William Nickols
| Snapshot Date: 2026-02-16 13:45 -0500 (Mon, 16 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 2026-02-18 11:57 -0500 (Wed, 18 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: 2026-02-17 01:41:44 -0500 (Tue, 17 Feb 2026) |
| EndedAt: 2026-02-17 02:03:14 -0500 (Tue, 17 Feb 2026) |
| EllapsedTime: 1290.3 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 44.357 0.262 44.577
maaslin_plot_results_from_output 43.696 0.293 43.993
maaslin3 20.472 0.533 21.008
maaslin_contrast_test 19.174 0.324 19.498
maaslin_write_results_lefse_format 14.946 0.101 15.049
maaslin_write_results 14.361 0.163 14.525
maaslin_fit 12.886 0.059 12.946
* 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")
2026-02-17 01:48:07.3397 WARNING::Fitting problem for feature 50 returning NA
2026-02-17 01:48:07.429611 WARNING::Fitting problem for feature 62 returning NA
2026-02-17 01:48:07.534571 WARNING::Fitting problem for feature 74 returning NA
2026-02-17 01:48:07.556338 WARNING::Fitting problem for feature 78 returning NA
2026-02-17 01:48:07.590669 WARNING::Fitting problem for feature 84 returning NA
2026-02-17 01:48:07.667209 WARNING::Fitting problem for feature 96 returning NA
2026-02-17 01:48:07.689463 WARNING::Fitting problem for feature 97 returning NA
2026-02-17 01:48:07.702285 WARNING::Fitting problem for feature 99 returning NA
2026-02-17 01:48:07.797914 WARNING::Fitting problem for feature 114 returning NA
2026-02-17 01:48:07.80314 WARNING::Fitting problem for feature 115 returning NA
2026-02-17 01:48:07.851779 WARNING::Fitting problem for feature 123 returning NA
2026-02-17 01:48:07.899564 WARNING::Fitting problem for feature 130 returning NA
2026-02-17 01:48:07.911503 WARNING::Fitting problem for feature 132 returning NA
2026-02-17 01:48:07.951499 WARNING::Fitting problem for feature 139 returning NA
2026-02-17 01:48:08.020697 WARNING::Fitting problem for feature 150 returning NA
2026-02-17 01:48:23.705085 WARNING::Fitting problem for feature 50 returning NA
2026-02-17 01:48:23.781731 WARNING::Fitting problem for feature 62 returning NA
2026-02-17 01:48:23.854335 WARNING::Fitting problem for feature 74 returning NA
2026-02-17 01:48:23.876343 WARNING::Fitting problem for feature 78 returning NA
2026-02-17 01:48:23.910522 WARNING::Fitting problem for feature 84 returning NA
2026-02-17 01:48:23.999125 WARNING::Fitting problem for feature 96 returning NA
2026-02-17 01:48:24.004396 WARNING::Fitting problem for feature 97 returning NA
2026-02-17 01:48:24.016096 WARNING::Fitting problem for feature 99 returning NA
2026-02-17 01:48:24.111126 WARNING::Fitting problem for feature 114 returning NA
2026-02-17 01:48:24.116372 WARNING::Fitting problem for feature 115 returning NA
2026-02-17 01:48:24.165572 WARNING::Fitting problem for feature 123 returning NA
2026-02-17 01:48:24.204854 WARNING::Fitting problem for feature 130 returning NA
2026-02-17 01:48:24.216405 WARNING::Fitting problem for feature 132 returning NA
2026-02-17 01:48:24.256231 WARNING::Fitting problem for feature 139 returning NA
2026-02-17 01:48:24.322372 WARNING::Fitting problem for feature 150 returning NA
2026-02-17 01:48:48.924832 WARNING::Fitting problem for feature 50 returning NA
