William Nickols
| Snapshot Date: 2026-02-12 13:45 -0500 (Thu, 12 Feb 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 2026-02-16 11:57 -0500 (Mon, 16 Feb 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" | 4889 |
| 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 | | ||||||||
| See other builds for maaslin3 in R Universe. | ||||||||||||||
|
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: 2026-02-13 01:44:52 -0500 (Fri, 13 Feb 2026) |
| EndedAt: 2026-02-13 02:06:28 -0500 (Fri, 13 Feb 2026) |
| EllapsedTime: 1295.4 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 44.370 0.387 44.762
maaslin_plot_results 43.069 0.276 43.318
maaslin3 20.208 0.510 20.721
maaslin_contrast_test 18.707 0.343 19.050
maaslin_write_results_lefse_format 13.829 0.055 13.886
maaslin_write_results 13.543 0.179 13.723
maaslin_fit 13.218 0.095 13.313
* 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")
2026-02-13 01:51:15.385745 WARNING::Fitting problem for feature 50 returning NA
2026-02-13 01:51:15.47071 WARNING::Fitting problem for feature 62 returning NA
2026-02-13 01:51:15.564049 WARNING::Fitting problem for feature 74 returning NA
2026-02-13 01:51:15.585346 WARNING::Fitting problem for feature 78 returning NA
2026-02-13 01:51:15.619704 WARNING::Fitting problem for feature 84 returning NA
2026-02-13 01:51:15.695194 WARNING::Fitting problem for feature 96 returning NA
2026-02-13 01:51:15.707968 WARNING::Fitting problem for feature 97 returning NA
2026-02-13 01:51:15.719609 WARNING::Fitting problem for feature 99 returning NA
2026-02-13 01:51:15.813791 WARNING::Fitting problem for feature 114 returning NA
2026-02-13 01:51:15.819389 WARNING::Fitting problem for feature 115 returning NA
2026-02-13 01:51:15.870699 WARNING::Fitting problem for feature 123 returning NA
2026-02-13 01:51:15.920063 WARNING::Fitting problem for feature 130 returning NA
2026-02-13 01:51:15.931587 WARNING::Fitting problem for feature 132 returning NA
2026-02-13 01:51:15.971164 WARNING::Fitting problem for feature 139 returning NA
2026-02-13 01:51:16.038209 WARNING::Fitting problem for feature 150 returning NA
2026-02-13 01:51:31.874177 WARNING::Fitting problem for feature 50 returning NA
2026-02-13 01:51:31.950172 WARNING::Fitting problem for feature 62 returning NA
2026-02-13 01:51:32.023453 WARNING::Fitting problem for feature 74 returning NA
2026-02-13 01:51:32.044976 WARNING::Fitting problem for feature 78 returning NA
2026-02-13 01:51:32.078408 WARNING::Fitting problem for feature 84 returning NA
2026-02-13 01:51:32.168082 WARNING::Fitting problem for feature 96 returning NA
2026-02-13 01:51:32.173575 WARNING::Fitting problem for feature 97 returning NA
2026-02-13 01:51:32.186201 WARNING::Fitting problem for feature 99 returning NA
2026-02-13 01:51:32.285631 WARNING::Fitting problem for feature 114 returning NA
2026-02-13 01:51:32.29106 WARNING::Fitting problem for feature 115 returning NA
2026-02-13 01:51:32.339456 WARNING::Fitting problem for feature 123 returning NA
2026-02-13 01:51:32.378229 WARNING::Fitting problem for feature 130 returning NA
2026-02-13 01:51:32.389772 WARNING::Fitting problem for feature 132 returning NA
2026-02-13 01:51:32.429181 WARNING::Fitting problem for feature 139 returning NA
2026-02-13 01:51:32.496355 WARNING::Fitting problem for feature 150 returning NA
2026-02-13 01:51:57.01822 WARNING::Fitting problem for feature 50 returning NA
2026-02-13 01:51:57.097959 WARNING::Fitting problem for feature 62 returning NA
2026-02-13 01:51:57.17429 WARNING::Fitting problem for feature 74 returning NA
2026-02-13 01:51:57.196486 WARNING::Fitting problem for feature 78 returning NA
2026-02-13 01:51:57.231219 WARNING::Fitting problem for feature 84 returning NA
2026-02-13 01:51:57.308475 WARNING::Fitting problem for feature 96 returning NA
2026-02-13 01:51:57.313959 WARNING::Fitting problem for feature 97 returning NA
2026-02-13 01:51:57.326019 WARNING::Fitting problem for feature 99 returning NA
