William Nickols
| Snapshot Date: 2026-01-22 13:45 -0500 (Thu, 22 Jan 2026) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: RELEASE_3_22 |
| git_last_commit: 9669f95 |
| git_last_commit_date: 2025-10-29 11:33:46 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-01-26 11:58 -0500 (Mon, 26 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4886 |
| 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 1170/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maaslin3 1.2.0 (landing page) William Nickols
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
|
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. |
| Package: maaslin3 |
| Version: 1.2.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings maaslin3_1.2.0.tar.gz |
| StartedAt: 2026-01-23 01:04:36 -0500 (Fri, 23 Jan 2026) |
| EndedAt: 2026-01-23 01:26:27 -0500 (Fri, 23 Jan 2026) |
| EllapsedTime: 1310.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maaslin3.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings maaslin3_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/maaslin3.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘1.2.0’
* 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 43.315 0.420 43.740
maaslin_plot_results 43.128 0.377 43.479
maaslin3 21.006 1.738 22.745
maaslin_contrast_test 18.989 0.722 19.713
maaslin_write_results_lefse_format 16.391 0.141 16.533
maaslin_write_results 13.746 0.137 13.883
maaslin_fit 12.686 0.125 12.812
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
maaslin3.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL maaslin3 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘maaslin3’ ... ** this is package ‘maaslin3’ version ‘1.2.0’ ** 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)
maaslin3.Rcheck/tests/testthat.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(maaslin3)
>
> test_check("maaslin3")
2026-01-23 01:10:55.332529 WARNING::Fitting problem for feature 50 returning NA
2026-01-23 01:10:55.408626 WARNING::Fitting problem for feature 62 returning NA
2026-01-23 01:10:55.501322 WARNING::Fitting problem for feature 74 returning NA
2026-01-23 01:10:55.52815 WARNING::Fitting problem for feature 78 returning NA
2026-01-23 01:10:55.585572 WARNING::Fitting problem for feature 84 returning NA
2026-01-23 01:10:55.661933 WARNING::Fitting problem for feature 96 returning NA
2026-01-23 01:10:55.66721 WARNING::Fitting problem for feature 97 returning NA
2026-01-23 01:10:55.678893 WARNING::Fitting problem for feature 99 returning NA
2026-01-23 01:10:55.792611 WARNING::Fitting problem for feature 114 returning NA
2026-01-23 01:10:55.797965 WARNING::Fitting problem for feature 115 returning NA
2026-01-23 01:10:55.846754 WARNING::Fitting problem for feature 123 returning NA
2026-01-23 01:10:55.88561 WARNING::Fitting problem for feature 130 returning NA
2026-01-23 01:10:55.89705 WARNING::Fitting problem for feature 132 returning NA
2026-01-23 01:10:55.936647 WARNING::Fitting problem for feature 139 returning NA
2026-01-23 01:10:56.012107 WARNING::Fitting problem for feature 150 returning NA
2026-01-23 01:11:11.756997 WARNING::Fitting problem for feature 50 returning NA
2026-01-23 01:11:11.830504 WARNING::Fitting problem for feature 62 returning NA
2026-01-23 01:11:11.902634 WARNING::Fitting problem for feature 74 returning NA
2026-01-23 01:11:11.923336 WARNING::Fitting problem for feature 78 returning NA
2026-01-23 01:11:11.955955 WARNING::Fitting problem for feature 84 returning NA
2026-01-23 01:11:12.029871 WARNING::Fitting problem for feature 96 returning NA
2026-01-23 01:11:12.035041 WARNING::Fitting problem for feature 97 returning NA
2026-01-23 01:11:12.046402 WARNING::Fitting problem for feature 99 returning NA
2026-01-23 01:11:12.153826 WARNING::Fitting problem for feature 114 returning NA
2026-01-23 01:11:12.159074 WARNING::Fitting problem for feature 115 returning NA
2026-01-23 01:11:12.207363 WARNING::Fitting problem for feature 123 returning NA
2026-01-23 01:11:12.246873 WARNING::Fitting problem for feature 130 returning NA
2026-01-23 01:11:12.25864 WARNING::Fitting problem for feature 132 returning NA
2026-01-23 01:11:12.29828 WARNING::Fitting problem for feature 139 returning NA