2026-02-17 01:48:49.004075 WARNING::Fitting problem for feature 62 returning NA
2026-02-17 01:48:49.078632 WARNING::Fitting problem for feature 74 returning NA
2026-02-17 01:48:49.10014 WARNING::Fitting problem for feature 78 returning NA
2026-02-17 01:48:49.134316 WARNING::Fitting problem for feature 84 returning NA
2026-02-17 01:48:49.209691 WARNING::Fitting problem for feature 96 returning NA
2026-02-17 01:48:49.214987 WARNING::Fitting problem for feature 97 returning NA
2026-02-17 01:48:49.226943 WARNING::Fitting problem for feature 99 returning NA
2026-02-17 01:48:49.320207 WARNING::Fitting problem for feature 114 returning NA
2026-02-17 01:48:49.325484 WARNING::Fitting problem for feature 115 returning NA
2026-02-17 01:48:49.374613 WARNING::Fitting problem for feature 123 returning NA
2026-02-17 01:48:49.415333 WARNING::Fitting problem for feature 130 returning NA
2026-02-17 01:48:49.427565 WARNING::Fitting problem for feature 132 returning NA
2026-02-17 01:48:49.468895 WARNING::Fitting problem for feature 139 returning NA
2026-02-17 01:48:49.537701 WARNING::Fitting problem for feature 150 returning NA
2026-02-17 01:49:02.969159 WARNING::Fitting problem for feature 50 returning NA
2026-02-17 01:49:03.072999 WARNING::Fitting problem for feature 62 returning NA
2026-02-17 01:49:03.151314 WARNING::Fitting problem for feature 74 returning NA
2026-02-17 01:49:03.173542 WARNING::Fitting problem for feature 78 returning NA
2026-02-17 01:49:03.208565 WARNING::Fitting problem for feature 84 returning NA
2026-02-17 01:49:03.283323 WARNING::Fitting problem for feature 96 returning NA
2026-02-17 01:49:03.288601 WARNING::Fitting problem for feature 97 returning NA
2026-02-17 01:49:03.300289 WARNING::Fitting problem for feature 99 returning NA
2026-02-17 01:49:03.395282 WARNING::Fitting problem for feature 114 returning NA
2026-02-17 01:49:03.400789 WARNING::Fitting problem for feature 115 returning NA
2026-02-17 01:49:03.451621 WARNING::Fitting problem for feature 123 returning NA
2026-02-17 01:49:03.49318 WARNING::Fitting problem for feature 130 returning NA
2026-02-17 01:49:03.505319 WARNING::Fitting problem for feature 132 returning NA
2026-02-17 01:49:03.546858 WARNING::Fitting problem for feature 139 returning NA
2026-02-17 01:49:03.617901 WARNING::Fitting problem for feature 150 returning NA
2026-02-17 01:49:03.822521 WARNING::Deleting existing residuals file: /tmp/RtmpN5h4M3/file1d3a0048deff05/fits/residuals_linear.rds
2026-02-17 01:49:03.883684 WARNING::Deleting existing fitted file: /tmp/RtmpN5h4M3/file1d3a0048deff05/fits/fitted_linear.rds
2026-02-17 01:49:03.946772 WARNING::Deleting existing residuals file: /tmp/RtmpN5h4M3/file1d3a0048deff05/fits/residuals_logistic.rds
2026-02-17 01:49:04.248409 WARNING::Deleting existing fitted file: /tmp/RtmpN5h4M3/file1d3a0048deff05/fits/fitted_logistic.rds
2026-02-17 01:49:26.74982 WARNING::Fitting problem for feature 50 returning NA
2026-02-17 01:49:26.840799 WARNING::Fitting problem for feature 62 returning NA
2026-02-17 01:49:26.957037 WARNING::Fitting problem for feature 74 returning NA
2026-02-17 01:49:26.979934 WARNING::Fitting problem for feature 78 returning NA
