARNING::Fitting problem for feature 74 returning NA
2025-08-15 04:53:06.420452 WARNING::Fitting problem for feature 78 returning NA
2025-08-15 04:53:06.491611 WARNING::Fitting problem for feature 84 returning NA
2025-08-15 04:53:06.645785 WARNING::Fitting problem for feature 96 returning NA
2025-08-15 04:53:06.65782 WARNING::Fitting problem for feature 97 returning NA
2025-08-15 04:53:06.683372 WARNING::Fitting problem for feature 99 returning NA
2025-08-15 04:53:06.871147 WARNING::Fitting problem for feature 114 returning NA
2025-08-15 04:53:06.882886 WARNING::Fitting problem for feature 115 returning NA
2025-08-15 04:53:06.986058 WARNING::Fitting problem for feature 123 returning NA
2025-08-15 04:53:07.06957 WARNING::Fitting problem for feature 130 returning NA
2025-08-15 04:53:07.0932 WARNING::Fitting problem for feature 132 returning NA
2025-08-15 04:53:07.177018 WARNING::Fitting problem for feature 139 returning NA
2025-08-15 04:53:07.316626 WARNING::Fitting problem for feature 150 returning NA
2025-08-15 04:53:31.889965 WARNING::Fitting problem for feature 124 returning NA
2025-08-15 04:53:47.029761 WARNING::Fitting problem for feature 124 returning NA
2025-08-15 04:54:13.072852 WARNING::Fitting problem for feature 124 returning NA
2025-08-15 04:54:28.107936 WARNING::Fitting problem for feature 124 returning NA
2025-08-15 04:54:28.877989 WARNING::Deleting existing residuals file: F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file82784ce2769/fits/residuals_linear.rds
2025-08-15 04:54:28.957192 WARNING::Deleting existing fitted file: F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file82784ce2769/fits/fitted_linear.rds
2025-08-15 04:54:29.006751 WARNING::Deleting existing residuals file: F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file82784ce2769/fits/residuals_logistic.rds
2025-08-15 04:54:29.098675 WARNING::Deleting existing fitted file: F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file82784ce2769/fits/fitted_logistic.rds
2025-08-15 04:54:52.583181 WARNING::Fitting problem for feature 124 returning NA
2025-08-15 04:55:02.402552 WARNING::Fitting problem for feature 124 returning NA
2025-08-15 04:55:02.934269 WARNING::Deleting existing residuals file: F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file82784ce2769/fits/residuals_linear.rds
2025-08-15 04:55:02.990194 WARNING::Deleting existing fitted file: F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file82784ce2769/fits/fitted_linear.rds
2025-08-15 04:55:03.025473 WARNING::Deleting existing residuals file: F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file82784ce2769/fits/residuals_logistic.rds
2025-08-15 04:55:03.092444 WARNING::Deleting existing fitted file: F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file82784ce2769/fits/fitted_logistic.rds
2025-08-15 04:55:23.433391 WARNING::Fitting problem for feature 124 returning NA
2025-08-15 04:55:33.411309 WARNING::Fitting problem for feature 124 returning NA
2025-08-15 04:55:33.821763 WARNING::Deleting existing residuals file: F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file82784ce2769/fits/residuals_linear.rds
2025-08-15 04:55:33.874363 WARNING::Deleting existing fitted file: F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file82784ce2769/fits/fitted_linear.rds
2025-08-15 04:55:33.908177 WARNING::Deleting existing residuals file: F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file82784ce2769/fits/residuals_logistic.rds
2025-08-15 04:55:33.968627 WARNING::Deleting existing fitted file: F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file82784ce2769/fits/fitted_logistic.rds
2025-08-15 04:55:52.511547 WARNING::Fitting problem for feature 50 returning NA
2025-08-15 04:55:52.639087 WARNING::Fitting problem for feature 62 returning NA
2025-08-15 04:55:52.732164 WARNING::Fitting problem for feature 74 returning NA
2025-08-15 04:55:52.762538 WARNING::Fitting problem for feature 78 returning NA
2025-08-15 04:55:52.812607 WARNING::Fitting problem for feature 84 returning NA
2025-08-15 04:55:52.915449 WARNING::Fitting problem for feature 96 returning NA
2025-08-15 04:55:52.923889 WARNING::Fitting problem for feature 97 returning NA
2025-08-15 04:55:52.94229 WARNING::Fitting problem for feature 99 returning NA
2025-08-15 04:55:53.083092 WARNING::Fitting problem for feature 114 returning NA
2025-08-15 04:55:53.093854 WARNING::Fitting problem for feature 115 returning NA
2025-08-15 04:55:53.157944 WARNING::Fitting problem for feature 123 returning NA
2025-08-15 04:55:53.225126 WARNING::Fitting problem for feature 130 returning NA
2025-08-15 04:55:53.240627 WARNING::Fitting problem for feature 132 returning NA
2025-08-15 04:55:53.369373 WARNING::Fitting problem for feature 139 returning NA
2025-08-15 04:55:53.504565 WARNING::Fitting problem for feature 150 returning NA
2025-08-15 04:56:10.561833 WARNING::Fitting problem for feature 50 returning NA