2026-01-23 01:11:12.365585 WARNING::Fitting problem for feature 150 returning NA
2026-01-23 01:11:36.852101 WARNING::Fitting problem for feature 50 returning NA
2026-01-23 01:11:36.928319 WARNING::Fitting problem for feature 62 returning NA
2026-01-23 01:11:37.002794 WARNING::Fitting problem for feature 74 returning NA
2026-01-23 01:11:37.02485 WARNING::Fitting problem for feature 78 returning NA
2026-01-23 01:11:37.059208 WARNING::Fitting problem for feature 84 returning NA
2026-01-23 01:11:37.135944 WARNING::Fitting problem for feature 96 returning NA
2026-01-23 01:11:37.14166 WARNING::Fitting problem for feature 97 returning NA
2026-01-23 01:11:37.154137 WARNING::Fitting problem for feature 99 returning NA
2026-01-23 01:11:37.25074 WARNING::Fitting problem for feature 114 returning NA
2026-01-23 01:11:37.256213 WARNING::Fitting problem for feature 115 returning NA
2026-01-23 01:11:37.307338 WARNING::Fitting problem for feature 123 returning NA
2026-01-23 01:11:37.348489 WARNING::Fitting problem for feature 130 returning NA
2026-01-23 01:11:37.360418 WARNING::Fitting problem for feature 132 returning NA
2026-01-23 01:11:37.403038 WARNING::Fitting problem for feature 139 returning NA
2026-01-23 01:11:37.476361 WARNING::Fitting problem for feature 150 returning NA
2026-01-23 01:11:50.139347 WARNING::Fitting problem for feature 50 returning NA
2026-01-23 01:11:50.231144 WARNING::Fitting problem for feature 62 returning NA
2026-01-23 01:11:50.3121 WARNING::Fitting problem for feature 74 returning NA
2026-01-23 01:11:50.335541 WARNING::Fitting problem for feature 78 returning NA
2026-01-23 01:11:50.372742 WARNING::Fitting problem for feature 84 returning NA
2026-01-23 01:11:50.450264 WARNING::Fitting problem for feature 96 returning NA
2026-01-23 01:11:50.455751 WARNING::Fitting problem for feature 97 returning NA
2026-01-23 01:11:50.467979 WARNING::Fitting problem for feature 99 returning NA
2026-01-23 01:11:50.5656 WARNING::Fitting problem for feature 114 returning NA
2026-01-23 01:11:50.571106 WARNING::Fitting problem for feature 115 returning NA
2026-01-23 01:11:50.622118 WARNING::Fitting problem for feature 123 returning NA
2026-01-23 01:11:50.662814 WARNING::Fitting problem for feature 130 returning NA
2026-01-23 01:11:50.674933 WARNING::Fitting problem for feature 132 returning NA
2026-01-23 01:11:50.715855 WARNING::Fitting problem for feature 139 returning NA
2026-01-23 01:11:50.785921 WARNING::Fitting problem for feature 150 returning NA
2026-01-23 01:11:50.997159 WARNING::Deleting existing residuals file: /tmp/RtmpLH6Orv/file20474778a3dc2e/fits/residuals_linear.rds
2026-01-23 01:11:51.058733 WARNING::Deleting existing fitted file: /tmp/RtmpLH6Orv/file20474778a3dc2e/fits/fitted_linear.rds
2026-01-23 01:11:51.121763 WARNING::Deleting existing residuals file: /tmp/RtmpLH6Orv/file20474778a3dc2e/fits/residuals_logistic.rds
2026-01-23 01:11:51.421472 WARNING::Deleting existing fitted file: /tmp/RtmpLH6Orv/file20474778a3dc2e/fits/fitted_logistic.rds
2026-01-23 01:12:13.142356 WARNING::Fitting problem for feature 50 returning NA
2026-01-23 01:12:13.217726 WARNING::Fitting problem for feature 62 returning NA
2026-01-23 01:12:13.292032 WARNING::Fitting problem for feature 74 returning NA
2026-01-23 01:12:13.313888 WARNING::Fitting problem for feature 78 returning NA
2026-01-23 01:12:13.348852 WARNING::Fitting problem for feature 84 returning NA
2026-01-23 01:12:13.428692 WARNING::Fitting problem for feature 96 returning NA
2026-01-23 01:12:13.43442 WARNING::Fitting problem for feature 97 returning NA
2026-01-23 01:12:13.446938 WARNING::Fitting problem for feature 99 returning NA
2026-01-23 01:12:13.546252 WARNING::Fitting problem for feature 114 returning NA
2026-01-23 01:12:13.551903 WARNING::Fitting problem for feature 115 returning NA
2026-01-23 01:12:13.60211 WARNING::Fitting problem for feature 123 returning NA
2026-01-23 01:12:13.645855 WARNING::Fitting problem for feature 130 returning NA
2026-01-23 01:12:13.658812 WARNING::Fitting problem for feature 132 returning NA
2026-01-23 01:12:13.701696 WARNING::Fitting problem for feature 139 returning NA
