William Nickols
| Snapshot Date: 2025-12-11 13:45 -0500 (Thu, 11 Dec 2025) |
| 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 Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-12-15 12:05 -0500 (Mon, 15 Dec 2025).
| 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" | 4882 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4673 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4607 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4671 |
| 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 | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | 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: 2025-12-12 01:52:40 -0500 (Fri, 12 Dec 2025) |
| EndedAt: 2025-12-12 02:14:42 -0500 (Fri, 12 Dec 2025) |
| EllapsedTime: 1322.4 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 44.146 0.371 44.476
maaslin_plot_results_from_output 43.924 0.314 44.242
maaslin3 20.403 0.576 20.982
maaslin_contrast_test 18.670 0.520 19.192
maaslin_write_results_lefse_format 14.336 0.129 14.465
maaslin_write_results 13.820 0.194 14.017
maaslin_fit 12.018 0.139 12.157
* 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")
2025-12-12 01:58:58.480969 WARNING::Fitting problem for feature 50 returning NA
2025-12-12 01:58:58.57069 WARNING::Fitting problem for feature 62 returning NA
2025-12-12 01:58:58.668964 WARNING::Fitting problem for feature 74 returning NA
2025-12-12 01:58:58.691052 WARNING::Fitting problem for feature 78 returning NA
2025-12-12 01:58:58.725983 WARNING::Fitting problem for feature 84 returning NA
2025-12-12 01:58:58.803059 WARNING::Fitting problem for feature 96 returning NA
2025-12-12 01:58:58.815022 WARNING::Fitting problem for feature 97 returning NA
2025-12-12 01:58:58.826826 WARNING::Fitting problem for feature 99 returning NA
2025-12-12 01:58:58.920992 WARNING::Fitting problem for feature 114 returning NA
2025-12-12 01:58:58.926358 WARNING::Fitting problem for feature 115 returning NA
2025-12-12 01:58:58.97682 WARNING::Fitting problem for feature 123 returning NA
2025-12-12 01:58:59.025911 WARNING::Fitting problem for feature 130 returning NA
2025-12-12 01:58:59.038452 WARNING::Fitting problem for feature 132 returning NA
2025-12-12 01:58:59.08 WARNING::Fitting problem for feature 139 returning NA
2025-12-12 01:58:59.150797 WARNING::Fitting problem for feature 150 returning NA
2025-12-12 01:59:14.187078 WARNING::Fitting problem for feature 50 returning NA
2025-12-12 01:59:14.278037 WARNING::Fitting problem for feature 62 returning NA
2025-12-12 01:59:14.350491 WARNING::Fitting problem for feature 74 returning NA
2025-12-12 01:59:14.371609 WARNING::Fitting problem for feature 78 returning NA
2025-12-12 01:59:14.404998 WARNING::Fitting problem for feature 84 returning NA
2025-12-12 01:59:14.478794 WARNING::Fitting problem for feature 96 returning NA
2025-12-12 01:59:14.483937 WARNING::Fitting problem for feature 97 returning NA
2025-12-12 01:59:14.495595 WARNING::Fitting problem for feature 99 returning NA
2025-12-12 01:59:14.588238 WARNING::Fitting problem for feature 114 returning NA
2025-12-12 01:59:14.593479 WARNING::Fitting problem for feature 115 returning NA
2025-12-12 01:59:14.641896 WARNING::Fitting problem for feature 123 returning NA
2025-12-12 01:59:14.680995 WARNING::Fitting problem for feature 130 returning NA
2025-12-12 01:59:14.692706 WARNING::Fitting problem for feature 132 returning NA
2025-12-12 01:59:14.733956 WARNING::Fitting problem for feature 139 returning NA
2025-12-12 01:59:14.818216 WARNING::Fitting problem for feature 150 returning NA
2025-12-12 01:59:40.476984 WARNING::Fitting problem for feature 50 returning NA
2025-12-12 01:59:40.55447 WARNING::Fitting problem for feature 62 returning NA
2025-12-12 01:59:40.631487 WARNING::Fitting problem for feature 74 returning NA
2025-12-12 01:59:40.65442 WARNING::Fitting problem for feature 78 returning NA
2025-12-12 01:59:40.689221 WARNING::Fitting problem for feature 84 returning NA
2025-12-12 01:59:40.767603 WARNING::Fitting problem for feature 96 returning NA