2025-08-15 04:56:10.694073 WARNING::Fitting problem for feature 62 returning NA
2025-08-15 04:56:10.83203 WARNING::Fitting problem for feature 74 returning NA
2025-08-15 04:56:10.863185 WARNING::Fitting problem for feature 78 returning NA
2025-08-15 04:56:10.918742 WARNING::Fitting problem for feature 84 returning NA
2025-08-15 04:56:11.04004 WARNING::Fitting problem for feature 96 returning NA
2025-08-15 04:56:11.047329 WARNING::Fitting problem for feature 97 returning NA
2025-08-15 04:56:11.06867 WARNING::Fitting problem for feature 99 returning NA
2025-08-15 04:56:11.195817 WARNING::Fitting problem for feature 114 returning NA
2025-08-15 04:56:11.204732 WARNING::Fitting problem for feature 115 returning NA
2025-08-15 04:56:11.28879 WARNING::Fitting problem for feature 123 returning NA
2025-08-15 04:56:11.371984 WARNING::Fitting problem for feature 130 returning NA
2025-08-15 04:56:11.39751 WARNING::Fitting problem for feature 132 returning NA
2025-08-15 04:56:11.47702 WARNING::Fitting problem for feature 139 returning NA
2025-08-15 04:56:11.608558 WARNING::Fitting problem for feature 150 returning NA
2025-08-15 04:56:12.078802 WARNING::Deleting existing residuals file: F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file82784ce2769/fits/residuals_linear.rds
2025-08-15 04:56:12.15256 WARNING::Deleting existing fitted file: F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file82784ce2769/fits/fitted_linear.rds
2025-08-15 04:56:12.229027 WARNING::Deleting existing residuals file: F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file82784ce2769/fits/residuals_logistic.rds
2025-08-15 04:56:12.589578 WARNING::Deleting existing fitted file: F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file82784ce2769/fits/fitted_logistic.rds
2025-08-15 04:56:31.926177 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-08-15 04:56:31.942435 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-08-15 04:56:31.953709 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-08-15 04:56:32.005497 ERROR::No fixed, group, or
                        ordered effects included in formula.
2025-08-15 04:56:32.021478 ERROR::Effect name not found in metadata: d
2025-08-15 04:56:32.032292 ERROR::No user formula provided
2025-08-15 04:56:32.065189 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-08-15 04:56:32.076478 ERROR::No fixed/group/ordered/
                        feature-specific effects provided.
2025-08-15 04:56:36.185804 INFO::Writing function arguments to log file
2025-08-15 04:56:36.220713 INFO::Verifying options selected are valid
2025-08-15 04:56:38.572144 INFO::Writing function arguments to log file
2025-08-15 04:56:38.613064 INFO::Verifying options selected are valid
2025-08-15 04:56:38.615916 INFO::Determining format of input files
2025-08-15 04:56:38.618552 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-15 04:56:38.624577 INFO::Running selected normalization method: TSS
2025-08-15 04:56:38.627951 INFO::Creating output feature tables folder
2025-08-15 04:56:38.630672 INFO::Writing normalized data to file F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file82787ea3391/features/data_norm.tsv
2025-08-15 04:56:38.634438 INFO::Filter data based on min abundance and min prevalence
2025-08-15 04:56:38.63705 INFO::Total samples in data: 16
2025-08-15 04:56:38.639681 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-08-15 04:56:38.643668 INFO::Total filtered features: 0
2025-08-15 04:56:38.646309 INFO::Filtered feature names from abundance and prevalence filtering:
2025-08-15 04:56:38.64925 INFO::Total features filtered by non-zero variance filtering: 0
2025-08-15 04:56:38.651924 INFO::Filtered feature names from variance filtering:
2025-08-15 04:56:38.654484 INFO::Writing filtered data to file F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file82787ea3391/features/filtered_data.tsv
2025-08-15 04:56:38.65851 INFO::Running selected transform method: LOG
2025-08-15 04:56:38.661691 INFO::Writing normalized, filtered, transformed data to file F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file82787ea3391/features/data_transformed.tsv
2025-08-15 04:56:38.666168 INFO::Applying z-score to standardize continuous metadata
2025-08-15 04:56:38.675419 INFO::Running the linear model component
2025-08-15 04:56:38.719199 INFO::Fitting model to feature number 1, a
2025-08-15 04:56:38.725527 INFO::Fitting model to feature number 2, b
2025-08-15 04:56:38.731554 INFO::Fitting model to feature number 3, c
2025-08-15 04:56:38.740374 INFO::Counting total values for each feature
2025-08-15 04:56:38.743224 INFO::Running the logistic model component
2025-08-15 04:56:38.788907 INFO::Fitting model to feature number 1, a
2025-08-15 04:56:38.802237 INFO::Fitting model to feature number 2, b
2025-08-15 04:56:38.815199 INFO::Fitting model to feature number 3, c