2026-01-23 01:12:13.873121 WARNING::Fitting problem for feature 150 returning NA
2026-01-23 01:12:26.698859 WARNING::Fitting problem for feature 50 returning NA
2026-01-23 01:12:26.774405 WARNING::Fitting problem for feature 62 returning NA
2026-01-23 01:12:26.847329 WARNING::Fitting problem for feature 74 returning NA
2026-01-23 01:12:26.868643 WARNING::Fitting problem for feature 78 returning NA
2026-01-23 01:12:26.902136 WARNING::Fitting problem for feature 84 returning NA
2026-01-23 01:12:26.976715 WARNING::Fitting problem for feature 96 returning NA
2026-01-23 01:12:26.981987 WARNING::Fitting problem for feature 97 returning NA
2026-01-23 01:12:27.0195 WARNING::Fitting problem for feature 99 returning NA
2026-01-23 01:12:27.118191 WARNING::Fitting problem for feature 114 returning NA
2026-01-23 01:12:27.12375 WARNING::Fitting problem for feature 115 returning NA
2026-01-23 01:12:27.173911 WARNING::Fitting problem for feature 123 returning NA
2026-01-23 01:12:27.213441 WARNING::Fitting problem for feature 130 returning NA
2026-01-23 01:12:27.225063 WARNING::Fitting problem for feature 132 returning NA
2026-01-23 01:12:27.264315 WARNING::Fitting problem for feature 139 returning NA
2026-01-23 01:12:27.330966 WARNING::Fitting problem for feature 150 returning NA
2026-01-23 01:12:27.520274 WARNING::Deleting existing residuals file: /tmp/RtmpLH6Orv/file20474778a3dc2e/fits/residuals_linear.rds
2026-01-23 01:12:27.581922 WARNING::Deleting existing fitted file: /tmp/RtmpLH6Orv/file20474778a3dc2e/fits/fitted_linear.rds
2026-01-23 01:12:27.644578 WARNING::Deleting existing residuals file: /tmp/RtmpLH6Orv/file20474778a3dc2e/fits/residuals_logistic.rds
2026-01-23 01:12:27.951828 WARNING::Deleting existing fitted file: /tmp/RtmpLH6Orv/file20474778a3dc2e/fits/fitted_logistic.rds
2026-01-23 01:12:49.714683 WARNING::Fitting problem for feature 50 returning NA
2026-01-23 01:12:49.79934 WARNING::Fitting problem for feature 62 returning NA
2026-01-23 01:12:49.88189 WARNING::Fitting problem for feature 74 returning NA
2026-01-23 01:12:49.939179 WARNING::Fitting problem for feature 78 returning NA
2026-01-23 01:12:49.977535 WARNING::Fitting problem for feature 84 returning NA
2026-01-23 01:12:50.057747 WARNING::Fitting problem for feature 96 returning NA
2026-01-23 01:12:50.063364 WARNING::Fitting problem for feature 97 returning NA
2026-01-23 01:12:50.075541 WARNING::Fitting problem for feature 99 returning NA
2026-01-23 01:12:50.172652 WARNING::Fitting problem for feature 114 returning NA
2026-01-23 01:12:50.178267 WARNING::Fitting problem for feature 115 returning NA
2026-01-23 01:12:50.228604 WARNING::Fitting problem for feature 123 returning NA
2026-01-23 01:12:50.269277 WARNING::Fitting problem for feature 130 returning NA
2026-01-23 01:12:50.281214 WARNING::Fitting problem for feature 132 returning NA
2026-01-23 01:12:50.322285 WARNING::Fitting problem for feature 139 returning NA
2026-01-23 01:12:50.39191 WARNING::Fitting problem for feature 150 returning NA
2026-01-23 01:13:02.86095 WARNING::Fitting problem for feature 50 returning NA
2026-01-23 01:13:02.944659 WARNING::Fitting problem for feature 62 returning NA
2026-01-23 01:13:03.022317 WARNING::Fitting problem for feature 74 returning NA
2026-01-23 01:13:03.044017 WARNING::Fitting problem for feature 78 returning NA
2026-01-23 01:13:03.080458 WARNING::Fitting problem for feature 84 returning NA
2026-01-23 01:13:03.159187 WARNING::Fitting problem for feature 96 returning NA
2026-01-23 01:13:03.16488 WARNING::Fitting problem for feature 97 returning NA
2026-01-23 01:13:03.176578 WARNING::Fitting problem for feature 99 returning NA
2026-01-23 01:13:03.27349 WARNING::Fitting problem for feature 114 returning NA
2026-01-23 01:13:03.278891 WARNING::Fitting problem for feature 115 returning NA
2026-01-23 01:13:03.329441 WARNING::Fitting problem for feature 123 returning NA
2026-01-23 01:13:03.370124 WARNING::Fitting problem for feature 130 returning NA
2026-01-23 01:13:03.382092 WARNING::Fitting problem for feature 132 returning NA
2026-01-23 01:13:03.456413 WARNING::Fitting problem for feature 139 returning NA
2026-01-23 01:13:03.526373 WARNING::Fitting problem for feature 150 returning NA