2026-02-13 01:51:57.422515 WARNING::Fitting problem for feature 114 returning NA
2026-02-13 01:51:57.428077 WARNING::Fitting problem for feature 115 returning NA
2026-02-13 01:51:57.480635 WARNING::Fitting problem for feature 123 returning NA
2026-02-13 01:51:57.522008 WARNING::Fitting problem for feature 130 returning NA
2026-02-13 01:51:57.534591 WARNING::Fitting problem for feature 132 returning NA
2026-02-13 01:51:57.576526 WARNING::Fitting problem for feature 139 returning NA
2026-02-13 01:51:57.650691 WARNING::Fitting problem for feature 150 returning NA
2026-02-13 01:52:10.308119 WARNING::Fitting problem for feature 50 returning NA
2026-02-13 01:52:10.407369 WARNING::Fitting problem for feature 62 returning NA
2026-02-13 01:52:10.480737 WARNING::Fitting problem for feature 74 returning NA
2026-02-13 01:52:10.501932 WARNING::Fitting problem for feature 78 returning NA
2026-02-13 01:52:10.535644 WARNING::Fitting problem for feature 84 returning NA
2026-02-13 01:52:10.610362 WARNING::Fitting problem for feature 96 returning NA
2026-02-13 01:52:10.615758 WARNING::Fitting problem for feature 97 returning NA
2026-02-13 01:52:10.627445 WARNING::Fitting problem for feature 99 returning NA
2026-02-13 01:52:10.72057 WARNING::Fitting problem for feature 114 returning NA
2026-02-13 01:52:10.725849 WARNING::Fitting problem for feature 115 returning NA
2026-02-13 01:52:10.77388 WARNING::Fitting problem for feature 123 returning NA
2026-02-13 01:52:10.813769 WARNING::Fitting problem for feature 130 returning NA
2026-02-13 01:52:10.825714 WARNING::Fitting problem for feature 132 returning NA
2026-02-13 01:52:10.86457 WARNING::Fitting problem for feature 139 returning NA
2026-02-13 01:52:10.930484 WARNING::Fitting problem for feature 150 returning NA
2026-02-13 01:52:11.127709 WARNING::Deleting existing residuals file: /tmp/RtmpYb0fyE/file1642cdc4b8bc3/fits/residuals_linear.rds
2026-02-13 01:52:11.189363 WARNING::Deleting existing fitted file: /tmp/RtmpYb0fyE/file1642cdc4b8bc3/fits/fitted_linear.rds
2026-02-13 01:52:11.252918 WARNING::Deleting existing residuals file: /tmp/RtmpYb0fyE/file1642cdc4b8bc3/fits/residuals_logistic.rds
2026-02-13 01:52:11.554481 WARNING::Deleting existing fitted file: /tmp/RtmpYb0fyE/file1642cdc4b8bc3/fits/fitted_logistic.rds
2026-02-13 01:52:33.673692 WARNING::Fitting problem for feature 50 returning NA
2026-02-13 01:52:33.751945 WARNING::Fitting problem for feature 62 returning NA
2026-02-13 01:52:33.855703 WARNING::Fitting problem for feature 74 returning NA
2026-02-13 01:52:33.877733 WARNING::Fitting problem for feature 78 returning NA
2026-02-13 01:52:33.912338 WARNING::Fitting problem for feature 84 returning NA
2026-02-13 01:52:33.989274 WARNING::Fitting problem for feature 96 returning NA
2026-02-13 01:52:33.994684 WARNING::Fitting problem for feature 97 returning NA
2026-02-13 01:52:34.006617 WARNING::Fitting problem for feature 99 returning NA
2026-02-13 01:52:34.104186 WARNING::Fitting problem for feature 114 returning NA
2026-02-13 01:52:34.109657 WARNING::Fitting problem for feature 115 returning NA
2026-02-13 01:52:34.15968 WARNING::Fitting problem for feature 123 returning NA
2026-02-13 01:52:34.201395 WARNING::Fitting problem for feature 130 returning NA
2026-02-13 01:52:34.213466 WARNING::Fitting problem for feature 132 returning NA
2026-02-13 01:52:34.254766 WARNING::Fitting problem for feature 139 returning NA
2026-02-13 01:52:34.323338 WARNING::Fitting problem for feature 150 returning NA
2026-02-13 01:52:46.569061 WARNING::Fitting problem for feature 50 returning NA
2026-02-13 01:52:46.654583 WARNING::Fitting problem for feature 62 returning NA
2026-02-13 01:52:46.738115 WARNING::Fitting problem for feature 74 returning NA
2026-02-13 01:52:46.762624 WARNING::Fitting problem for feature 78 returning NA
2026-02-13 01:52:46.801554 WARNING::Fitting problem for feature 84 returning NA
2026-02-13 01:52:46.884134 WARNING::Fitting problem for feature 96 returning NA
2026-02-13 01:52:46.890039 WARNING::Fitting problem for feature 97 returning NA