2026-02-17 01:49:27.015768 WARNING::Fitting problem for feature 84 returning NA
2026-02-17 01:49:27.094923 WARNING::Fitting problem for feature 96 returning NA
2026-02-17 01:49:27.100277 WARNING::Fitting problem for feature 97 returning NA
2026-02-17 01:49:27.112151 WARNING::Fitting problem for feature 99 returning NA
2026-02-17 01:49:27.208819 WARNING::Fitting problem for feature 114 returning NA
2026-02-17 01:49:27.214417 WARNING::Fitting problem for feature 115 returning NA
2026-02-17 01:49:27.26402 WARNING::Fitting problem for feature 123 returning NA
2026-02-17 01:49:27.304539 WARNING::Fitting problem for feature 130 returning NA
2026-02-17 01:49:27.317004 WARNING::Fitting problem for feature 132 returning NA
2026-02-17 01:49:27.358678 WARNING::Fitting problem for feature 139 returning NA
2026-02-17 01:49:27.431325 WARNING::Fitting problem for feature 150 returning NA
2026-02-17 01:49:39.585297 WARNING::Fitting problem for feature 50 returning NA
2026-02-17 01:49:39.670777 WARNING::Fitting problem for feature 62 returning NA
2026-02-17 01:49:39.755328 WARNING::Fitting problem for feature 74 returning NA
2026-02-17 01:49:39.781005 WARNING::Fitting problem for feature 78 returning NA
2026-02-17 01:49:39.81946 WARNING::Fitting problem for feature 84 returning NA
2026-02-17 01:49:39.899655 WARNING::Fitting problem for feature 96 returning NA
2026-02-17 01:49:39.905158 WARNING::Fitting problem for feature 97 returning NA
2026-02-17 01:49:39.917483 WARNING::Fitting problem for feature 99 returning NA
2026-02-17 01:49:40.016374 WARNING::Fitting problem for feature 114 returning NA
2026-02-17 01:49:40.022053 WARNING::Fitting problem for feature 115 returning NA
2026-02-17 01:49:40.07327 WARNING::Fitting problem for feature 123 returning NA
2026-02-17 01:49:40.115607 WARNING::Fitting problem for feature 130 returning NA
2026-02-17 01:49:40.127989 WARNING::Fitting problem for feature 132 returning NA
2026-02-17 01:49:40.171052 WARNING::Fitting problem for feature 139 returning NA
2026-02-17 01:49:40.24108 WARNING::Fitting problem for feature 150 returning NA
2026-02-17 01:49:40.448693 WARNING::Deleting existing residuals file: /tmp/RtmpN5h4M3/file1d3a0048deff05/fits/residuals_linear.rds
2026-02-17 01:49:40.509915 WARNING::Deleting existing fitted file: /tmp/RtmpN5h4M3/file1d3a0048deff05/fits/fitted_linear.rds
2026-02-17 01:49:40.572454 WARNING::Deleting existing residuals file: /tmp/RtmpN5h4M3/file1d3a0048deff05/fits/residuals_logistic.rds
2026-02-17 01:49:40.872408 WARNING::Deleting existing fitted file: /tmp/RtmpN5h4M3/file1d3a0048deff05/fits/fitted_logistic.rds
2026-02-17 01:50:02.657194 WARNING::Fitting problem for feature 50 returning NA
2026-02-17 01:50:02.753734 WARNING::Fitting problem for feature 62 returning NA
2026-02-17 01:50:02.845116 WARNING::Fitting problem for feature 74 returning NA
2026-02-17 01:50:02.872584 WARNING::Fitting problem for feature 78 returning NA
2026-02-17 01:50:02.913291 WARNING::Fitting problem for feature 84 returning NA
2026-02-17 01:50:03.043204 WARNING::Fitting problem for feature 96 returning NA
2026-02-17 01:50:03.050687 WARNING::Fitting problem for feature 97 returning NA
