William Nickols
| Snapshot Date: 2026-02-22 13:45 -0500 (Sun, 22 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 2026-02-23 11:57 -0500 (Mon, 23 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" | 4890 |
| 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: 2026-02-23 01:12:33 -0500 (Mon, 23 Feb 2026) |
| EndedAt: 2026-02-23 01:34:22 -0500 (Mon, 23 Feb 2026) |
| EllapsedTime: 1308.4 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 44.226 0.249 44.480
maaslin_plot_results 43.733 0.263 43.957
maaslin3 20.948 0.491 21.449
maaslin_contrast_test 19.468 0.408 19.878
maaslin_write_results_lefse_format 14.667 0.136 14.805
maaslin_write_results 12.990 0.162 13.152
maaslin_fit 12.604 0.083 12.692
* 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")
2026-02-23 01:18:52.689974 WARNING::Fitting problem for feature 50 returning NA
2026-02-23 01:18:52.776441 WARNING::Fitting problem for feature 62 returning NA
2026-02-23 01:18:52.872083 WARNING::Fitting problem for feature 74 returning NA
2026-02-23 01:18:52.893834 WARNING::Fitting problem for feature 78 returning NA
2026-02-23 01:18:52.92874 WARNING::Fitting problem for feature 84 returning NA
2026-02-23 01:18:53.00441 WARNING::Fitting problem for feature 96 returning NA
2026-02-23 01:18:53.016568 WARNING::Fitting problem for feature 97 returning NA
2026-02-23 01:18:53.028232 WARNING::Fitting problem for feature 99 returning NA
2026-02-23 01:18:53.120976 WARNING::Fitting problem for feature 114 returning NA
2026-02-23 01:18:53.126288 WARNING::Fitting problem for feature 115 returning NA
2026-02-23 01:18:53.185438 WARNING::Fitting problem for feature 123 returning NA
2026-02-23 01:18:53.241376 WARNING::Fitting problem for feature 130 returning NA
2026-02-23 01:18:53.252988 WARNING::Fitting problem for feature 132 returning NA
2026-02-23 01:18:53.292201 WARNING::Fitting problem for feature 139 returning NA
2026-02-23 01:18:53.361769 WARNING::Fitting problem for feature 150 returning NA
2026-02-23 01:19:09.301085 WARNING::Fitting problem for feature 50 returning NA
2026-02-23 01:19:09.376626 WARNING::Fitting problem for feature 62 returning NA
2026-02-23 01:19:09.452411 WARNING::Fitting problem for feature 74 returning NA
2026-02-23 01:19:09.474327 WARNING::Fitting problem for feature 78 returning NA
2026-02-23 01:19:09.509531 WARNING::Fitting problem for feature 84 returning NA
2026-02-23 01:19:09.605256 WARNING::Fitting problem for feature 96 returning NA
2026-02-23 01:19:09.610817 WARNING::Fitting problem for feature 97 returning NA
2026-02-23 01:19:09.623265 WARNING::Fitting problem for feature 99 returning NA
2026-02-23 01:19:09.71741 WARNING::Fitting problem for feature 114 returning NA
2026-02-23 01:19:09.722731 WARNING::Fitting problem for feature 115 returning NA
2026-02-23 01:19:09.77157 WARNING::Fitting problem for feature 123 returning NA
2026-02-23 01:19:09.810354 WARNING::Fitting problem for feature 130 returning NA
2026-02-23 01:19:09.821917 WARNING::Fitting problem for feature 132 returning NA
2026-02-23 01:19:09.861796 WARNING::Fitting problem for feature 139 returning NA
2026-02-23 01:19:09.930719 WARNING::Fitting problem for feature 150 returning NA
2026-02-23 01:19:34.353912 WARNING::Fitting problem for feature 50 returning NA
2026-02-23 01:19:34.428671 WARNING::Fitting problem for feature 62 returning NA
2026-02-23 01:19:34.503285 WARNING::Fitting problem for feature 74 returning NA
2026-02-23 01:19:34.524776 WARNING::Fitting problem for feature 78 returning NA
2026-02-23 01:19:34.558793 WARNING::Fitting problem for feature 84 returning NA
2026-02-23 01:19:34.634546 WARNING::Fitting problem for feature 96 returning NA
2026-02-23 01:19:34.639912 WARNING::Fitting problem for feature 97 returning NA
2026-02-23 01:19:34.65186 WARNING::Fitting problem for feature 99 returning NA
2026-02-23 01:19:34.74681 WARNING::Fitting problem for feature 114 returning NA
2026-02-23 01:19:34.752246 WARNING::Fitting problem for feature 115 returning NA