2026-01-23 01:13:03.721769 WARNING::Deleting existing residuals file: /tmp/RtmpLH6Orv/file20474778a3dc2e/fits/residuals_linear.rds
2026-01-23 01:13:03.783551 WARNING::Deleting existing fitted file: /tmp/RtmpLH6Orv/file20474778a3dc2e/fits/fitted_linear.rds
2026-01-23 01:13:03.846402 WARNING::Deleting existing residuals file: /tmp/RtmpLH6Orv/file20474778a3dc2e/fits/residuals_logistic.rds
2026-01-23 01:13:04.144866 WARNING::Deleting existing fitted file: /tmp/RtmpLH6Orv/file20474778a3dc2e/fits/fitted_logistic.rds
2026-01-23 01:13:25.803791 WARNING::Fitting problem for feature 50 returning NA
2026-01-23 01:13:25.883479 WARNING::Fitting problem for feature 62 returning NA
2026-01-23 01:13:25.963921 WARNING::Fitting problem for feature 74 returning NA
2026-01-23 01:13:25.987461 WARNING::Fitting problem for feature 78 returning NA
2026-01-23 01:13:26.025878 WARNING::Fitting problem for feature 84 returning NA
2026-01-23 01:13:26.110441 WARNING::Fitting problem for feature 96 returning NA
2026-01-23 01:13:26.116862 WARNING::Fitting problem for feature 97 returning NA
2026-01-23 01:13:26.130906 WARNING::Fitting problem for feature 99 returning NA
2026-01-23 01:13:26.26978 WARNING::Fitting problem for feature 114 returning NA
2026-01-23 01:13:26.275894 WARNING::Fitting problem for feature 115 returning NA
2026-01-23 01:13:26.328212 WARNING::Fitting problem for feature 123 returning NA
2026-01-23 01:13:26.369416 WARNING::Fitting problem for feature 130 returning NA
2026-01-23 01:13:26.381736 WARNING::Fitting problem for feature 132 returning NA
2026-01-23 01:13:26.422463 WARNING::Fitting problem for feature 139 returning NA
2026-01-23 01:13:26.493673 WARNING::Fitting problem for feature 150 returning NA
2026-01-23 01:13:38.623698 WARNING::Fitting problem for feature 50 returning NA
2026-01-23 01:13:38.702622 WARNING::Fitting problem for feature 62 returning NA
2026-01-23 01:13:38.781151 WARNING::Fitting problem for feature 74 returning NA
2026-01-23 01:13:38.803849 WARNING::Fitting problem for feature 78 returning NA
2026-01-23 01:13:38.838972 WARNING::Fitting problem for feature 84 returning NA
2026-01-23 01:13:38.922233 WARNING::Fitting problem for feature 96 returning NA
2026-01-23 01:13:38.927666 WARNING::Fitting problem for feature 97 returning NA
2026-01-23 01:13:38.939545 WARNING::Fitting problem for feature 99 returning NA
2026-01-23 01:13:39.036588 WARNING::Fitting problem for feature 114 returning NA
2026-01-23 01:13:39.042182 WARNING::Fitting problem for feature 115 returning NA
2026-01-23 01:13:39.093356 WARNING::Fitting problem for feature 123 returning NA
2026-01-23 01:13:39.133889 WARNING::Fitting problem for feature 130 returning NA
2026-01-23 01:13:39.145639 WARNING::Fitting problem for feature 132 returning NA
2026-01-23 01:13:39.185911 WARNING::Fitting problem for feature 139 returning NA
2026-01-23 01:13:39.256964 WARNING::Fitting problem for feature 150 returning NA
2026-01-23 01:14:03.696801 WARNING::Fitting problem for feature 124 returning NA
2026-01-23 01:14:13.533655 WARNING::Fitting problem for feature 124 returning NA
2026-01-23 01:14:38.281755 WARNING::Fitting problem for feature 124 returning NA
2026-01-23 01:14:48.368465 WARNING::Fitting problem for feature 124 returning NA
2026-01-23 01:14:48.975162 WARNING::Deleting existing residuals file: /tmp/RtmpLH6Orv/file2047473dee01de/fits/residuals_linear.rds
2026-01-23 01:14:49.03657 WARNING::Deleting existing fitted file: /tmp/RtmpLH6Orv/file2047473dee01de/fits/fitted_linear.rds
2026-01-23 01:14:49.074932 WARNING::Deleting existing residuals file: /tmp/RtmpLH6Orv/file2047473dee01de/fits/residuals_logistic.rds
2026-01-23 01:14:49.143581 WARNING::Deleting existing fitted file: /tmp/RtmpLH6Orv/file2047473dee01de/fits/fitted_logistic.rds
2026-01-23 01:15:11.960857 WARNING::Fitting problem for feature 124 returning NA
2026-01-23 01:15:18.530469 WARNING::Fitting problem for feature 124 returning NA
2026-01-23 01:15:18.845008 WARNING::Deleting existing residuals file: /tmp/RtmpLH6Orv/file2047473dee01de/fits/residuals_linear.rds
2026-01-23 01:15:18.907587 WARNING::Deleting existing fitted file: /tmp/RtmpLH6Orv/file2047473dee01de/fits/fitted_linear.rds