2025-12-12 01:59:40.772953 WARNING::Fitting problem for feature 97 returning NA
2025-12-12 01:59:40.784787 WARNING::Fitting problem for feature 99 returning NA
2025-12-12 01:59:40.881801 WARNING::Fitting problem for feature 114 returning NA
2025-12-12 01:59:40.887408 WARNING::Fitting problem for feature 115 returning NA
2025-12-12 01:59:40.938065 WARNING::Fitting problem for feature 123 returning NA
2025-12-12 01:59:40.977418 WARNING::Fitting problem for feature 130 returning NA
2025-12-12 01:59:40.988976 WARNING::Fitting problem for feature 132 returning NA
2025-12-12 01:59:41.029139 WARNING::Fitting problem for feature 139 returning NA
2025-12-12 01:59:41.098622 WARNING::Fitting problem for feature 150 returning NA
2025-12-12 01:59:53.872086 WARNING::Fitting problem for feature 50 returning NA
2025-12-12 01:59:53.949525 WARNING::Fitting problem for feature 62 returning NA
2025-12-12 01:59:54.028521 WARNING::Fitting problem for feature 74 returning NA
2025-12-12 01:59:54.052992 WARNING::Fitting problem for feature 78 returning NA
2025-12-12 01:59:54.088015 WARNING::Fitting problem for feature 84 returning NA
2025-12-12 01:59:54.164481 WARNING::Fitting problem for feature 96 returning NA
2025-12-12 01:59:54.169777 WARNING::Fitting problem for feature 97 returning NA
2025-12-12 01:59:54.181767 WARNING::Fitting problem for feature 99 returning NA
2025-12-12 01:59:54.276686 WARNING::Fitting problem for feature 114 returning NA
2025-12-12 01:59:54.282017 WARNING::Fitting problem for feature 115 returning NA
2025-12-12 01:59:54.331551 WARNING::Fitting problem for feature 123 returning NA
2025-12-12 01:59:54.376936 WARNING::Fitting problem for feature 130 returning NA
2025-12-12 01:59:54.389154 WARNING::Fitting problem for feature 132 returning NA
2025-12-12 01:59:54.430005 WARNING::Fitting problem for feature 139 returning NA
2025-12-12 01:59:54.500501 WARNING::Fitting problem for feature 150 returning NA
2025-12-12 01:59:54.726769 WARNING::Deleting existing residuals file: /tmp/RtmpUKQWJM/fileeabec7808bd28/fits/residuals_linear.rds
2025-12-12 01:59:54.788488 WARNING::Deleting existing fitted file: /tmp/RtmpUKQWJM/fileeabec7808bd28/fits/fitted_linear.rds
2025-12-12 01:59:54.852411 WARNING::Deleting existing residuals file: /tmp/RtmpUKQWJM/fileeabec7808bd28/fits/residuals_logistic.rds
2025-12-12 01:59:55.159639 WARNING::Deleting existing fitted file: /tmp/RtmpUKQWJM/fileeabec7808bd28/fits/fitted_logistic.rds
2025-12-12 02:00:18.042905 WARNING::Fitting problem for feature 50 returning NA
2025-12-12 02:00:18.135861 WARNING::Fitting problem for feature 62 returning NA
2025-12-12 02:00:18.222394 WARNING::Fitting problem for feature 74 returning NA
2025-12-12 02:00:18.247383 WARNING::Fitting problem for feature 78 returning NA
2025-12-12 02:00:18.286655 WARNING::Fitting problem for feature 84 returning NA
2025-12-12 02:00:18.373858 WARNING::Fitting problem for feature 96 returning NA
2025-12-12 02:00:18.380053 WARNING::Fitting problem for feature 97 returning NA
2025-12-12 02:00:18.393785 WARNING::Fitting problem for feature 99 returning NA
2025-12-12 02:00:18.506165 WARNING::Fitting problem for feature 114 returning NA
2025-12-12 02:00:18.513106 WARNING::Fitting problem for feature 115 returning NA
2025-12-12 02:00:18.572933 WARNING::Fitting problem for feature 123 returning NA
2025-12-12 02:00:18.621049 WARNING::Fitting problem for feature 130 returning NA
2025-12-12 02:00:18.635144 WARNING::Fitting problem for feature 132 returning NA
2025-12-12 02:00:18.68252 WARNING::Fitting problem for feature 139 returning NA
2025-12-12 02:00:18.763424 WARNING::Fitting problem for feature 150 returning NA
2025-12-12 02:00:30.531728 WARNING::Fitting problem for feature 50 returning NA
2025-12-12 02:00:30.607734 WARNING::Fitting problem for feature 62 returning NA
2025-12-12 02:00:30.681998 WARNING::Fitting problem for feature 74 returning NA
2025-12-12 02:00:30.703846 WARNING::Fitting problem for feature 78 returning NA
2025-12-12 02:00:30.737551 WARNING::Fitting problem for feature 84 returning NA