2026-02-13 01:52:46.903597 WARNING::Fitting problem for feature 99 returning NA
2026-02-13 01:52:47.009649 WARNING::Fitting problem for feature 114 returning NA
2026-02-13 01:52:47.015723 WARNING::Fitting problem for feature 115 returning NA
2026-02-13 01:52:47.072464 WARNING::Fitting problem for feature 123 returning NA
2026-02-13 01:52:47.115475 WARNING::Fitting problem for feature 130 returning NA
2026-02-13 01:52:47.12866 WARNING::Fitting problem for feature 132 returning NA
2026-02-13 01:52:47.171994 WARNING::Fitting problem for feature 139 returning NA
2026-02-13 01:52:47.243581 WARNING::Fitting problem for feature 150 returning NA
2026-02-13 01:52:47.452342 WARNING::Deleting existing residuals file: /tmp/RtmpYb0fyE/file1642cdc4b8bc3/fits/residuals_linear.rds
2026-02-13 01:52:47.513524 WARNING::Deleting existing fitted file: /tmp/RtmpYb0fyE/file1642cdc4b8bc3/fits/fitted_linear.rds
2026-02-13 01:52:47.576624 WARNING::Deleting existing residuals file: /tmp/RtmpYb0fyE/file1642cdc4b8bc3/fits/residuals_logistic.rds
2026-02-13 01:52:47.876286 WARNING::Deleting existing fitted file: /tmp/RtmpYb0fyE/file1642cdc4b8bc3/fits/fitted_logistic.rds
2026-02-13 01:53:09.466124 WARNING::Fitting problem for feature 50 returning NA
2026-02-13 01:53:09.54845 WARNING::Fitting problem for feature 62 returning NA
2026-02-13 01:53:09.630291 WARNING::Fitting problem for feature 74 returning NA
2026-02-13 01:53:09.655949 WARNING::Fitting problem for feature 78 returning NA
2026-02-13 01:53:09.692569 WARNING::Fitting problem for feature 84 returning NA
2026-02-13 01:53:09.792156 WARNING::Fitting problem for feature 96 returning NA
2026-02-13 01:53:09.79756 WARNING::Fitting problem for feature 97 returning NA
2026-02-13 01:53:09.809413 WARNING::Fitting problem for feature 99 returning NA
2026-02-13 01:53:09.906442 WARNING::Fitting problem for feature 114 returning NA
2026-02-13 01:53:09.912121 WARNING::Fitting problem for feature 115 returning NA
2026-02-13 01:53:09.963572 WARNING::Fitting problem for feature 123 returning NA
2026-02-13 01:53:10.004391 WARNING::Fitting problem for feature 130 returning NA
2026-02-13 01:53:10.016568 WARNING::Fitting problem for feature 132 returning NA
2026-02-13 01:53:10.057768 WARNING::Fitting problem for feature 139 returning NA
2026-02-13 01:53:10.128065 WARNING::Fitting problem for feature 150 returning NA
2026-02-13 01:53:23.463585 WARNING::Fitting problem for feature 50 returning NA
2026-02-13 01:53:23.548852 WARNING::Fitting problem for feature 62 returning NA
2026-02-13 01:53:23.633832 WARNING::Fitting problem for feature 74 returning NA
2026-02-13 01:53:23.658951 WARNING::Fitting problem for feature 78 returning NA
2026-02-13 01:53:23.697939 WARNING::Fitting problem for feature 84 returning NA
2026-02-13 01:53:23.782918 WARNING::Fitting problem for feature 96 returning NA
2026-02-13 01:53:23.788913 WARNING::Fitting problem for feature 97 returning NA
2026-02-13 01:53:23.801721 WARNING::Fitting problem for feature 99 returning NA
2026-02-13 01:53:23.904054 WARNING::Fitting problem for feature 114 returning NA
2026-02-13 01:53:23.910635 WARNING::Fitting problem for feature 115 returning NA
2026-02-13 01:53:23.967426 WARNING::Fitting problem for feature 123 returning NA
2026-02-13 01:53:24.015429 WARNING::Fitting problem for feature 130 returning NA
2026-02-13 01:53:24.029274 WARNING::Fitting problem for feature 132 returning NA
2026-02-13 01:53:24.077362 WARNING::Fitting problem for feature 139 returning NA
2026-02-13 01:53:24.159156 WARNING::Fitting problem for feature 150 returning NA
2026-02-13 01:53:24.38747 WARNING::Deleting existing residuals file: /tmp/RtmpYb0fyE/file1642cdc4b8bc3/fits/residuals_linear.rds
2026-02-13 01:53:24.448683 WARNING::Deleting existing fitted file: /tmp/RtmpYb0fyE/file1642cdc4b8bc3/fits/fitted_linear.rds
2026-02-13 01:53:24.511984 WARNING::Deleting existing residuals file: /tmp/RtmpYb0fyE/file1642cdc4b8bc3/fits/residuals_logistic.rds