2026-01-23 01:15:18.946056 WARNING::Deleting existing residuals file: /tmp/RtmpLH6Orv/file2047473dee01de/fits/residuals_logistic.rds
2026-01-23 01:15:19.015022 WARNING::Deleting existing fitted file: /tmp/RtmpLH6Orv/file2047473dee01de/fits/fitted_logistic.rds
2026-01-23 01:15:37.575526 WARNING::Fitting problem for feature 124 returning NA
2026-01-23 01:15:43.998335 WARNING::Fitting problem for feature 124 returning NA
2026-01-23 01:15:44.302548 WARNING::Deleting existing residuals file: /tmp/RtmpLH6Orv/file2047473dee01de/fits/residuals_linear.rds
2026-01-23 01:15:44.364899 WARNING::Deleting existing fitted file: /tmp/RtmpLH6Orv/file2047473dee01de/fits/fitted_linear.rds
2026-01-23 01:15:44.403873 WARNING::Deleting existing residuals file: /tmp/RtmpLH6Orv/file2047473dee01de/fits/residuals_logistic.rds
2026-01-23 01:15:44.475049 WARNING::Deleting existing fitted file: /tmp/RtmpLH6Orv/file2047473dee01de/fits/fitted_logistic.rds
2026-01-23 01:16:02.844483 WARNING::Fitting problem for feature 50 returning NA
2026-01-23 01:16:02.926291 WARNING::Fitting problem for feature 62 returning NA
2026-01-23 01:16:03.009744 WARNING::Fitting problem for feature 74 returning NA
2026-01-23 01:16:03.032699 WARNING::Fitting problem for feature 78 returning NA
2026-01-23 01:16:03.092971 WARNING::Fitting problem for feature 84 returning NA
2026-01-23 01:16:03.170801 WARNING::Fitting problem for feature 96 returning NA
2026-01-23 01:16:03.17624 WARNING::Fitting problem for feature 97 returning NA
2026-01-23 01:16:03.188319 WARNING::Fitting problem for feature 99 returning NA
2026-01-23 01:16:03.285869 WARNING::Fitting problem for feature 114 returning NA
2026-01-23 01:16:03.291456 WARNING::Fitting problem for feature 115 returning NA
2026-01-23 01:16:03.342065 WARNING::Fitting problem for feature 123 returning NA
2026-01-23 01:16:03.382591 WARNING::Fitting problem for feature 130 returning NA
2026-01-23 01:16:03.394602 WARNING::Fitting problem for feature 132 returning NA
2026-01-23 01:16:03.43632 WARNING::Fitting problem for feature 139 returning NA
2026-01-23 01:16:03.506369 WARNING::Fitting problem for feature 150 returning NA
2026-01-23 01:16:15.683854 WARNING::Fitting problem for feature 50 returning NA
2026-01-23 01:16:15.760027 WARNING::Fitting problem for feature 62 returning NA
2026-01-23 01:16:15.835346 WARNING::Fitting problem for feature 74 returning NA
2026-01-23 01:16:15.857708 WARNING::Fitting problem for feature 78 returning NA
2026-01-23 01:16:15.893589 WARNING::Fitting problem for feature 84 returning NA
2026-01-23 01:16:15.971648 WARNING::Fitting problem for feature 96 returning NA
2026-01-23 01:16:15.977018 WARNING::Fitting problem for feature 97 returning NA
2026-01-23 01:16:15.988913 WARNING::Fitting problem for feature 99 returning NA
2026-01-23 01:16:16.084785 WARNING::Fitting problem for feature 114 returning NA
2026-01-23 01:16:16.090241 WARNING::Fitting problem for feature 115 returning NA
2026-01-23 01:16:16.140365 WARNING::Fitting problem for feature 123 returning NA
2026-01-23 01:16:16.182019 WARNING::Fitting problem for feature 130 returning NA
2026-01-23 01:16:16.194394 WARNING::Fitting problem for feature 132 returning NA
2026-01-23 01:16:16.236231 WARNING::Fitting problem for feature 139 returning NA
2026-01-23 01:16:16.309648 WARNING::Fitting problem for feature 150 returning NA
2026-01-23 01:16:16.572389 WARNING::Deleting existing residuals file: /tmp/RtmpLH6Orv/file2047473dee01de/fits/residuals_linear.rds
2026-01-23 01:16:16.633662 WARNING::Deleting existing fitted file: /tmp/RtmpLH6Orv/file2047473dee01de/fits/fitted_linear.rds
2026-01-23 01:16:16.696493 WARNING::Deleting existing residuals file: /tmp/RtmpLH6Orv/file2047473dee01de/fits/residuals_logistic.rds
2026-01-23 01:16:16.994725 WARNING::Deleting existing fitted file: /tmp/RtmpLH6Orv/file2047473dee01de/fits/fitted_logistic.rds
2026-01-23 01:16:37.507389 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2026-01-23 01:16:37.525466 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2026-01-23 01:16:37.538306 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2026-01-23 01:16:37.590878 ERROR::No fixed, group, or
ordered effects included in formula.