2025-12-12 02:00:30.81213 WARNING::Fitting problem for feature 96 returning NA
2025-12-12 02:00:30.817539 WARNING::Fitting problem for feature 97 returning NA
2025-12-12 02:00:30.829386 WARNING::Fitting problem for feature 99 returning NA
2025-12-12 02:00:30.924459 WARNING::Fitting problem for feature 114 returning NA
2025-12-12 02:00:30.929878 WARNING::Fitting problem for feature 115 returning NA
2025-12-12 02:00:31.005501 WARNING::Fitting problem for feature 123 returning NA
2025-12-12 02:00:31.045918 WARNING::Fitting problem for feature 130 returning NA
2025-12-12 02:00:31.057721 WARNING::Fitting problem for feature 132 returning NA
2025-12-12 02:00:31.098236 WARNING::Fitting problem for feature 139 returning NA
2025-12-12 02:00:31.168684 WARNING::Fitting problem for feature 150 returning NA
2025-12-12 02:00:31.372021 WARNING::Deleting existing residuals file: /tmp/RtmpUKQWJM/fileeabec7808bd28/fits/residuals_linear.rds
2025-12-12 02:00:31.433177 WARNING::Deleting existing fitted file: /tmp/RtmpUKQWJM/fileeabec7808bd28/fits/fitted_linear.rds
2025-12-12 02:00:31.49607 WARNING::Deleting existing residuals file: /tmp/RtmpUKQWJM/fileeabec7808bd28/fits/residuals_logistic.rds
2025-12-12 02:00:31.795269 WARNING::Deleting existing fitted file: /tmp/RtmpUKQWJM/fileeabec7808bd28/fits/fitted_logistic.rds
2025-12-12 02:00:53.407081 WARNING::Fitting problem for feature 50 returning NA
2025-12-12 02:00:53.48681 WARNING::Fitting problem for feature 62 returning NA
2025-12-12 02:00:53.565224 WARNING::Fitting problem for feature 74 returning NA
2025-12-12 02:00:53.589149 WARNING::Fitting problem for feature 78 returning NA
2025-12-12 02:00:53.626062 WARNING::Fitting problem for feature 84 returning NA
2025-12-12 02:00:53.705628 WARNING::Fitting problem for feature 96 returning NA
2025-12-12 02:00:53.711177 WARNING::Fitting problem for feature 97 returning NA
2025-12-12 02:00:53.72343 WARNING::Fitting problem for feature 99 returning NA
2025-12-12 02:00:53.821329 WARNING::Fitting problem for feature 114 returning NA
2025-12-12 02:00:53.826973 WARNING::Fitting problem for feature 115 returning NA
2025-12-12 02:00:53.878096 WARNING::Fitting problem for feature 123 returning NA
2025-12-12 02:00:53.919679 WARNING::Fitting problem for feature 130 returning NA
2025-12-12 02:00:53.932447 WARNING::Fitting problem for feature 132 returning NA
2025-12-12 02:00:53.978885 WARNING::Fitting problem for feature 139 returning NA
2025-12-12 02:00:54.049182 WARNING::Fitting problem for feature 150 returning NA
2025-12-12 02:01:06.928386 WARNING::Fitting problem for feature 50 returning NA
2025-12-12 02:01:07.003789 WARNING::Fitting problem for feature 62 returning NA
2025-12-12 02:01:07.077465 WARNING::Fitting problem for feature 74 returning NA
2025-12-12 02:01:07.099331 WARNING::Fitting problem for feature 78 returning NA
2025-12-12 02:01:07.138012 WARNING::Fitting problem for feature 84 returning NA
2025-12-12 02:01:07.218446 WARNING::Fitting problem for feature 96 returning NA
2025-12-12 02:01:07.223708 WARNING::Fitting problem for feature 97 returning NA
2025-12-12 02:01:07.235368 WARNING::Fitting problem for feature 99 returning NA
2025-12-12 02:01:07.331396 WARNING::Fitting problem for feature 114 returning NA
2025-12-12 02:01:07.336776 WARNING::Fitting problem for feature 115 returning NA
2025-12-12 02:01:07.384855 WARNING::Fitting problem for feature 123 returning NA
2025-12-12 02:01:07.423831 WARNING::Fitting problem for feature 130 returning NA
2025-12-12 02:01:07.435466 WARNING::Fitting problem for feature 132 returning NA
2025-12-12 02:01:07.474818 WARNING::Fitting problem for feature 139 returning NA
2025-12-12 02:01:07.543482 WARNING::Fitting problem for feature 150 returning NA
2025-12-12 02:01:07.763814 WARNING::Deleting existing residuals file: /tmp/RtmpUKQWJM/fileeabec7808bd28/fits/residuals_linear.rds
2025-12-12 02:01:07.824679 WARNING::Deleting existing fitted file: /tmp/RtmpUKQWJM/fileeabec7808bd28/fits/fitted_linear.rds