2025-08-15 04:56:38.832802 INFO::Counting total values for each feature
2025-08-15 04:56:38.837959 INFO::Re-running abundances for warn_prevalence
2025-08-15 04:56:38.840903 INFO::Running selected normalization method: TSS
2025-08-15 04:56:38.844804 INFO::Running selected transform method: LOG
2025-08-15 04:56:38.892768 INFO::Fitting model to feature number 1, a
2025-08-15 04:56:38.899417 INFO::Fitting model to feature number 2, b
2025-08-15 04:56:38.906433 INFO::Fitting model to feature number 3, c
2025-08-15 04:56:39.017191 INFO::Creating fits folder
2025-08-15 04:56:39.019574 INFO::Writing residuals to file F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file82787ea3391/fits/residuals_linear.rds
2025-08-15 04:56:39.022954 INFO::Writing fitted values to file F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file82787ea3391/fits/fitted_linear.rds
2025-08-15 04:56:39.026377 INFO::Writing residuals to file F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file82787ea3391/fits/residuals_logistic.rds
2025-08-15 04:56:39.028885 INFO::Writing fitted values to file F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file82787ea3391/fits/fitted_logistic.rds
2025-08-15 04:56:39.033925 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file82787ea3391/all_results.tsv
2025-08-15 04:56:39.038492 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): F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file82787ea3391/significant_results.tsv
2025-08-15 04:56:39.042221 INFO::Creating output figures folder
2025-08-15 04:56:39.045593 INFO::Writing summary plot of significant
                        results to file: F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file82787ea3391/figures/summary_plot.pdf
2025-08-15 04:56:40.513736 INFO::Writing association plots (one for each significant association) to output folder: F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file82787ea3391/figures
2025-08-15 04:56:40.516327 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-15 04:56:40.522261 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-15 04:56:40.935673 INFO::Writing summary plot of
                        significant results to file: F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file82787ea3391/figures/summary_plot.pdf
2025-08-15 04:56:42.270131 INFO::Writing association plots (one for each significant association) to output folder: F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file82787ea3391/figures
2025-08-15 04:56:42.272844 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-15 04:56:42.280605 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-15 04:56:42.817908 INFO::Running the linear model component
2025-08-15 04:56:42.832785 INFO::Fitting model to feature number 1, a
2025-08-15 04:56:42.838286 INFO::Fitting model to feature number 2, b
2025-08-15 04:56:42.8435 INFO::Fitting model to feature number 3, c
2025-08-15 04:56:42.851618 INFO::Counting total values for each feature
2025-08-15 04:56:42.853671 INFO::Running the logistic model component
2025-08-15 04:56:42.86602 INFO::Fitting model to feature number 1, a
2025-08-15 04:56:42.873286 INFO::Fitting model to feature number 2, b
2025-08-15 04:56:42.8803 INFO::Fitting model to feature number 3, c
2025-08-15 04:56:42.890712 INFO::Counting total values for each feature
2025-08-15 04:56:42.893296 INFO::Re-running abundances for warn_prevalence
2025-08-15 04:56:42.894481 INFO::Running selected normalization method: TSS
2025-08-15 04:56:42.896175 INFO::Running selected transform method: LOG
2025-08-15 04:56:42.910855 INFO::Fitting model to feature number 1, a
2025-08-15 04:56:42.916223 INFO::Fitting model to feature number 2, b
2025-08-15 04:56:42.921329 INFO::Fitting model to feature number 3, c
2025-08-15 04:56:43.014112 INFO::Creating output folder
2025-08-15 04:56:43.015599 INFO::Creating output figures folder
2025-08-15 04:56:43.017408 INFO::Writing summary plot of significant
                        results to file: F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file82786ea42744/figures/summary_plot.pdf
2025-08-15 04:56:44.281343 INFO::Writing association plots (one for each significant association) to output folder: F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file82786ea42744/figures
2025-08-15 04:56:44.28331 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-15 04:56:44.288453 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-15 04:56:45.3832 INFO::Applying z-score to standardize continuous metadata
2025-08-15 04:56:45.393005 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-08-15 04:56:45.394845 INFO::Bypass z-score application to metadata
2025-08-15 04:56:45.399447 INFO::Bypass z-score application to metadata
2025-08-15 04:56:45.467092 INFO::Determining format of input files