2026-02-23 01:19:34.803705 WARNING::Fitting problem for feature 123 returning NA
2026-02-23 01:19:34.844891 WARNING::Fitting problem for feature 130 returning NA
2026-02-23 01:19:34.857041 WARNING::Fitting problem for feature 132 returning NA
2026-02-23 01:19:34.897789 WARNING::Fitting problem for feature 139 returning NA
2026-02-23 01:19:34.97138 WARNING::Fitting problem for feature 150 returning NA
2026-02-23 01:19:47.747019 WARNING::Fitting problem for feature 50 returning NA
2026-02-23 01:19:47.850141 WARNING::Fitting problem for feature 62 returning NA
2026-02-23 01:19:47.926665 WARNING::Fitting problem for feature 74 returning NA
2026-02-23 01:19:47.948605 WARNING::Fitting problem for feature 78 returning NA
2026-02-23 01:19:47.983057 WARNING::Fitting problem for feature 84 returning NA
2026-02-23 01:19:48.058712 WARNING::Fitting problem for feature 96 returning NA
2026-02-23 01:19:48.063989 WARNING::Fitting problem for feature 97 returning NA
2026-02-23 01:19:48.07566 WARNING::Fitting problem for feature 99 returning NA
2026-02-23 01:19:48.171026 WARNING::Fitting problem for feature 114 returning NA
2026-02-23 01:19:48.176445 WARNING::Fitting problem for feature 115 returning NA
2026-02-23 01:19:48.226763 WARNING::Fitting problem for feature 123 returning NA
2026-02-23 01:19:48.267263 WARNING::Fitting problem for feature 130 returning NA
2026-02-23 01:19:48.279301 WARNING::Fitting problem for feature 132 returning NA
2026-02-23 01:19:48.319848 WARNING::Fitting problem for feature 139 returning NA
2026-02-23 01:19:48.388653 WARNING::Fitting problem for feature 150 returning NA
2026-02-23 01:19:48.583487 WARNING::Deleting existing residuals file: /tmp/RtmpgIGj1a/file54206708e4d60/fits/residuals_linear.rds
2026-02-23 01:19:48.644622 WARNING::Deleting existing fitted file: /tmp/RtmpgIGj1a/file54206708e4d60/fits/fitted_linear.rds
2026-02-23 01:19:48.707572 WARNING::Deleting existing residuals file: /tmp/RtmpgIGj1a/file54206708e4d60/fits/residuals_logistic.rds
2026-02-23 01:19:49.006802 WARNING::Deleting existing fitted file: /tmp/RtmpgIGj1a/file54206708e4d60/fits/fitted_logistic.rds
2026-02-23 01:20:11.226337 WARNING::Fitting problem for feature 50 returning NA
2026-02-23 01:20:11.308265 WARNING::Fitting problem for feature 62 returning NA
2026-02-23 01:20:11.410065 WARNING::Fitting problem for feature 74 returning NA
2026-02-23 01:20:11.431703 WARNING::Fitting problem for feature 78 returning NA
2026-02-23 01:20:11.466115 WARNING::Fitting problem for feature 84 returning NA
2026-02-23 01:20:11.542959 WARNING::Fitting problem for feature 96 returning NA
2026-02-23 01:20:11.548533 WARNING::Fitting problem for feature 97 returning NA
2026-02-23 01:20:11.560796 WARNING::Fitting problem for feature 99 returning NA
2026-02-23 01:20:11.660037 WARNING::Fitting problem for feature 114 returning NA
2026-02-23 01:20:11.665841 WARNING::Fitting problem for feature 115 returning NA
2026-02-23 01:20:11.716992 WARNING::Fitting problem for feature 123 returning NA
2026-02-23 01:20:11.758842 WARNING::Fitting problem for feature 130 returning NA
2026-02-23 01:20:11.771256 WARNING::Fitting problem for feature 132 returning NA
2026-02-23 01:20:11.813905 WARNING::Fitting problem for feature 139 returning NA
2026-02-23 01:20:11.887567 WARNING::Fitting problem for feature 150 returning NA
2026-02-23 01:20:24.059864 WARNING::Fitting problem for feature 50 returning NA
2026-02-23 01:20:24.135711 WARNING::Fitting problem for feature 62 returning NA
2026-02-23 01:20:24.21056 WARNING::Fitting problem for feature 74 returning NA
2026-02-23 01:20:24.232455 WARNING::Fitting problem for feature 78 returning NA
2026-02-23 01:20:24.267959 WARNING::Fitting problem for feature 84 returning NA
2026-02-23 01:20:24.345138 WARNING::Fitting problem for feature 96 returning NA
2026-02-23 01:20:24.3506 WARNING::Fitting problem for feature 97 returning NA
2026-02-23 01:20:24.362735 WARNING::Fitting problem for feature 99 returning NA