2026-02-17 01:50:03.067759 WARNING::Fitting problem for feature 99 returning NA
2026-02-17 01:50:03.181332 WARNING::Fitting problem for feature 114 returning NA
2026-02-17 01:50:03.187654 WARNING::Fitting problem for feature 115 returning NA
2026-02-17 01:50:03.243192 WARNING::Fitting problem for feature 123 returning NA
2026-02-17 01:50:03.286583 WARNING::Fitting problem for feature 130 returning NA
2026-02-17 01:50:03.300026 WARNING::Fitting problem for feature 132 returning NA
2026-02-17 01:50:03.344412 WARNING::Fitting problem for feature 139 returning NA
2026-02-17 01:50:03.419842 WARNING::Fitting problem for feature 150 returning NA
2026-02-17 01:50:15.465429 WARNING::Fitting problem for feature 50 returning NA
2026-02-17 01:50:15.548661 WARNING::Fitting problem for feature 62 returning NA
2026-02-17 01:50:15.631932 WARNING::Fitting problem for feature 74 returning NA
2026-02-17 01:50:15.654699 WARNING::Fitting problem for feature 78 returning NA
2026-02-17 01:50:15.690388 WARNING::Fitting problem for feature 84 returning NA
2026-02-17 01:50:15.769298 WARNING::Fitting problem for feature 96 returning NA
2026-02-17 01:50:15.774784 WARNING::Fitting problem for feature 97 returning NA
2026-02-17 01:50:15.78716 WARNING::Fitting problem for feature 99 returning NA
2026-02-17 01:50:15.885246 WARNING::Fitting problem for feature 114 returning NA
2026-02-17 01:50:15.890941 WARNING::Fitting problem for feature 115 returning NA
2026-02-17 01:50:15.942206 WARNING::Fitting problem for feature 123 returning NA
2026-02-17 01:50:15.984865 WARNING::Fitting problem for feature 130 returning NA
2026-02-17 01:50:15.997213 WARNING::Fitting problem for feature 132 returning NA
2026-02-17 01:50:16.038924 WARNING::Fitting problem for feature 139 returning NA
2026-02-17 01:50:16.111807 WARNING::Fitting problem for feature 150 returning NA
2026-02-17 01:50:16.31421 WARNING::Deleting existing residuals file: /tmp/RtmpN5h4M3/file1d3a0048deff05/fits/residuals_linear.rds
2026-02-17 01:50:16.374983 WARNING::Deleting existing fitted file: /tmp/RtmpN5h4M3/file1d3a0048deff05/fits/fitted_linear.rds
2026-02-17 01:50:16.43771 WARNING::Deleting existing residuals file: /tmp/RtmpN5h4M3/file1d3a0048deff05/fits/residuals_logistic.rds
2026-02-17 01:50:16.737339 WARNING::Deleting existing fitted file: /tmp/RtmpN5h4M3/file1d3a0048deff05/fits/fitted_logistic.rds
2026-02-17 01:50:38.780461 WARNING::Fitting problem for feature 50 returning NA
2026-02-17 01:50:38.863292 WARNING::Fitting problem for feature 62 returning NA
2026-02-17 01:50:38.946461 WARNING::Fitting problem for feature 74 returning NA
2026-02-17 01:50:38.974055 WARNING::Fitting problem for feature 78 returning NA
2026-02-17 01:50:39.015019 WARNING::Fitting problem for feature 84 returning NA
2026-02-17 01:50:39.097066 WARNING::Fitting problem for feature 96 returning NA
2026-02-17 01:50:39.103236 WARNING::Fitting problem for feature 97 returning NA
2026-02-17 01:50:39.116327 WARNING::Fitting problem for feature 99 returning NA
2026-02-17 01:50:39.224285 WARNING::Fitting problem for feature 114 returning NA
2026-02-17 01:50:39.230368 WARNING::Fitting problem for feature 115 returning NA
2026-02-17 01:50:39.286498 WARNING::Fitting problem for feature 123 returning NA