2026-02-13 01:53:24.812403 WARNING::Deleting existing fitted file: /tmp/RtmpYb0fyE/file1642cdc4b8bc3/fits/fitted_logistic.rds
2026-02-13 01:53:46.214247 WARNING::Fitting problem for feature 50 returning NA
2026-02-13 01:53:46.297634 WARNING::Fitting problem for feature 62 returning NA
2026-02-13 01:53:46.376672 WARNING::Fitting problem for feature 74 returning NA
2026-02-13 01:53:46.399829 WARNING::Fitting problem for feature 78 returning NA
2026-02-13 01:53:46.434853 WARNING::Fitting problem for feature 84 returning NA
2026-02-13 01:53:46.512031 WARNING::Fitting problem for feature 96 returning NA
2026-02-13 01:53:46.517915 WARNING::Fitting problem for feature 97 returning NA
2026-02-13 01:53:46.530461 WARNING::Fitting problem for feature 99 returning NA
2026-02-13 01:53:46.631781 WARNING::Fitting problem for feature 114 returning NA
2026-02-13 01:53:46.6379 WARNING::Fitting problem for feature 115 returning NA
2026-02-13 01:53:46.69112 WARNING::Fitting problem for feature 123 returning NA
2026-02-13 01:53:46.763619 WARNING::Fitting problem for feature 130 returning NA
2026-02-13 01:53:46.776719 WARNING::Fitting problem for feature 132 returning NA
2026-02-13 01:53:46.821601 WARNING::Fitting problem for feature 139 returning NA
2026-02-13 01:53:46.893105 WARNING::Fitting problem for feature 150 returning NA
2026-02-13 01:53:57.569264 WARNING::Fitting problem for feature 50 returning NA
2026-02-13 01:53:57.644649 WARNING::Fitting problem for feature 62 returning NA
2026-02-13 01:53:57.718468 WARNING::Fitting problem for feature 74 returning NA
2026-02-13 01:53:57.740324 WARNING::Fitting problem for feature 78 returning NA
2026-02-13 01:53:57.774719 WARNING::Fitting problem for feature 84 returning NA
2026-02-13 01:53:57.850559 WARNING::Fitting problem for feature 96 returning NA
2026-02-13 01:53:57.85592 WARNING::Fitting problem for feature 97 returning NA
2026-02-13 01:53:57.86752 WARNING::Fitting problem for feature 99 returning NA
2026-02-13 01:53:57.963234 WARNING::Fitting problem for feature 114 returning NA
2026-02-13 01:53:57.969043 WARNING::Fitting problem for feature 115 returning NA
2026-02-13 01:53:58.020016 WARNING::Fitting problem for feature 123 returning NA
2026-02-13 01:53:58.060982 WARNING::Fitting problem for feature 130 returning NA
2026-02-13 01:53:58.073228 WARNING::Fitting problem for feature 132 returning NA
2026-02-13 01:53:58.193061 WARNING::Fitting problem for feature 139 returning NA
2026-02-13 01:53:58.263118 WARNING::Fitting problem for feature 150 returning NA
2026-02-13 01:54:23.751768 WARNING::Fitting problem for feature 124 returning NA
2026-02-13 01:54:32.889958 WARNING::Fitting problem for feature 124 returning NA
2026-02-13 01:54:58.121614 WARNING::Fitting problem for feature 124 returning NA
2026-02-13 01:55:08.082804 WARNING::Fitting problem for feature 124 returning NA
2026-02-13 01:55:08.69119 WARNING::Deleting existing residuals file: /tmp/RtmpYb0fyE/file1642cd2345b3c3/fits/residuals_linear.rds
2026-02-13 01:55:08.753273 WARNING::Deleting existing fitted file: /tmp/RtmpYb0fyE/file1642cd2345b3c3/fits/fitted_linear.rds
2026-02-13 01:55:08.791718 WARNING::Deleting existing residuals file: /tmp/RtmpYb0fyE/file1642cd2345b3c3/fits/residuals_logistic.rds
2026-02-13 01:55:08.860438 WARNING::Deleting existing fitted file: /tmp/RtmpYb0fyE/file1642cd2345b3c3/fits/fitted_logistic.rds
2026-02-13 01:55:31.861579 WARNING::Fitting problem for feature 124 returning NA
2026-02-13 01:55:37.052283 WARNING::Fitting problem for feature 124 returning NA
2026-02-13 01:55:37.369907 WARNING::Deleting existing residuals file: /tmp/RtmpYb0fyE/file1642cd2345b3c3/fits/residuals_linear.rds
2026-02-13 01:55:37.432154 WARNING::Deleting existing fitted file: /tmp/RtmpYb0fyE/file1642cd2345b3c3/fits/fitted_linear.rds
2026-02-13 01:55:37.470584 WARNING::Deleting existing residuals file: /tmp/RtmpYb0fyE/file1642cd2345b3c3/fits/residuals_logistic.rds
2026-02-13 01:55:37.539433 WARNING::Deleting existing fitted file: /tmp/RtmpYb0fyE/file1642cd2345b3c3/fits/fitted_logistic.rds