2026-02-23 01:20:24.460766 WARNING::Fitting problem for feature 114 returning NA
2026-02-23 01:20:24.466205 WARNING::Fitting problem for feature 115 returning NA
2026-02-23 01:20:24.515192 WARNING::Fitting problem for feature 123 returning NA
2026-02-23 01:20:24.554942 WARNING::Fitting problem for feature 130 returning NA
2026-02-23 01:20:24.566776 WARNING::Fitting problem for feature 132 returning NA
2026-02-23 01:20:24.608194 WARNING::Fitting problem for feature 139 returning NA
2026-02-23 01:20:24.681124 WARNING::Fitting problem for feature 150 returning NA
2026-02-23 01:20:24.899399 WARNING::Deleting existing residuals file: /tmp/RtmpgIGj1a/file54206708e4d60/fits/residuals_linear.rds
2026-02-23 01:20:24.960707 WARNING::Deleting existing fitted file: /tmp/RtmpgIGj1a/file54206708e4d60/fits/fitted_linear.rds
2026-02-23 01:20:25.023581 WARNING::Deleting existing residuals file: /tmp/RtmpgIGj1a/file54206708e4d60/fits/residuals_logistic.rds
2026-02-23 01:20:25.323078 WARNING::Deleting existing fitted file: /tmp/RtmpgIGj1a/file54206708e4d60/fits/fitted_logistic.rds
2026-02-23 01:20:47.038697 WARNING::Fitting problem for feature 50 returning NA
2026-02-23 01:20:47.118702 WARNING::Fitting problem for feature 62 returning NA
2026-02-23 01:20:47.197818 WARNING::Fitting problem for feature 74 returning NA
2026-02-23 01:20:47.221575 WARNING::Fitting problem for feature 78 returning NA
2026-02-23 01:20:47.258003 WARNING::Fitting problem for feature 84 returning NA
2026-02-23 01:20:47.356651 WARNING::Fitting problem for feature 96 returning NA
2026-02-23 01:20:47.362114 WARNING::Fitting problem for feature 97 returning NA
2026-02-23 01:20:47.374088 WARNING::Fitting problem for feature 99 returning NA
2026-02-23 01:20:47.470748 WARNING::Fitting problem for feature 114 returning NA
2026-02-23 01:20:47.476488 WARNING::Fitting problem for feature 115 returning NA
2026-02-23 01:20:47.528547 WARNING::Fitting problem for feature 123 returning NA
2026-02-23 01:20:47.569669 WARNING::Fitting problem for feature 130 returning NA
2026-02-23 01:20:47.581911 WARNING::Fitting problem for feature 132 returning NA
2026-02-23 01:20:47.623187 WARNING::Fitting problem for feature 139 returning NA
2026-02-23 01:20:47.693228 WARNING::Fitting problem for feature 150 returning NA
2026-02-23 01:20:59.767357 WARNING::Fitting problem for feature 50 returning NA
2026-02-23 01:20:59.846972 WARNING::Fitting problem for feature 62 returning NA
2026-02-23 01:20:59.928812 WARNING::Fitting problem for feature 74 returning NA
2026-02-23 01:20:59.952974 WARNING::Fitting problem for feature 78 returning NA
2026-02-23 01:20:59.990627 WARNING::Fitting problem for feature 84 returning NA
2026-02-23 01:21:00.068024 WARNING::Fitting problem for feature 96 returning NA
2026-02-23 01:21:00.073494 WARNING::Fitting problem for feature 97 returning NA
2026-02-23 01:21:00.085494 WARNING::Fitting problem for feature 99 returning NA
2026-02-23 01:21:00.184799 WARNING::Fitting problem for feature 114 returning NA
2026-02-23 01:21:00.190679 WARNING::Fitting problem for feature 115 returning NA
2026-02-23 01:21:00.242206 WARNING::Fitting problem for feature 123 returning NA
2026-02-23 01:21:00.283521 WARNING::Fitting problem for feature 130 returning NA
2026-02-23 01:21:00.295754 WARNING::Fitting problem for feature 132 returning NA
2026-02-23 01:21:00.336812 WARNING::Fitting problem for feature 139 returning NA
2026-02-23 01:21:00.409043 WARNING::Fitting problem for feature 150 returning NA
2026-02-23 01:21:00.614131 WARNING::Deleting existing residuals file: /tmp/RtmpgIGj1a/file54206708e4d60/fits/residuals_linear.rds
2026-02-23 01:21:00.675114 WARNING::Deleting existing fitted file: /tmp/RtmpgIGj1a/file54206708e4d60/fits/fitted_linear.rds
2026-02-23 01:21:00.74868 WARNING::Deleting existing residuals file: /tmp/RtmpgIGj1a/file54206708e4d60/fits/residuals_logistic.rds