2025-08-15 04:56:45.468413 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-15 04:56:45.469589 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-08-15 04:56:45.477593 INFO::Determining format of input files
2025-08-15 04:56:45.478976 INFO::Input format is data samples as columns and metadata samples as rows
2025-08-15 04:56:45.480589 INFO::Input format is feature_specific_covariate samples as columns
2025-08-15 04:56:45.488981 INFO::Determining format of input files
2025-08-15 04:56:45.490223 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-15 04:56:45.491537 INFO::Input format is feature_specific_covariate samples as columns
2025-08-15 04:56:45.493527 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-08-15 04:56:45.494553 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-08-15 04:56:45.508372 INFO::Running selected transform method: LOG
2025-08-15 04:56:45.510006 INFO::Creating output feature tables folder
2025-08-15 04:56:45.511487 INFO::Writing normalized, filtered, transformed data to file F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file82785174186f/features/data_transformed.tsv
2025-08-15 04:56:45.51633 INFO::Running selected transform method: LOG
2025-08-15 04:56:45.517783 INFO::Writing normalized, filtered, transformed data to file F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file82785174186f/features/data_transformed.tsv
2025-08-15 04:56:45.532412 INFO::Running selected transform method: PLOG
2025-08-15 04:56:45.534921 INFO::Writing normalized, filtered, transformed data to file F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file82785174186f/features/data_transformed.tsv
2025-08-15 04:56:45.539334 INFO::Running selected transform method: NONE
2025-08-15 04:56:45.541154 INFO::Writing normalized, filtered, transformed data to file F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file82785174186f/features/data_transformed.tsv
2025-08-15 04:56:45.552177 INFO::Running the linear model component
2025-08-15 04:56:45.568257 INFO::Fitting model to feature number 1, a
2025-08-15 04:56:45.573868 INFO::Fitting model to feature number 2, b
2025-08-15 04:56:45.57903 INFO::Fitting model to feature number 3, c
2025-08-15 04:56:45.587291 INFO::Counting total values for each feature
2025-08-15 04:56:45.589391 INFO::Running the logistic model component
2025-08-15 04:56:45.603046 INFO::Fitting model to feature number 1, a
2025-08-15 04:56:45.61039 INFO::Fitting model to feature number 2, b
2025-08-15 04:56:45.617461 INFO::Fitting model to feature number 3, c
2025-08-15 04:56:45.627452 INFO::Counting total values for each feature
2025-08-15 04:56:45.630613 INFO::Re-running abundances for warn_prevalence
2025-08-15 04:56:45.631821 INFO::Running selected normalization method: TSS
2025-08-15 04:56:45.633586 INFO::Running selected transform method: LOG
2025-08-15 04:56:45.646547 INFO::Fitting model to feature number 1, a
2025-08-15 04:56:45.65215 INFO::Fitting model to feature number 2, b
2025-08-15 04:56:45.657303 INFO::Fitting model to feature number 3, c
2025-08-15 04:56:45.790922 INFO::Creating output folder
2025-08-15 04:56:45.792577 INFO::Creating fits folder
2025-08-15 04:56:45.794056 INFO::Writing residuals to file F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file82784c7faf9/fits/residuals_linear.rds
2025-08-15 04:56:45.79583 INFO::Writing fitted values to file F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file82784c7faf9/fits/fitted_linear.rds
2025-08-15 04:56:45.79758 INFO::Writing residuals to file F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file82784c7faf9/fits/residuals_logistic.rds
2025-08-15 04:56:45.79925 INFO::Writing fitted values to file F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file82784c7faf9/fits/fitted_logistic.rds
2025-08-15 04:56:45.802391 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file82784c7faf9/all_results.tsv
2025-08-15 04:56:45.804936 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): F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp8wyPfi\file82784c7faf9/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]

[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
> 
> 
> proc.time()
   user  system elapsed 
 417.39   15.03  432.62

Example timings

maaslin3.Rcheck/maaslin3-Ex.timings

nameusersystemelapsed
maaslin325.14 1.4229.42
maaslin_check_arguments0.180.000.25
maaslin_check_formula0.350.000.36
maaslin_compute_formula0.260.010.29
maaslin_contrast_test27.52 1.9729.50
maaslin_filter1.590.031.64
maaslin_fit20.02 1.1321.11
maaslin_log_arguments0.260.020.28
maaslin_normalize0.900.030.92
maaslin_plot_results48.68 2.7352.44
maaslin_plot_results_from_output45.57 2.2747.84
maaslin_process_metadata1.430.071.53
maaslin_read_data0.320.020.33
maaslin_reorder_data0.260.000.26
maaslin_transform2.000.062.07
maaslin_write_results21.34 1.7723.14
maaslin_write_results_lefse_format21.75 2.1523.94
preprocess_dna_mtx0.020.000.01
preprocess_taxa_mtx000