2026-01-23 01:16:37.60723 ERROR::Effect name not found in metadata: d
2026-01-23 01:16:37.618197 ERROR::No user formula provided
2026-01-23 01:16:37.64879 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2026-01-23 01:16:37.660198 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2026-01-23 01:16:40.495755 INFO::Writing function arguments to log file
2026-01-23 01:16:40.509781 INFO::Verifying options selected are valid
2026-01-23 01:16:42.833602 INFO::Writing function arguments to log file
2026-01-23 01:16:42.845375 INFO::Verifying options selected are valid
2026-01-23 01:16:42.846451 INFO::Determining format of input files
2026-01-23 01:16:42.847424 INFO::Input format is data samples as rows and metadata samples as rows
2026-01-23 01:16:42.849702 INFO::Running selected normalization method: TSS
2026-01-23 01:16:42.851117 INFO::Creating output feature tables folder
2026-01-23 01:16:42.852054 INFO::Writing normalized data to file /tmp/RtmpLH6Orv/file2047473a8e2926/features/data_norm.tsv
2026-01-23 01:16:42.853493 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2026-01-23 01:16:42.854368 INFO::Total samples in data: 16
2026-01-23 01:16:42.855215 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2026-01-23 01:16:42.856054 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2026-01-23 01:16:42.857963 INFO::Total filtered features: 0
2026-01-23 01:16:42.858913 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2026-01-23 01:16:42.860038 INFO::Total features filtered by non-zero variance filtering: 0
2026-01-23 01:16:42.860963 INFO::Filtered feature names from variance filtering:
2026-01-23 01:16:42.861831 INFO::Writing filtered data to file /tmp/RtmpLH6Orv/file2047473a8e2926/features/filtered_data.tsv
2026-01-23 01:16:42.863291 INFO::Running selected transform method: LOG
2026-01-23 01:16:42.864462 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpLH6Orv/file2047473a8e2926/features/data_transformed.tsv
2026-01-23 01:16:42.866099 INFO::Applying z-score to standardize continuous metadata
2026-01-23 01:16:42.870624 INFO::Running the linear model component
2026-01-23 01:16:42.884045 INFO::Fitting model to feature number 1, a
2026-01-23 01:16:42.888645 INFO::Fitting model to feature number 2, b
2026-01-23 01:16:42.893033 INFO::Fitting model to feature number 3, c
2026-01-23 01:16:42.900442 INFO::Counting total values for each feature
2026-01-23 01:16:42.90231 INFO::Running the logistic model component
2026-01-23 01:16:42.915877 INFO::Fitting model to feature number 1, a
2026-01-23 01:16:42.922417 INFO::Fitting model to feature number 2, b
2026-01-23 01:16:42.928632 INFO::Fitting model to feature number 3, c
2026-01-23 01:16:42.937793 INFO::Counting total values for each feature
2026-01-23 01:16:42.940071 INFO::Re-running abundances for warn_prevalence
2026-01-23 01:16:42.941067 INFO::Running selected normalization method: TSS
2026-01-23 01:16:42.942609 INFO::Running selected transform method: LOG
2026-01-23 01:16:42.956311 INFO::Fitting model to feature number 1, a
2026-01-23 01:16:42.960837 INFO::Fitting model to feature number 2, b
2026-01-23 01:16:42.965091 INFO::Fitting model to feature number 3, c
2026-01-23 01:16:43.054784 INFO::Creating fits folder
2026-01-23 01:16:43.055925 INFO::Writing residuals to file /tmp/RtmpLH6Orv/file2047473a8e2926/fits/residuals_linear.rds
2026-01-23 01:16:43.057055 INFO::Writing fitted values to file /tmp/RtmpLH6Orv/file2047473a8e2926/fits/fitted_linear.rds
2026-01-23 01:16:43.058259 INFO::Writing residuals to file /tmp/RtmpLH6Orv/file2047473a8e2926/fits/residuals_logistic.rds
2026-01-23 01:16:43.059446 INFO::Writing fitted values to file /tmp/RtmpLH6Orv/file2047473a8e2926/fits/fitted_logistic.rds
2026-01-23 01:16:43.062105 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpLH6Orv/file2047473a8e2926/all_results.tsv
2026-01-23 01:16:43.063697 INFO::Writing the significant results without errors (those which have joint q-values less than or equal to the threshold of 0.100000 ) to file (ordered by increasing individual q-values): /tmp/RtmpLH6Orv/file2047473a8e2926/significant_results.tsv