2026-02-23 01:21:01.048952 WARNING::Deleting existing fitted file: /tmp/RtmpgIGj1a/file54206708e4d60/fits/fitted_logistic.rds
2026-02-23 01:21:23.045455 WARNING::Fitting problem for feature 50 returning NA
2026-02-23 01:21:23.12434 WARNING::Fitting problem for feature 62 returning NA
2026-02-23 01:21:23.203007 WARNING::Fitting problem for feature 74 returning NA
2026-02-23 01:21:23.226114 WARNING::Fitting problem for feature 78 returning NA
2026-02-23 01:21:23.262316 WARNING::Fitting problem for feature 84 returning NA
2026-02-23 01:21:23.344069 WARNING::Fitting problem for feature 96 returning NA
2026-02-23 01:21:23.350149 WARNING::Fitting problem for feature 97 returning NA
2026-02-23 01:21:23.363499 WARNING::Fitting problem for feature 99 returning NA
2026-02-23 01:21:23.469989 WARNING::Fitting problem for feature 114 returning NA
2026-02-23 01:21:23.476229 WARNING::Fitting problem for feature 115 returning NA
2026-02-23 01:21:23.532229 WARNING::Fitting problem for feature 123 returning NA
2026-02-23 01:21:23.578377 WARNING::Fitting problem for feature 130 returning NA
2026-02-23 01:21:23.591998 WARNING::Fitting problem for feature 132 returning NA
2026-02-23 01:21:23.63811 WARNING::Fitting problem for feature 139 returning NA
2026-02-23 01:21:23.720754 WARNING::Fitting problem for feature 150 returning NA
2026-02-23 01:21:36.633386 WARNING::Fitting problem for feature 50 returning NA
2026-02-23 01:21:36.734409 WARNING::Fitting problem for feature 62 returning NA
2026-02-23 01:21:36.830425 WARNING::Fitting problem for feature 74 returning NA
2026-02-23 01:21:36.857751 WARNING::Fitting problem for feature 78 returning NA
2026-02-23 01:21:36.901795 WARNING::Fitting problem for feature 84 returning NA
2026-02-23 01:21:36.995826 WARNING::Fitting problem for feature 96 returning NA
2026-02-23 01:21:37.002291 WARNING::Fitting problem for feature 97 returning NA
2026-02-23 01:21:37.016472 WARNING::Fitting problem for feature 99 returning NA
2026-02-23 01:21:37.127788 WARNING::Fitting problem for feature 114 returning NA
2026-02-23 01:21:37.134207 WARNING::Fitting problem for feature 115 returning NA
2026-02-23 01:21:37.19183 WARNING::Fitting problem for feature 123 returning NA
2026-02-23 01:21:37.245876 WARNING::Fitting problem for feature 130 returning NA
2026-02-23 01:21:37.260178 WARNING::Fitting problem for feature 132 returning NA
2026-02-23 01:21:37.308606 WARNING::Fitting problem for feature 139 returning NA
2026-02-23 01:21:37.390539 WARNING::Fitting problem for feature 150 returning NA
2026-02-23 01:22:04.329404 WARNING::Fitting problem for feature 124 returning NA
2026-02-23 01:22:13.540542 WARNING::Fitting problem for feature 124 returning NA
2026-02-23 01:22:38.996458 WARNING::Fitting problem for feature 124 returning NA
2026-02-23 01:22:49.548653 WARNING::Fitting problem for feature 124 returning NA
2026-02-23 01:22:50.223044 WARNING::Deleting existing residuals file: /tmp/RtmpgIGj1a/file542062c0ef485/fits/residuals_linear.rds
2026-02-23 01:22:50.284992 WARNING::Deleting existing fitted file: /tmp/RtmpgIGj1a/file542062c0ef485/fits/fitted_linear.rds
2026-02-23 01:22:50.324175 WARNING::Deleting existing residuals file: /tmp/RtmpgIGj1a/file542062c0ef485/fits/residuals_logistic.rds
2026-02-23 01:22:50.394152 WARNING::Deleting existing fitted file: /tmp/RtmpgIGj1a/file542062c0ef485/fits/fitted_logistic.rds
2026-02-23 01:23:13.932821 WARNING::Fitting problem for feature 124 returning NA
2026-02-23 01:23:19.372859 WARNING::Fitting problem for feature 124 returning NA
2026-02-23 01:23:19.694674 WARNING::Deleting existing residuals file: /tmp/RtmpgIGj1a/file542062c0ef485/fits/residuals_linear.rds
2026-02-23 01:23:19.75613 WARNING::Deleting existing fitted file: /tmp/RtmpgIGj1a/file542062c0ef485/fits/fitted_linear.rds
2026-02-23 01:23:19.794688 WARNING::Deleting existing residuals file: /tmp/RtmpgIGj1a/file542062c0ef485/fits/residuals_logistic.rds
2026-02-23 01:23:19.881501 WARNING::Deleting existing fitted file: /tmp/RtmpgIGj1a/file542062c0ef485/fits/fitted_logistic.rds