2026-02-13 01:55:56.776533 WARNING::Fitting problem for feature 124 returning NA
2026-02-13 01:56:03.385461 WARNING::Fitting problem for feature 124 returning NA
2026-02-13 01:56:03.680492 WARNING::Deleting existing residuals file: /tmp/RtmpYb0fyE/file1642cd2345b3c3/fits/residuals_linear.rds
2026-02-13 01:56:03.742724 WARNING::Deleting existing fitted file: /tmp/RtmpYb0fyE/file1642cd2345b3c3/fits/fitted_linear.rds
2026-02-13 01:56:03.782205 WARNING::Deleting existing residuals file: /tmp/RtmpYb0fyE/file1642cd2345b3c3/fits/residuals_logistic.rds
2026-02-13 01:56:03.851192 WARNING::Deleting existing fitted file: /tmp/RtmpYb0fyE/file1642cd2345b3c3/fits/fitted_logistic.rds
2026-02-13 01:56:22.7695 WARNING::Fitting problem for feature 50 returning NA
2026-02-13 01:56:22.851982 WARNING::Fitting problem for feature 62 returning NA
2026-02-13 01:56:22.92975 WARNING::Fitting problem for feature 74 returning NA
2026-02-13 01:56:22.952502 WARNING::Fitting problem for feature 78 returning NA
2026-02-13 01:56:22.989653 WARNING::Fitting problem for feature 84 returning NA
2026-02-13 01:56:23.072099 WARNING::Fitting problem for feature 96 returning NA
2026-02-13 01:56:23.078145 WARNING::Fitting problem for feature 97 returning NA
2026-02-13 01:56:23.090931 WARNING::Fitting problem for feature 99 returning NA
2026-02-13 01:56:23.195594 WARNING::Fitting problem for feature 114 returning NA
2026-02-13 01:56:23.234149 WARNING::Fitting problem for feature 115 returning NA
2026-02-13 01:56:23.298156 WARNING::Fitting problem for feature 123 returning NA
2026-02-13 01:56:23.340852 WARNING::Fitting problem for feature 130 returning NA
2026-02-13 01:56:23.353427 WARNING::Fitting problem for feature 132 returning NA
2026-02-13 01:56:23.393674 WARNING::Fitting problem for feature 139 returning NA
2026-02-13 01:56:23.461911 WARNING::Fitting problem for feature 150 returning NA
2026-02-13 01:56:34.177831 WARNING::Fitting problem for feature 50 returning NA
2026-02-13 01:56:34.253721 WARNING::Fitting problem for feature 62 returning NA
2026-02-13 01:56:34.327909 WARNING::Fitting problem for feature 74 returning NA
2026-02-13 01:56:34.349211 WARNING::Fitting problem for feature 78 returning NA
2026-02-13 01:56:34.383332 WARNING::Fitting problem for feature 84 returning NA
2026-02-13 01:56:34.458383 WARNING::Fitting problem for feature 96 returning NA
2026-02-13 01:56:34.463678 WARNING::Fitting problem for feature 97 returning NA
2026-02-13 01:56:34.475639 WARNING::Fitting problem for feature 99 returning NA
2026-02-13 01:56:34.569882 WARNING::Fitting problem for feature 114 returning NA
2026-02-13 01:56:34.575186 WARNING::Fitting problem for feature 115 returning NA
2026-02-13 01:56:34.62393 WARNING::Fitting problem for feature 123 returning NA
2026-02-13 01:56:34.66398 WARNING::Fitting problem for feature 130 returning NA
2026-02-13 01:56:34.67623 WARNING::Fitting problem for feature 132 returning NA
2026-02-13 01:56:34.716141 WARNING::Fitting problem for feature 139 returning NA
2026-02-13 01:56:34.785764 WARNING::Fitting problem for feature 150 returning NA
2026-02-13 01:56:35.068435 WARNING::Deleting existing residuals file: /tmp/RtmpYb0fyE/file1642cd2345b3c3/fits/residuals_linear.rds
2026-02-13 01:56:35.129334 WARNING::Deleting existing fitted file: /tmp/RtmpYb0fyE/file1642cd2345b3c3/fits/fitted_linear.rds
2026-02-13 01:56:35.192026 WARNING::Deleting existing residuals file: /tmp/RtmpYb0fyE/file1642cd2345b3c3/fits/residuals_logistic.rds
2026-02-13 01:56:35.491009 WARNING::Deleting existing fitted file: /tmp/RtmpYb0fyE/file1642cd2345b3c3/fits/fitted_logistic.rds
2026-02-13 01:56:56.305359 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2026-02-13 01:56:56.323282 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2026-02-13 01:56:56.335757 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2026-02-13 01:56:56.389891 ERROR::No fixed, group, or
ordered effects included in formula.