2025-12-12 02:01:07.887792 WARNING::Deleting existing residuals file: /tmp/RtmpUKQWJM/fileeabec7808bd28/fits/residuals_logistic.rds
2025-12-12 02:01:08.187616 WARNING::Deleting existing fitted file: /tmp/RtmpUKQWJM/fileeabec7808bd28/fits/fitted_logistic.rds
2025-12-12 02:01:30.370671 WARNING::Fitting problem for feature 50 returning NA
2025-12-12 02:01:30.452376 WARNING::Fitting problem for feature 62 returning NA
2025-12-12 02:01:30.539697 WARNING::Fitting problem for feature 74 returning NA
2025-12-12 02:01:30.563999 WARNING::Fitting problem for feature 78 returning NA
2025-12-12 02:01:30.601316 WARNING::Fitting problem for feature 84 returning NA
2025-12-12 02:01:30.687236 WARNING::Fitting problem for feature 96 returning NA
2025-12-12 02:01:30.693552 WARNING::Fitting problem for feature 97 returning NA
2025-12-12 02:01:30.707314 WARNING::Fitting problem for feature 99 returning NA
2025-12-12 02:01:30.84279 WARNING::Fitting problem for feature 114 returning NA
2025-12-12 02:01:30.848745 WARNING::Fitting problem for feature 115 returning NA
2025-12-12 02:01:30.904048 WARNING::Fitting problem for feature 123 returning NA
2025-12-12 02:01:30.946931 WARNING::Fitting problem for feature 130 returning NA
2025-12-12 02:01:30.959407 WARNING::Fitting problem for feature 132 returning NA
2025-12-12 02:01:31.002893 WARNING::Fitting problem for feature 139 returning NA
2025-12-12 02:01:31.083082 WARNING::Fitting problem for feature 150 returning NA
2025-12-12 02:01:42.338533 WARNING::Fitting problem for feature 50 returning NA
2025-12-12 02:01:42.420909 WARNING::Fitting problem for feature 62 returning NA
2025-12-12 02:01:42.539951 WARNING::Fitting problem for feature 74 returning NA
2025-12-12 02:01:42.56766 WARNING::Fitting problem for feature 78 returning NA
2025-12-12 02:01:42.6069 WARNING::Fitting problem for feature 84 returning NA
2025-12-12 02:01:42.693673 WARNING::Fitting problem for feature 96 returning NA
2025-12-12 02:01:42.699682 WARNING::Fitting problem for feature 97 returning NA
2025-12-12 02:01:42.712387 WARNING::Fitting problem for feature 99 returning NA
2025-12-12 02:01:42.812333 WARNING::Fitting problem for feature 114 returning NA
2025-12-12 02:01:42.817998 WARNING::Fitting problem for feature 115 returning NA
2025-12-12 02:01:42.870585 WARNING::Fitting problem for feature 123 returning NA
2025-12-12 02:01:42.913689 WARNING::Fitting problem for feature 130 returning NA
2025-12-12 02:01:42.927421 WARNING::Fitting problem for feature 132 returning NA
2025-12-12 02:01:42.970066 WARNING::Fitting problem for feature 139 returning NA
2025-12-12 02:01:43.042621 WARNING::Fitting problem for feature 150 returning NA
2025-12-12 02:02:08.582989 WARNING::Fitting problem for feature 124 returning NA
2025-12-12 02:02:18.243026 WARNING::Fitting problem for feature 124 returning NA
2025-12-12 02:02:45.133918 WARNING::Fitting problem for feature 124 returning NA
2025-12-12 02:02:54.526208 WARNING::Fitting problem for feature 124 returning NA
2025-12-12 02:02:55.178146 WARNING::Deleting existing residuals file: /tmp/RtmpUKQWJM/fileeabec238f3331/fits/residuals_linear.rds
2025-12-12 02:02:55.244322 WARNING::Deleting existing fitted file: /tmp/RtmpUKQWJM/fileeabec238f3331/fits/fitted_linear.rds
2025-12-12 02:02:55.284036 WARNING::Deleting existing residuals file: /tmp/RtmpUKQWJM/fileeabec238f3331/fits/residuals_logistic.rds
2025-12-12 02:02:55.354706 WARNING::Deleting existing fitted file: /tmp/RtmpUKQWJM/fileeabec238f3331/fits/fitted_logistic.rds
2025-12-12 02:03:19.673524 WARNING::Fitting problem for feature 124 returning NA
2025-12-12 02:03:24.880356 WARNING::Fitting problem for feature 124 returning NA
2025-12-12 02:03:25.273948 WARNING::Deleting existing residuals file: /tmp/RtmpUKQWJM/fileeabec238f3331/fits/residuals_linear.rds
2025-12-12 02:03:25.336581 WARNING::Deleting existing fitted file: /tmp/RtmpUKQWJM/fileeabec238f3331/fits/fitted_linear.rds
2025-12-12 02:03:25.375065 WARNING::Deleting existing residuals file: /tmp/RtmpUKQWJM/fileeabec238f3331/fits/residuals_logistic.rds