2026-02-23 01:23:39.257449 WARNING::Fitting problem for feature 124 returning NA
2026-02-23 01:23:45.896891 WARNING::Fitting problem for feature 124 returning NA
2026-02-23 01:23:46.200851 WARNING::Deleting existing residuals file: /tmp/RtmpgIGj1a/file542062c0ef485/fits/residuals_linear.rds
2026-02-23 01:23:46.262419 WARNING::Deleting existing fitted file: /tmp/RtmpgIGj1a/file542062c0ef485/fits/fitted_linear.rds
2026-02-23 01:23:46.301322 WARNING::Deleting existing residuals file: /tmp/RtmpgIGj1a/file542062c0ef485/fits/residuals_logistic.rds
2026-02-23 01:23:46.371529 WARNING::Deleting existing fitted file: /tmp/RtmpgIGj1a/file542062c0ef485/fits/fitted_logistic.rds
2026-02-23 01:24:06.060084 WARNING::Fitting problem for feature 50 returning NA
2026-02-23 01:24:06.141485 WARNING::Fitting problem for feature 62 returning NA
2026-02-23 01:24:06.222556 WARNING::Fitting problem for feature 74 returning NA
2026-02-23 01:24:06.246808 WARNING::Fitting problem for feature 78 returning NA
2026-02-23 01:24:06.284985 WARNING::Fitting problem for feature 84 returning NA
2026-02-23 01:24:06.390643 WARNING::Fitting problem for feature 96 returning NA
2026-02-23 01:24:06.396827 WARNING::Fitting problem for feature 97 returning NA
2026-02-23 01:24:06.411059 WARNING::Fitting problem for feature 99 returning NA
2026-02-23 01:24:06.520598 WARNING::Fitting problem for feature 114 returning NA
2026-02-23 01:24:06.526871 WARNING::Fitting problem for feature 115 returning NA
2026-02-23 01:24:06.622601 WARNING::Fitting problem for feature 123 returning NA
2026-02-23 01:24:06.666687 WARNING::Fitting problem for feature 130 returning NA
2026-02-23 01:24:06.679374 WARNING::Fitting problem for feature 132 returning NA
2026-02-23 01:24:06.725596 WARNING::Fitting problem for feature 139 returning NA
2026-02-23 01:24:06.802072 WARNING::Fitting problem for feature 150 returning NA
2026-02-23 01:24:17.786872 WARNING::Fitting problem for feature 50 returning NA
2026-02-23 01:24:17.863584 WARNING::Fitting problem for feature 62 returning NA
2026-02-23 01:24:17.94066 WARNING::Fitting problem for feature 74 returning NA
2026-02-23 01:24:17.963158 WARNING::Fitting problem for feature 78 returning NA
2026-02-23 01:24:17.998867 WARNING::Fitting problem for feature 84 returning NA
2026-02-23 01:24:18.078974 WARNING::Fitting problem for feature 96 returning NA
2026-02-23 01:24:18.084607 WARNING::Fitting problem for feature 97 returning NA
2026-02-23 01:24:18.098285 WARNING::Fitting problem for feature 99 returning NA
2026-02-23 01:24:18.201045 WARNING::Fitting problem for feature 114 returning NA
2026-02-23 01:24:18.206813 WARNING::Fitting problem for feature 115 returning NA
2026-02-23 01:24:18.260049 WARNING::Fitting problem for feature 123 returning NA
2026-02-23 01:24:18.302498 WARNING::Fitting problem for feature 130 returning NA
2026-02-23 01:24:18.31521 WARNING::Fitting problem for feature 132 returning NA
2026-02-23 01:24:18.358279 WARNING::Fitting problem for feature 139 returning NA
2026-02-23 01:24:18.432442 WARNING::Fitting problem for feature 150 returning NA
2026-02-23 01:24:18.756225 WARNING::Deleting existing residuals file: /tmp/RtmpgIGj1a/file542062c0ef485/fits/residuals_linear.rds
2026-02-23 01:24:18.818154 WARNING::Deleting existing fitted file: /tmp/RtmpgIGj1a/file542062c0ef485/fits/fitted_linear.rds
2026-02-23 01:24:18.881675 WARNING::Deleting existing residuals file: /tmp/RtmpgIGj1a/file542062c0ef485/fits/residuals_logistic.rds
2026-02-23 01:24:19.180742 WARNING::Deleting existing fitted file: /tmp/RtmpgIGj1a/file542062c0ef485/fits/fitted_logistic.rds
2026-02-23 01:24:40.14347 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2026-02-23 01:24:40.161695 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2026-02-23 01:24:40.173625 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2026-02-23 01:24:40.226376 ERROR::No fixed, group, or
ordered effects included in formula.