2026-01-23 01:16:43.064979 INFO::Creating output figures folder
2026-01-23 01:16:43.066303 INFO::Writing summary plot of significant
results to file: /tmp/RtmpLH6Orv/file2047473a8e2926/figures/summary_plot.pdf
2026-01-23 01:16:44.691422 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpLH6Orv/file2047473a8e2926/figures
2026-01-23 01:16:44.693501 INFO::Plotting associations from most to least significant, grouped by metadata
2026-01-23 01:16:44.698801 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-01-23 01:16:45.228104 INFO::Writing summary plot of
significant results to file: /tmp/RtmpLH6Orv/file2047473a8e2926/figures/summary_plot.pdf
2026-01-23 01:16:46.861868 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpLH6Orv/file2047473a8e2926/figures
2026-01-23 01:16:46.863377 INFO::Plotting associations from most to least significant, grouped by metadata
2026-01-23 01:16:46.86817 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-01-23 01:16:47.384351 INFO::Running the linear model component
2026-01-23 01:16:47.393186 INFO::Fitting model to feature number 1, a
2026-01-23 01:16:47.397493 INFO::Fitting model to feature number 2, b
2026-01-23 01:16:47.401516 INFO::Fitting model to feature number 3, c
2026-01-23 01:16:47.408553 INFO::Counting total values for each feature
2026-01-23 01:16:47.410239 INFO::Running the logistic model component
2026-01-23 01:16:47.418773 INFO::Fitting model to feature number 1, a
2026-01-23 01:16:47.425221 INFO::Fitting model to feature number 2, b
2026-01-23 01:16:47.431285 INFO::Fitting model to feature number 3, c
2026-01-23 01:16:47.440241 INFO::Counting total values for each feature
2026-01-23 01:16:47.442313 INFO::Re-running abundances for warn_prevalence
2026-01-23 01:16:47.443128 INFO::Running selected normalization method: TSS
2026-01-23 01:16:47.444458 INFO::Running selected transform method: LOG
2026-01-23 01:16:47.453031 INFO::Fitting model to feature number 1, a
2026-01-23 01:16:47.457136 INFO::Fitting model to feature number 2, b
2026-01-23 01:16:47.461082 INFO::Fitting model to feature number 3, c
2026-01-23 01:16:47.538309 INFO::Creating output folder
2026-01-23 01:16:47.539293 INFO::Creating output figures folder
2026-01-23 01:16:47.540539 INFO::Writing summary plot of significant
results to file: /tmp/RtmpLH6Orv/file20474720b037ad/figures/summary_plot.pdf
2026-01-23 01:16:49.21509 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpLH6Orv/file20474720b037ad/figures
2026-01-23 01:16:49.217031 INFO::Plotting associations from most to least significant, grouped by metadata
2026-01-23 01:16:49.222483 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-01-23 01:16:50.228522 INFO::Applying z-score to standardize continuous metadata
2026-01-23 01:16:50.236056 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2026-01-23 01:16:50.237015 INFO::Bypass z-score application to metadata
2026-01-23 01:16:50.239847 INFO::Bypass z-score application to metadata
2026-01-23 01:16:50.259498 INFO::Determining format of input files
2026-01-23 01:16:50.260487 INFO::Input format is data samples as rows and metadata samples as rows
2026-01-23 01:16:50.261365 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2026-01-23 01:16:50.269193 INFO::Determining format of input files
2026-01-23 01:16:50.270255 INFO::Input format is data samples as columns and metadata samples as rows
2026-01-23 01:16:50.271575 INFO::Input format is feature_specific_covariate samples as columns
2026-01-23 01:16:50.280178 INFO::Determining format of input files
2026-01-23 01:16:50.281136 INFO::Input format is data samples as rows and metadata samples as rows
2026-01-23 01:16:50.2822 INFO::Input format is feature_specific_covariate samples as columns
2026-01-23 01:16:50.283949 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2026-01-23 01:16:50.284773 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2026-01-23 01:16:50.297127 INFO::Running selected transform method: LOG