2025-12-12 02:03:25.44417 WARNING::Deleting existing fitted file: /tmp/RtmpUKQWJM/fileeabec238f3331/fits/fitted_logistic.rds
2025-12-12 02:03:44.653171 WARNING::Fitting problem for feature 124 returning NA
2025-12-12 02:03:51.020893 WARNING::Fitting problem for feature 124 returning NA
2025-12-12 02:03:51.339221 WARNING::Deleting existing residuals file: /tmp/RtmpUKQWJM/fileeabec238f3331/fits/residuals_linear.rds
2025-12-12 02:03:51.402993 WARNING::Deleting existing fitted file: /tmp/RtmpUKQWJM/fileeabec238f3331/fits/fitted_linear.rds
2025-12-12 02:03:51.443481 WARNING::Deleting existing residuals file: /tmp/RtmpUKQWJM/fileeabec238f3331/fits/residuals_logistic.rds
2025-12-12 02:03:51.516084 WARNING::Deleting existing fitted file: /tmp/RtmpUKQWJM/fileeabec238f3331/fits/fitted_logistic.rds
2025-12-12 02:04:09.900894 WARNING::Fitting problem for feature 50 returning NA
2025-12-12 02:04:10.006144 WARNING::Fitting problem for feature 62 returning NA
2025-12-12 02:04:10.083247 WARNING::Fitting problem for feature 74 returning NA
2025-12-12 02:04:10.105461 WARNING::Fitting problem for feature 78 returning NA
2025-12-12 02:04:10.140545 WARNING::Fitting problem for feature 84 returning NA
2025-12-12 02:04:10.218693 WARNING::Fitting problem for feature 96 returning NA
2025-12-12 02:04:10.224231 WARNING::Fitting problem for feature 97 returning NA
2025-12-12 02:04:10.236477 WARNING::Fitting problem for feature 99 returning NA
2025-12-12 02:04:10.336805 WARNING::Fitting problem for feature 114 returning NA
2025-12-12 02:04:10.342278 WARNING::Fitting problem for feature 115 returning NA
2025-12-12 02:04:10.393335 WARNING::Fitting problem for feature 123 returning NA
2025-12-12 02:04:10.435904 WARNING::Fitting problem for feature 130 returning NA
2025-12-12 02:04:10.448383 WARNING::Fitting problem for feature 132 returning NA
2025-12-12 02:04:10.488664 WARNING::Fitting problem for feature 139 returning NA
2025-12-12 02:04:10.556892 WARNING::Fitting problem for feature 150 returning NA
2025-12-12 02:04:22.824635 WARNING::Fitting problem for feature 50 returning NA
2025-12-12 02:04:22.903711 WARNING::Fitting problem for feature 62 returning NA
2025-12-12 02:04:22.981298 WARNING::Fitting problem for feature 74 returning NA
2025-12-12 02:04:23.003832 WARNING::Fitting problem for feature 78 returning NA
2025-12-12 02:04:23.039903 WARNING::Fitting problem for feature 84 returning NA
2025-12-12 02:04:23.121299 WARNING::Fitting problem for feature 96 returning NA
2025-12-12 02:04:23.126934 WARNING::Fitting problem for feature 97 returning NA
2025-12-12 02:04:23.139612 WARNING::Fitting problem for feature 99 returning NA
2025-12-12 02:04:23.239578 WARNING::Fitting problem for feature 114 returning NA
2025-12-12 02:04:23.245157 WARNING::Fitting problem for feature 115 returning NA
2025-12-12 02:04:23.296127 WARNING::Fitting problem for feature 123 returning NA
2025-12-12 02:04:23.338791 WARNING::Fitting problem for feature 130 returning NA
2025-12-12 02:04:23.351062 WARNING::Fitting problem for feature 132 returning NA
2025-12-12 02:04:23.392424 WARNING::Fitting problem for feature 139 returning NA
2025-12-12 02:04:23.46434 WARNING::Fitting problem for feature 150 returning NA
2025-12-12 02:04:23.726586 WARNING::Deleting existing residuals file: /tmp/RtmpUKQWJM/fileeabec238f3331/fits/residuals_linear.rds
2025-12-12 02:04:23.787779 WARNING::Deleting existing fitted file: /tmp/RtmpUKQWJM/fileeabec238f3331/fits/fitted_linear.rds
2025-12-12 02:04:23.851142 WARNING::Deleting existing residuals file: /tmp/RtmpUKQWJM/fileeabec238f3331/fits/residuals_logistic.rds
2025-12-12 02:04:24.150666 WARNING::Deleting existing fitted file: /tmp/RtmpUKQWJM/fileeabec238f3331/fits/fitted_logistic.rds
2025-12-12 02:04:45.262944 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-12-12 02:04:45.280691 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-12-12 02:04:45.292744 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-12-12 02:04:45.348895 ERROR::No fixed, group, or
ordered effects included in formula.