2026-02-23 01:24:40.243459 ERROR::Effect name not found in metadata: d
2026-02-23 01:24:40.255018 ERROR::No user formula provided
2026-02-23 01:24:40.28705 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2026-02-23 01:24:40.298929 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2026-02-23 01:24:43.210529 INFO::Writing function arguments to log file
2026-02-23 01:24:43.225398 INFO::Verifying options selected are valid
2026-02-23 01:24:45.612079 INFO::Writing function arguments to log file
2026-02-23 01:24:45.624787 INFO::Verifying options selected are valid
2026-02-23 01:24:45.625972 INFO::Determining format of input files
2026-02-23 01:24:45.627041 INFO::Input format is data samples as rows and metadata samples as rows
2026-02-23 01:24:45.62958 INFO::Running selected normalization method: TSS
2026-02-23 01:24:45.631151 INFO::Creating output feature tables folder
2026-02-23 01:24:45.632137 INFO::Writing normalized data to file /tmp/RtmpgIGj1a/file542063165392b/features/data_norm.tsv
2026-02-23 01:24:45.633666 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2026-02-23 01:24:45.634603 INFO::Total samples in data: 16
2026-02-23 01:24:45.635487 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2026-02-23 01:24:45.636351 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2026-02-23 01:24:45.63833 INFO::Total filtered features: 0
2026-02-23 01:24:45.639302 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2026-02-23 01:24:45.640484 INFO::Total features filtered by non-zero variance filtering: 0
2026-02-23 01:24:45.641453 INFO::Filtered feature names from variance filtering:
2026-02-23 01:24:45.642352 INFO::Writing filtered data to file /tmp/RtmpgIGj1a/file542063165392b/features/filtered_data.tsv
2026-02-23 01:24:45.643833 INFO::Running selected transform method: LOG
2026-02-23 01:24:45.645027 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpgIGj1a/file542063165392b/features/data_transformed.tsv
2026-02-23 01:24:45.646692 INFO::Applying z-score to standardize continuous metadata
2026-02-23 01:24:45.651412 INFO::Running the linear model component
2026-02-23 01:24:45.665898 INFO::Fitting model to feature number 1, a
2026-02-23 01:24:45.670695 INFO::Fitting model to feature number 2, b
2026-02-23 01:24:45.675186 INFO::Fitting model to feature number 3, c
2026-02-23 01:24:45.682646 INFO::Counting total values for each feature
2026-02-23 01:24:45.68454 INFO::Running the logistic model component
2026-02-23 01:24:45.699249 INFO::Fitting model to feature number 1, a
2026-02-23 01:24:45.706327 INFO::Fitting model to feature number 2, b
2026-02-23 01:24:45.713163 INFO::Fitting model to feature number 3, c
2026-02-23 01:24:45.72327 INFO::Counting total values for each feature
2026-02-23 01:24:45.72578 INFO::Re-running abundances for warn_prevalence
2026-02-23 01:24:45.726859 INFO::Running selected normalization method: TSS
2026-02-23 01:24:45.728527 INFO::Running selected transform method: LOG
2026-02-23 01:24:45.743637 INFO::Fitting model to feature number 1, a
2026-02-23 01:24:45.748688 INFO::Fitting model to feature number 2, b
2026-02-23 01:24:45.753495 INFO::Fitting model to feature number 3, c
2026-02-23 01:24:45.839053 INFO::Creating fits folder
2026-02-23 01:24:45.840356 INFO::Writing residuals to file /tmp/RtmpgIGj1a/file542063165392b/fits/residuals_linear.rds
2026-02-23 01:24:45.841603 INFO::Writing fitted values to file /tmp/RtmpgIGj1a/file542063165392b/fits/fitted_linear.rds
2026-02-23 01:24:45.843023 INFO::Writing residuals to file /tmp/RtmpgIGj1a/file542063165392b/fits/residuals_logistic.rds
2026-02-23 01:24:45.844354 INFO::Writing fitted values to file /tmp/RtmpgIGj1a/file542063165392b/fits/fitted_logistic.rds
2026-02-23 01:24:45.847044 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpgIGj1a/file542063165392b/all_results.tsv
2026-02-23 01:24:45.84884 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/RtmpgIGj1a/file542063165392b/significant_results.tsv