2026-02-13 01:56:56.406625 ERROR::Effect name not found in metadata: d
2026-02-13 01:56:56.418374 ERROR::No user formula provided
2026-02-13 01:56:56.450469 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2026-02-13 01:56:56.463275 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2026-02-13 01:56:59.350714 INFO::Writing function arguments to log file
2026-02-13 01:56:59.365834 INFO::Verifying options selected are valid
2026-02-13 01:57:01.746333 INFO::Writing function arguments to log file
2026-02-13 01:57:01.758882 INFO::Verifying options selected are valid
2026-02-13 01:57:01.760001 INFO::Determining format of input files
2026-02-13 01:57:01.761014 INFO::Input format is data samples as rows and metadata samples as rows
2026-02-13 01:57:01.763469 INFO::Running selected normalization method: TSS
2026-02-13 01:57:01.764987 INFO::Creating output feature tables folder
2026-02-13 01:57:01.765981 INFO::Writing normalized data to file /tmp/RtmpYb0fyE/file1642cd3c2a1b19/features/data_norm.tsv
2026-02-13 01:57:01.767481 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2026-02-13 01:57:01.768375 INFO::Total samples in data: 16
2026-02-13 01:57:01.769251 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2026-02-13 01:57:01.770126 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2026-02-13 01:57:01.772166 INFO::Total filtered features: 0
2026-02-13 01:57:01.773203 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2026-02-13 01:57:01.774481 INFO::Total features filtered by non-zero variance filtering: 0
2026-02-13 01:57:01.775544 INFO::Filtered feature names from variance filtering:
2026-02-13 01:57:01.77655 INFO::Writing filtered data to file /tmp/RtmpYb0fyE/file1642cd3c2a1b19/features/filtered_data.tsv
2026-02-13 01:57:01.778257 INFO::Running selected transform method: LOG
2026-02-13 01:57:01.779611 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpYb0fyE/file1642cd3c2a1b19/features/data_transformed.tsv
2026-02-13 01:57:01.781559 INFO::Applying z-score to standardize continuous metadata
2026-02-13 01:57:01.78689 INFO::Running the linear model component
2026-02-13 01:57:01.80206 INFO::Fitting model to feature number 1, a
2026-02-13 01:57:01.806974 INFO::Fitting model to feature number 2, b
2026-02-13 01:57:01.811518 INFO::Fitting model to feature number 3, c
2026-02-13 01:57:01.819181 INFO::Counting total values for each feature
2026-02-13 01:57:01.821079 INFO::Running the logistic model component
2026-02-13 01:57:01.835574 INFO::Fitting model to feature number 1, a
2026-02-13 01:57:01.842619 INFO::Fitting model to feature number 2, b
2026-02-13 01:57:01.84921 INFO::Fitting model to feature number 3, c
2026-02-13 01:57:01.859481 INFO::Counting total values for each feature
2026-02-13 01:57:01.862139 INFO::Re-running abundances for warn_prevalence
2026-02-13 01:57:01.863187 INFO::Running selected normalization method: TSS
2026-02-13 01:57:01.864796 INFO::Running selected transform method: LOG
2026-02-13 01:57:01.879277 INFO::Fitting model to feature number 1, a
2026-02-13 01:57:01.883889 INFO::Fitting model to feature number 2, b
2026-02-13 01:57:01.888306 INFO::Fitting model to feature number 3, c
2026-02-13 01:57:01.967778 INFO::Creating fits folder
2026-02-13 01:57:01.968988 INFO::Writing residuals to file /tmp/RtmpYb0fyE/file1642cd3c2a1b19/fits/residuals_linear.rds
2026-02-13 01:57:01.970154 INFO::Writing fitted values to file /tmp/RtmpYb0fyE/file1642cd3c2a1b19/fits/fitted_linear.rds
2026-02-13 01:57:01.971349 INFO::Writing residuals to file /tmp/RtmpYb0fyE/file1642cd3c2a1b19/fits/residuals_logistic.rds
2026-02-13 01:57:01.972541 INFO::Writing fitted values to file /tmp/RtmpYb0fyE/file1642cd3c2a1b19/fits/fitted_logistic.rds
2026-02-13 01:57:01.974945 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpYb0fyE/file1642cd3c2a1b19/all_results.tsv
2026-02-13 01:57:01.976591 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/RtmpYb0fyE/file1642cd3c2a1b19/significant_results.tsv