2025-12-12 02:04:45.366218 ERROR::Effect name not found in metadata: d
2025-12-12 02:04:45.377796 ERROR::No user formula provided
2025-12-12 02:04:45.409912 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-12-12 02:04:45.422602 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-12-12 02:04:48.385117 INFO::Writing function arguments to log file
2025-12-12 02:04:48.399412 INFO::Verifying options selected are valid
2025-12-12 02:04:50.816137 INFO::Writing function arguments to log file
2025-12-12 02:04:50.828218 INFO::Verifying options selected are valid
2025-12-12 02:04:50.8294 INFO::Determining format of input files
2025-12-12 02:04:50.830453 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-12 02:04:50.83291 INFO::Running selected normalization method: TSS
2025-12-12 02:04:50.834465 INFO::Creating output feature tables folder
2025-12-12 02:04:50.835487 INFO::Writing normalized data to file /tmp/RtmpUKQWJM/fileeabec265233ad/features/data_norm.tsv
2025-12-12 02:04:50.837163 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-12-12 02:04:50.838131 INFO::Total samples in data: 16
2025-12-12 02:04:50.839037 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-12-12 02:04:50.839908 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-12-12 02:04:50.841931 INFO::Total filtered features: 0
2025-12-12 02:04:50.842893 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-12-12 02:04:50.844028 INFO::Total features filtered by non-zero variance filtering: 0
2025-12-12 02:04:50.844962 INFO::Filtered feature names from variance filtering:
2025-12-12 02:04:50.84583 INFO::Writing filtered data to file /tmp/RtmpUKQWJM/fileeabec265233ad/features/filtered_data.tsv
2025-12-12 02:04:50.847426 INFO::Running selected transform method: LOG
2025-12-12 02:04:50.848712 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpUKQWJM/fileeabec265233ad/features/data_transformed.tsv
2025-12-12 02:04:50.850476 INFO::Applying z-score to standardize continuous metadata
2025-12-12 02:04:50.856175 INFO::Running the linear model component
2025-12-12 02:04:50.870034 INFO::Fitting model to feature number 1, a
2025-12-12 02:04:50.874977 INFO::Fitting model to feature number 2, b
2025-12-12 02:04:50.879516 INFO::Fitting model to feature number 3, c
2025-12-12 02:04:50.886999 INFO::Counting total values for each feature
2025-12-12 02:04:50.888874 INFO::Running the logistic model component
2025-12-12 02:04:50.902634 INFO::Fitting model to feature number 1, a
2025-12-12 02:04:50.909414 INFO::Fitting model to feature number 2, b
2025-12-12 02:04:50.916131 INFO::Fitting model to feature number 3, c
2025-12-12 02:04:50.925314 INFO::Counting total values for each feature
2025-12-12 02:04:50.927605 INFO::Re-running abundances for warn_prevalence
2025-12-12 02:04:50.928564 INFO::Running selected normalization method: TSS
2025-12-12 02:04:50.930053 INFO::Running selected transform method: LOG
2025-12-12 02:04:50.943793 INFO::Fitting model to feature number 1, a
2025-12-12 02:04:50.948451 INFO::Fitting model to feature number 2, b
2025-12-12 02:04:50.952834 INFO::Fitting model to feature number 3, c
2025-12-12 02:04:51.044739 INFO::Creating fits folder
2025-12-12 02:04:51.045964 INFO::Writing residuals to file /tmp/RtmpUKQWJM/fileeabec265233ad/fits/residuals_linear.rds
2025-12-12 02:04:51.047158 INFO::Writing fitted values to file /tmp/RtmpUKQWJM/fileeabec265233ad/fits/fitted_linear.rds
2025-12-12 02:04:51.048407 INFO::Writing residuals to file /tmp/RtmpUKQWJM/fileeabec265233ad/fits/residuals_logistic.rds
2025-12-12 02:04:51.049595 INFO::Writing fitted values to file /tmp/RtmpUKQWJM/fileeabec265233ad/fits/fitted_logistic.rds
2025-12-12 02:04:51.052264 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpUKQWJM/fileeabec265233ad/all_results.tsv
2025-12-12 02:04:51.05391 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/RtmpUKQWJM/fileeabec265233ad/significant_results.tsv