2026-02-23 01:24:45.850287 INFO::Creating output figures folder
2026-02-23 01:24:45.85176 INFO::Writing summary plot of significant
results to file: /tmp/RtmpgIGj1a/file542063165392b/figures/summary_plot.pdf
2026-02-23 01:24:47.502437 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpgIGj1a/file542063165392b/figures
2026-02-23 01:24:47.504435 INFO::Plotting associations from most to least significant, grouped by metadata
2026-02-23 01:24:47.509586 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-02-23 01:24:48.030473 INFO::Writing summary plot of
significant results to file: /tmp/RtmpgIGj1a/file542063165392b/figures/summary_plot.pdf
2026-02-23 01:24:49.655379 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpgIGj1a/file542063165392b/figures
2026-02-23 01:24:49.657195 INFO::Plotting associations from most to least significant, grouped by metadata
2026-02-23 01:24:49.662678 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-02-23 01:24:50.200893 INFO::Running the linear model component
2026-02-23 01:24:50.210912 INFO::Fitting model to feature number 1, a
2026-02-23 01:24:50.215798 INFO::Fitting model to feature number 2, b
2026-02-23 01:24:50.220456 INFO::Fitting model to feature number 3, c
2026-02-23 01:24:50.228043 INFO::Counting total values for each feature
2026-02-23 01:24:50.229793 INFO::Running the logistic model component
2026-02-23 01:24:50.238546 INFO::Fitting model to feature number 1, a
2026-02-23 01:24:50.245109 INFO::Fitting model to feature number 2, b
2026-02-23 01:24:50.251355 INFO::Fitting model to feature number 3, c
2026-02-23 01:24:50.261051 INFO::Counting total values for each feature
2026-02-23 01:24:50.26327 INFO::Re-running abundances for warn_prevalence
2026-02-23 01:24:50.264088 INFO::Running selected normalization method: TSS
2026-02-23 01:24:50.265486 INFO::Running selected transform method: LOG
2026-02-23 01:24:50.274315 INFO::Fitting model to feature number 1, a
2026-02-23 01:24:50.278774 INFO::Fitting model to feature number 2, b
2026-02-23 01:24:50.282997 INFO::Fitting model to feature number 3, c
2026-02-23 01:24:50.364639 INFO::Creating output folder
2026-02-23 01:24:50.365826 INFO::Creating output figures folder
2026-02-23 01:24:50.367256 INFO::Writing summary plot of significant
results to file: /tmp/RtmpgIGj1a/file5420649a51746/figures/summary_plot.pdf
2026-02-23 01:24:52.030465 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpgIGj1a/file5420649a51746/figures
2026-02-23 01:24:52.032487 INFO::Plotting associations from most to least significant, grouped by metadata
2026-02-23 01:24:52.037914 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-02-23 01:24:53.036547 INFO::Applying z-score to standardize continuous metadata
2026-02-23 01:24:53.044062 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2026-02-23 01:24:53.045021 INFO::Bypass z-score application to metadata
2026-02-23 01:24:53.047935 INFO::Bypass z-score application to metadata
2026-02-23 01:24:53.081478 INFO::Determining format of input files
2026-02-23 01:24:53.083611 INFO::Input format is data samples as rows and metadata samples as rows
2026-02-23 01:24:53.084861 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2026-02-23 01:24:53.094734 INFO::Determining format of input files
2026-02-23 01:24:53.095814 INFO::Input format is data samples as columns and metadata samples as rows
2026-02-23 01:24:53.097137 INFO::Input format is feature_specific_covariate samples as columns
2026-02-23 01:24:53.105339 INFO::Determining format of input files
2026-02-23 01:24:53.106261 INFO::Input format is data samples as rows and metadata samples as rows
2026-02-23 01:24:53.107278 INFO::Input format is feature_specific_covariate samples as columns
2026-02-23 01:24:53.108931 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2026-02-23 01:24:53.109709 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2026-02-23 01:24:53.121433 INFO::Running selected transform method: LOG