2026-02-13 01:57:01.977952 INFO::Creating output figures folder
2026-02-13 01:57:01.979309 INFO::Writing summary plot of significant
results to file: /tmp/RtmpYb0fyE/file1642cd3c2a1b19/figures/summary_plot.pdf
2026-02-13 01:57:03.633131 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpYb0fyE/file1642cd3c2a1b19/figures
2026-02-13 01:57:03.635204 INFO::Plotting associations from most to least significant, grouped by metadata
2026-02-13 01:57:03.640318 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-02-13 01:57:04.157331 INFO::Writing summary plot of
significant results to file: /tmp/RtmpYb0fyE/file1642cd3c2a1b19/figures/summary_plot.pdf
2026-02-13 01:57:05.850118 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpYb0fyE/file1642cd3c2a1b19/figures
2026-02-13 01:57:05.851807 INFO::Plotting associations from most to least significant, grouped by metadata
2026-02-13 01:57:05.857455 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-02-13 01:57:06.392333 INFO::Running the linear model component
2026-02-13 01:57:06.401542 INFO::Fitting model to feature number 1, a
2026-02-13 01:57:06.406305 INFO::Fitting model to feature number 2, b
2026-02-13 01:57:06.410535 INFO::Fitting model to feature number 3, c
2026-02-13 01:57:06.417784 INFO::Counting total values for each feature
2026-02-13 01:57:06.419489 INFO::Running the logistic model component
2026-02-13 01:57:06.427916 INFO::Fitting model to feature number 1, a
2026-02-13 01:57:06.434118 INFO::Fitting model to feature number 2, b
2026-02-13 01:57:06.439923 INFO::Fitting model to feature number 3, c
2026-02-13 01:57:06.448602 INFO::Counting total values for each feature
2026-02-13 01:57:06.450672 INFO::Re-running abundances for warn_prevalence
2026-02-13 01:57:06.451465 INFO::Running selected normalization method: TSS
2026-02-13 01:57:06.45284 INFO::Running selected transform method: LOG
2026-02-13 01:57:06.461395 INFO::Fitting model to feature number 1, a
2026-02-13 01:57:06.465476 INFO::Fitting model to feature number 2, b
2026-02-13 01:57:06.469456 INFO::Fitting model to feature number 3, c
2026-02-13 01:57:06.547463 INFO::Creating output folder
2026-02-13 01:57:06.548437 INFO::Creating output figures folder
2026-02-13 01:57:06.549679 INFO::Writing summary plot of significant
results to file: /tmp/RtmpYb0fyE/file1642cd55da983d/figures/summary_plot.pdf
2026-02-13 01:57:08.172903 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpYb0fyE/file1642cd55da983d/figures
2026-02-13 01:57:08.174731 INFO::Plotting associations from most to least significant, grouped by metadata
2026-02-13 01:57:08.179822 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-02-13 01:57:09.149259 INFO::Applying z-score to standardize continuous metadata
2026-02-13 01:57:09.156377 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2026-02-13 01:57:09.157274 INFO::Bypass z-score application to metadata
2026-02-13 01:57:09.159896 INFO::Bypass z-score application to metadata
2026-02-13 01:57:09.179451 INFO::Determining format of input files
2026-02-13 01:57:09.180462 INFO::Input format is data samples as rows and metadata samples as rows
2026-02-13 01:57:09.181346 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2026-02-13 01:57:09.189018 INFO::Determining format of input files
2026-02-13 01:57:09.190108 INFO::Input format is data samples as columns and metadata samples as rows
2026-02-13 01:57:09.191423 INFO::Input format is feature_specific_covariate samples as columns
2026-02-13 01:57:09.215316 INFO::Determining format of input files
2026-02-13 01:57:09.216796 INFO::Input format is data samples as rows and metadata samples as rows
2026-02-13 01:57:09.218284 INFO::Input format is feature_specific_covariate samples as columns
2026-02-13 01:57:09.220598 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2026-02-13 01:57:09.221515 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2026-02-13 01:57:09.233604 INFO::Running selected transform method: LOG