2025-12-12 02:04:51.055253 INFO::Creating output figures folder
2025-12-12 02:04:51.056615 INFO::Writing summary plot of significant
results to file: /tmp/RtmpUKQWJM/fileeabec265233ad/figures/summary_plot.pdf
2025-12-12 02:04:52.76154 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpUKQWJM/fileeabec265233ad/figures
2025-12-12 02:04:52.76368 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-12 02:04:52.76888 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-12 02:04:53.343807 INFO::Writing summary plot of
significant results to file: /tmp/RtmpUKQWJM/fileeabec265233ad/figures/summary_plot.pdf
2025-12-12 02:04:55.050132 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpUKQWJM/fileeabec265233ad/figures
2025-12-12 02:04:55.051919 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-12 02:04:55.057591 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-12 02:04:55.64276 INFO::Running the linear model component
2025-12-12 02:04:55.652435 INFO::Fitting model to feature number 1, a
2025-12-12 02:04:55.657244 INFO::Fitting model to feature number 2, b
2025-12-12 02:04:55.661631 INFO::Fitting model to feature number 3, c
2025-12-12 02:04:55.669104 INFO::Counting total values for each feature
2025-12-12 02:04:55.670922 INFO::Running the logistic model component
2025-12-12 02:04:55.679489 INFO::Fitting model to feature number 1, a
2025-12-12 02:04:55.685994 INFO::Fitting model to feature number 2, b
2025-12-12 02:04:55.692094 INFO::Fitting model to feature number 3, c
2025-12-12 02:04:55.70119 INFO::Counting total values for each feature
2025-12-12 02:04:55.703306 INFO::Re-running abundances for warn_prevalence
2025-12-12 02:04:55.704114 INFO::Running selected normalization method: TSS
2025-12-12 02:04:55.705468 INFO::Running selected transform method: LOG
2025-12-12 02:04:55.714207 INFO::Fitting model to feature number 1, a
2025-12-12 02:04:55.718612 INFO::Fitting model to feature number 2, b
2025-12-12 02:04:55.722796 INFO::Fitting model to feature number 3, c
2025-12-12 02:04:55.819228 INFO::Creating output folder
2025-12-12 02:04:55.820364 INFO::Creating output figures folder
2025-12-12 02:04:55.821786 INFO::Writing summary plot of significant
results to file: /tmp/RtmpUKQWJM/fileeabec22715c97/figures/summary_plot.pdf
2025-12-12 02:04:57.549483 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpUKQWJM/fileeabec22715c97/figures
2025-12-12 02:04:57.551201 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-12 02:04:57.556158 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-12 02:04:58.534555 INFO::Applying z-score to standardize continuous metadata
2025-12-12 02:04:58.543625 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-12-12 02:04:58.54468 INFO::Bypass z-score application to metadata
2025-12-12 02:04:58.564295 INFO::Bypass z-score application to metadata
2025-12-12 02:04:58.58545 INFO::Determining format of input files
2025-12-12 02:04:58.586452 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-12 02:04:58.587316 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-12-12 02:04:58.59485 INFO::Determining format of input files
2025-12-12 02:04:58.595942 INFO::Input format is data samples as columns and metadata samples as rows
2025-12-12 02:04:58.597273 INFO::Input format is feature_specific_covariate samples as columns
2025-12-12 02:04:58.605638 INFO::Determining format of input files
2025-12-12 02:04:58.606669 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-12 02:04:58.607707 INFO::Input format is feature_specific_covariate samples as columns
2025-12-12 02:04:58.609374 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-12-12 02:04:58.610154 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-12-12 02:04:58.622045 INFO::Running selected transform method: LOG