2026-02-23 01:24:53.122576 INFO::Creating output feature tables folder
2026-02-23 01:24:53.123392 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpgIGj1a/file542066c8b9555/features/data_transformed.tsv
2026-02-23 01:24:53.127163 INFO::Running selected transform method: LOG
2026-02-23 01:24:53.128161 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpgIGj1a/file542066c8b9555/features/data_transformed.tsv
2026-02-23 01:24:53.132196 INFO::Running selected transform method: PLOG
2026-02-23 01:24:53.133807 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpgIGj1a/file542066c8b9555/features/data_transformed.tsv
2026-02-23 01:24:53.136745 INFO::Running selected transform method: NONE
2026-02-23 01:24:53.137475 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpgIGj1a/file542066c8b9555/features/data_transformed.tsv
2026-02-23 01:24:53.145151 INFO::Running the linear model component
2026-02-23 01:24:53.153542 INFO::Fitting model to feature number 1, a
2026-02-23 01:24:53.157825 INFO::Fitting model to feature number 2, b
2026-02-23 01:24:53.161887 INFO::Fitting model to feature number 3, c
2026-02-23 01:24:53.168835 INFO::Counting total values for each feature
2026-02-23 01:24:53.170455 INFO::Running the logistic model component
2026-02-23 01:24:53.178885 INFO::Fitting model to feature number 1, a
2026-02-23 01:24:53.185204 INFO::Fitting model to feature number 2, b
2026-02-23 01:24:53.191087 INFO::Fitting model to feature number 3, c
2026-02-23 01:24:53.199788 INFO::Counting total values for each feature
2026-02-23 01:24:53.201789 INFO::Re-running abundances for warn_prevalence
2026-02-23 01:24:53.202592 INFO::Running selected normalization method: TSS
2026-02-23 01:24:53.203933 INFO::Running selected transform method: LOG
2026-02-23 01:24:53.212399 INFO::Fitting model to feature number 1, a
2026-02-23 01:24:53.21664 INFO::Fitting model to feature number 2, b
2026-02-23 01:24:53.2207 INFO::Fitting model to feature number 3, c
2026-02-23 01:24:53.297293 INFO::Creating output folder
2026-02-23 01:24:53.298274 INFO::Creating fits folder
2026-02-23 01:24:53.299109 INFO::Writing residuals to file /tmp/RtmpgIGj1a/file54206109a877c/fits/residuals_linear.rds
2026-02-23 01:24:53.300088 INFO::Writing fitted values to file /tmp/RtmpgIGj1a/file54206109a877c/fits/fitted_linear.rds
2026-02-23 01:24:53.301176 INFO::Writing residuals to file /tmp/RtmpgIGj1a/file54206109a877c/fits/residuals_logistic.rds
2026-02-23 01:24:53.302228 INFO::Writing fitted values to file /tmp/RtmpgIGj1a/file54206109a877c/fits/fitted_logistic.rds
2026-02-23 01:24:53.30442 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpgIGj1a/file54206109a877c/all_results.tsv
2026-02-23 01:24:53.305974 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/RtmpgIGj1a/file54206109a877c/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
363.457 8.129 371.590
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 20.948 | 0.491 | 21.449 | |
| maaslin_check_arguments | 0.143 | 0.000 | 0.143 | |
| maaslin_check_formula | 0.157 | 0.003 | 0.160 | |
| maaslin_compute_formula | 0.146 | 0.004 | 0.150 | |
| maaslin_contrast_test | 19.468 | 0.408 | 19.878 | |
| maaslin_filter | 0.441 | 0.010 | 0.452 | |
| maaslin_fit | 12.604 | 0.083 | 12.692 | |
| maaslin_log_arguments | 0.146 | 0.002 | 0.147 | |
| maaslin_normalize | 0.260 | 0.005 | 0.265 | |
| maaslin_plot_results | 43.733 | 0.263 | 43.957 | |
| maaslin_plot_results_from_output | 44.226 | 0.249 | 44.480 | |
| maaslin_process_metadata | 0.431 | 0.009 | 0.440 | |
| maaslin_read_data | 0.122 | 0.001 | 0.123 | |
| maaslin_reorder_data | 0.124 | 0.004 | 0.128 | |
| maaslin_transform | 0.547 | 0.011 | 0.558 | |
| maaslin_write_results | 12.990 | 0.162 | 13.152 | |
| maaslin_write_results_lefse_format | 14.667 | 0.136 | 14.805 | |
| preprocess_dna_mtx | 0.004 | 0.000 | 0.004 | |
| preprocess_taxa_mtx | 0.004 | 0.000 | 0.004 | |