2026-01-23 01:16:50.298324 INFO::Creating output feature tables folder
2026-01-23 01:16:50.299215 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpLH6Orv/file20474779725744/features/data_transformed.tsv
2026-01-23 01:16:50.303295 INFO::Running selected transform method: LOG
2026-01-23 01:16:50.304388 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpLH6Orv/file20474779725744/features/data_transformed.tsv
2026-01-23 01:16:50.308599 INFO::Running selected transform method: PLOG
2026-01-23 01:16:50.310211 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpLH6Orv/file20474779725744/features/data_transformed.tsv
2026-01-23 01:16:50.313255 INFO::Running selected transform method: NONE
2026-01-23 01:16:50.314006 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpLH6Orv/file20474779725744/features/data_transformed.tsv
2026-01-23 01:16:50.321877 INFO::Running the linear model component
2026-01-23 01:16:50.331 INFO::Fitting model to feature number 1, a
2026-01-23 01:16:50.335413 INFO::Fitting model to feature number 2, b
2026-01-23 01:16:50.339587 INFO::Fitting model to feature number 3, c
2026-01-23 01:16:50.346905 INFO::Counting total values for each feature
2026-01-23 01:16:50.348647 INFO::Running the logistic model component
2026-01-23 01:16:50.35745 INFO::Fitting model to feature number 1, a
2026-01-23 01:16:50.364153 INFO::Fitting model to feature number 2, b
2026-01-23 01:16:50.37067 INFO::Fitting model to feature number 3, c
2026-01-23 01:16:50.380186 INFO::Counting total values for each feature
2026-01-23 01:16:50.382385 INFO::Re-running abundances for warn_prevalence
2026-01-23 01:16:50.383246 INFO::Running selected normalization method: TSS
2026-01-23 01:16:50.384699 INFO::Running selected transform method: LOG
2026-01-23 01:16:50.393887 INFO::Fitting model to feature number 1, a
2026-01-23 01:16:50.398669 INFO::Fitting model to feature number 2, b
2026-01-23 01:16:50.403027 INFO::Fitting model to feature number 3, c
2026-01-23 01:16:50.487421 INFO::Creating output folder
2026-01-23 01:16:50.488478 INFO::Creating fits folder
2026-01-23 01:16:50.489398 INFO::Writing residuals to file /tmp/RtmpLH6Orv/file204747fec5497/fits/residuals_linear.rds
2026-01-23 01:16:50.49041 INFO::Writing fitted values to file /tmp/RtmpLH6Orv/file204747fec5497/fits/fitted_linear.rds
2026-01-23 01:16:50.491638 INFO::Writing residuals to file /tmp/RtmpLH6Orv/file204747fec5497/fits/residuals_logistic.rds
2026-01-23 01:16:50.492764 INFO::Writing fitted values to file /tmp/RtmpLH6Orv/file204747fec5497/fits/fitted_logistic.rds
2026-01-23 01:16:50.495621 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpLH6Orv/file204747fec5497/all_results.tsv
2026-01-23 01:16:50.497237 INFO::Writing the significant results without errors (those which have joint q-values less than or equal to the threshold of 0.100000 ) to file (ordered by increasing individual q-values): /tmp/RtmpLH6Orv/file204747fec5497/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
360.920 5.466 366.371
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 21.006 | 1.738 | 22.745 | |
| maaslin_check_arguments | 0.138 | 0.004 | 0.141 | |
| maaslin_check_formula | 0.161 | 0.006 | 0.168 | |
| maaslin_compute_formula | 0.153 | 0.002 | 0.154 | |
| maaslin_contrast_test | 18.989 | 0.722 | 19.713 | |
| maaslin_filter | 0.437 | 0.040 | 0.477 | |
| maaslin_fit | 12.686 | 0.125 | 12.812 | |
| maaslin_log_arguments | 0.129 | 0.001 | 0.129 | |
| maaslin_normalize | 0.260 | 0.002 | 0.262 | |
| maaslin_plot_results | 43.128 | 0.377 | 43.479 | |
| maaslin_plot_results_from_output | 43.315 | 0.420 | 43.740 | |
| maaslin_process_metadata | 0.459 | 0.014 | 0.473 | |
| maaslin_read_data | 0.130 | 0.006 | 0.136 | |
| maaslin_reorder_data | 0.143 | 0.001 | 0.144 | |
| maaslin_transform | 0.554 | 0.012 | 0.566 | |
| maaslin_write_results | 13.746 | 0.137 | 13.883 | |
| maaslin_write_results_lefse_format | 16.391 | 0.141 | 16.533 | |
| preprocess_dna_mtx | 0.003 | 0.000 | 0.004 | |
| preprocess_taxa_mtx | 0.004 | 0.000 | 0.004 | |