2025-12-12 02:04:58.623271 INFO::Creating output feature tables folder
2025-12-12 02:04:58.624161 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpUKQWJM/fileeabec51414acb/features/data_transformed.tsv
2025-12-12 02:04:58.628279 INFO::Running selected transform method: LOG
2025-12-12 02:04:58.629385 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpUKQWJM/fileeabec51414acb/features/data_transformed.tsv
2025-12-12 02:04:58.633583 INFO::Running selected transform method: PLOG
2025-12-12 02:04:58.635248 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpUKQWJM/fileeabec51414acb/features/data_transformed.tsv
2025-12-12 02:04:58.638255 INFO::Running selected transform method: NONE
2025-12-12 02:04:58.639005 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpUKQWJM/fileeabec51414acb/features/data_transformed.tsv
2025-12-12 02:04:58.646949 INFO::Running the linear model component
2025-12-12 02:04:58.655944 INFO::Fitting model to feature number 1, a
2025-12-12 02:04:58.660264 INFO::Fitting model to feature number 2, b
2025-12-12 02:04:58.66436 INFO::Fitting model to feature number 3, c
2025-12-12 02:04:58.671402 INFO::Counting total values for each feature
2025-12-12 02:04:58.673121 INFO::Running the logistic model component
2025-12-12 02:04:58.68169 INFO::Fitting model to feature number 1, a
2025-12-12 02:04:58.688186 INFO::Fitting model to feature number 2, b
2025-12-12 02:04:58.694291 INFO::Fitting model to feature number 3, c
2025-12-12 02:04:58.703765 INFO::Counting total values for each feature
2025-12-12 02:04:58.705861 INFO::Re-running abundances for warn_prevalence
2025-12-12 02:04:58.706679 INFO::Running selected normalization method: TSS
2025-12-12 02:04:58.708046 INFO::Running selected transform method: LOG
2025-12-12 02:04:58.716622 INFO::Fitting model to feature number 1, a
2025-12-12 02:04:58.721032 INFO::Fitting model to feature number 2, b
2025-12-12 02:04:58.725113 INFO::Fitting model to feature number 3, c
2025-12-12 02:04:58.819129 INFO::Creating output folder
2025-12-12 02:04:58.820189 INFO::Creating fits folder
2025-12-12 02:04:58.821033 INFO::Writing residuals to file /tmp/RtmpUKQWJM/fileeabec770399d4/fits/residuals_linear.rds
2025-12-12 02:04:58.822056 INFO::Writing fitted values to file /tmp/RtmpUKQWJM/fileeabec770399d4/fits/fitted_linear.rds
2025-12-12 02:04:58.823195 INFO::Writing residuals to file /tmp/RtmpUKQWJM/fileeabec770399d4/fits/residuals_logistic.rds
2025-12-12 02:04:58.824252 INFO::Writing fitted values to file /tmp/RtmpUKQWJM/fileeabec770399d4/fits/fitted_logistic.rds
2025-12-12 02:04:58.82675 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpUKQWJM/fileeabec770399d4/all_results.tsv
2025-12-12 02:04:58.828212 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/RtmpUKQWJM/fileeabec770399d4/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
363.513 8.133 371.637
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 20.403 | 0.576 | 20.982 | |
| maaslin_check_arguments | 0.138 | 0.000 | 0.138 | |
| maaslin_check_formula | 0.137 | 0.001 | 0.139 | |
| maaslin_compute_formula | 0.156 | 0.003 | 0.159 | |
| maaslin_contrast_test | 18.670 | 0.520 | 19.192 | |
| maaslin_filter | 0.421 | 0.006 | 0.426 | |
| maaslin_fit | 12.018 | 0.139 | 12.157 | |
| maaslin_log_arguments | 0.129 | 0.002 | 0.130 | |
| maaslin_normalize | 0.271 | 0.018 | 0.289 | |
| maaslin_plot_results | 44.146 | 0.371 | 44.476 | |
| maaslin_plot_results_from_output | 43.924 | 0.314 | 44.242 | |
| maaslin_process_metadata | 0.450 | 0.005 | 0.457 | |
| maaslin_read_data | 0.121 | 0.003 | 0.123 | |
| maaslin_reorder_data | 0.130 | 0.002 | 0.132 | |
| maaslin_transform | 0.575 | 0.009 | 0.585 | |
| maaslin_write_results | 13.820 | 0.194 | 14.017 | |
| maaslin_write_results_lefse_format | 14.336 | 0.129 | 14.465 | |
| preprocess_dna_mtx | 0.005 | 0.000 | 0.004 | |
| preprocess_taxa_mtx | 0.004 | 0.000 | 0.003 | |