2026-02-13 01:57:09.234805 INFO::Creating output feature tables folder
2026-02-13 01:57:09.235675 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpYb0fyE/file1642cd1804ef84/features/data_transformed.tsv
2026-02-13 01:57:09.239607 INFO::Running selected transform method: LOG
2026-02-13 01:57:09.240634 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpYb0fyE/file1642cd1804ef84/features/data_transformed.tsv
2026-02-13 01:57:09.244584 INFO::Running selected transform method: PLOG
2026-02-13 01:57:09.246176 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpYb0fyE/file1642cd1804ef84/features/data_transformed.tsv
2026-02-13 01:57:09.249101 INFO::Running selected transform method: NONE
2026-02-13 01:57:09.249858 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpYb0fyE/file1642cd1804ef84/features/data_transformed.tsv
2026-02-13 01:57:09.257634 INFO::Running the linear model component
2026-02-13 01:57:09.266401 INFO::Fitting model to feature number 1, a
2026-02-13 01:57:09.270678 INFO::Fitting model to feature number 2, b
2026-02-13 01:57:09.274685 INFO::Fitting model to feature number 3, c
2026-02-13 01:57:09.281635 INFO::Counting total values for each feature
2026-02-13 01:57:09.28328 INFO::Running the logistic model component
2026-02-13 01:57:09.291693 INFO::Fitting model to feature number 1, a
2026-02-13 01:57:09.298155 INFO::Fitting model to feature number 2, b
2026-02-13 01:57:09.303962 INFO::Fitting model to feature number 3, c
2026-02-13 01:57:09.312641 INFO::Counting total values for each feature
2026-02-13 01:57:09.314638 INFO::Re-running abundances for warn_prevalence
2026-02-13 01:57:09.315406 INFO::Running selected normalization method: TSS
2026-02-13 01:57:09.316731 INFO::Running selected transform method: LOG
2026-02-13 01:57:09.325325 INFO::Fitting model to feature number 1, a
2026-02-13 01:57:09.330026 INFO::Fitting model to feature number 2, b
2026-02-13 01:57:09.33439 INFO::Fitting model to feature number 3, c
2026-02-13 01:57:09.413453 INFO::Creating output folder
2026-02-13 01:57:09.414444 INFO::Creating fits folder
2026-02-13 01:57:09.41529 INFO::Writing residuals to file /tmp/RtmpYb0fyE/file1642cd2585aba9/fits/residuals_linear.rds
2026-02-13 01:57:09.416264 INFO::Writing fitted values to file /tmp/RtmpYb0fyE/file1642cd2585aba9/fits/fitted_linear.rds
2026-02-13 01:57:09.417317 INFO::Writing residuals to file /tmp/RtmpYb0fyE/file1642cd2585aba9/fits/residuals_logistic.rds
2026-02-13 01:57:09.418317 INFO::Writing fitted values to file /tmp/RtmpYb0fyE/file1642cd2585aba9/fits/fitted_logistic.rds
2026-02-13 01:57:09.420589 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpYb0fyE/file1642cd2585aba9/all_results.tsv
2026-02-13 01:57:09.422079 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/RtmpYb0fyE/file1642cd2585aba9/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
360.215 4.751 364.947
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 20.208 | 0.510 | 20.721 | |
| maaslin_check_arguments | 0.145 | 0.002 | 0.147 | |
| maaslin_check_formula | 0.158 | 0.001 | 0.159 | |
| maaslin_compute_formula | 0.142 | 0.001 | 0.143 | |
| maaslin_contrast_test | 18.707 | 0.343 | 19.050 | |
| maaslin_filter | 0.441 | 0.037 | 0.477 | |
| maaslin_fit | 13.218 | 0.095 | 13.313 | |
| maaslin_log_arguments | 0.126 | 0.003 | 0.129 | |
| maaslin_normalize | 0.261 | 0.002 | 0.263 | |
| maaslin_plot_results | 43.069 | 0.276 | 43.318 | |
| maaslin_plot_results_from_output | 44.370 | 0.387 | 44.762 | |
| maaslin_process_metadata | 0.438 | 0.006 | 0.444 | |
| maaslin_read_data | 0.125 | 0.003 | 0.129 | |
| maaslin_reorder_data | 0.130 | 0.002 | 0.131 | |
| maaslin_transform | 0.534 | 0.004 | 0.537 | |
| maaslin_write_results | 13.543 | 0.179 | 13.723 | |
| maaslin_write_results_lefse_format | 13.829 | 0.055 | 13.886 | |
| preprocess_dna_mtx | 0.002 | 0.001 | 0.004 | |
| preprocess_taxa_mtx | 0.004 | 0.000 | 0.004 | |