2026-02-17 01:50:39.333922 WARNING::Fitting problem for feature 130 returning NA
2026-02-17 01:50:39.347692 WARNING::Fitting problem for feature 132 returning NA
2026-02-17 01:50:39.393078 WARNING::Fitting problem for feature 139 returning NA
2026-02-17 01:50:39.474294 WARNING::Fitting problem for feature 150 returning NA
2026-02-17 01:50:51.891684 WARNING::Fitting problem for feature 50 returning NA
2026-02-17 01:50:51.973416 WARNING::Fitting problem for feature 62 returning NA
2026-02-17 01:50:52.052093 WARNING::Fitting problem for feature 74 returning NA
2026-02-17 01:50:52.075007 WARNING::Fitting problem for feature 78 returning NA
2026-02-17 01:50:52.111165 WARNING::Fitting problem for feature 84 returning NA
2026-02-17 01:50:52.191759 WARNING::Fitting problem for feature 96 returning NA
2026-02-17 01:50:52.1977 WARNING::Fitting problem for feature 97 returning NA
2026-02-17 01:50:52.210715 WARNING::Fitting problem for feature 99 returning NA
2026-02-17 01:50:52.314157 WARNING::Fitting problem for feature 114 returning NA
2026-02-17 01:50:52.319856 WARNING::Fitting problem for feature 115 returning NA
2026-02-17 01:50:52.3727 WARNING::Fitting problem for feature 123 returning NA
2026-02-17 01:50:52.416248 WARNING::Fitting problem for feature 130 returning NA
2026-02-17 01:50:52.429428 WARNING::Fitting problem for feature 132 returning NA
2026-02-17 01:50:52.475627 WARNING::Fitting problem for feature 139 returning NA
2026-02-17 01:50:52.553919 WARNING::Fitting problem for feature 150 returning NA
2026-02-17 01:51:18.817245 WARNING::Fitting problem for feature 124 returning NA
2026-02-17 01:51:27.740413 WARNING::Fitting problem for feature 124 returning NA
2026-02-17 01:51:52.814742 WARNING::Fitting problem for feature 124 returning NA
2026-02-17 01:52:02.733166 WARNING::Fitting problem for feature 124 returning NA
2026-02-17 01:52:03.337722 WARNING::Deleting existing residuals file: /tmp/RtmpN5h4M3/file1d3a0067ab0bc5/fits/residuals_linear.rds
2026-02-17 01:52:03.399289 WARNING::Deleting existing fitted file: /tmp/RtmpN5h4M3/file1d3a0067ab0bc5/fits/fitted_linear.rds
2026-02-17 01:52:03.438478 WARNING::Deleting existing residuals file: /tmp/RtmpN5h4M3/file1d3a0067ab0bc5/fits/residuals_logistic.rds
2026-02-17 01:52:03.508159 WARNING::Deleting existing fitted file: /tmp/RtmpN5h4M3/file1d3a0067ab0bc5/fits/fitted_logistic.rds
2026-02-17 01:52:25.972431 WARNING::Fitting problem for feature 124 returning NA
2026-02-17 01:52:31.092085 WARNING::Fitting problem for feature 124 returning NA
2026-02-17 01:52:31.403477 WARNING::Deleting existing residuals file: /tmp/RtmpN5h4M3/file1d3a0067ab0bc5/fits/residuals_linear.rds
2026-02-17 01:52:31.465608 WARNING::Deleting existing fitted file: /tmp/RtmpN5h4M3/file1d3a0067ab0bc5/fits/fitted_linear.rds
2026-02-17 01:52:31.504444 WARNING::Deleting existing residuals file: /tmp/RtmpN5h4M3/file1d3a0067ab0bc5/fits/residuals_logistic.rds
2026-02-17 01:52:31.573818 WARNING::Deleting existing fitted file: /tmp/RtmpN5h4M3/file1d3a0067ab0bc5/fits/fitted_logistic.rds
2026-02-17 01:52:50.504063 WARNING::Fitting problem for feature 124 returning NA
2026-02-17 01:52:56.936689 WARNING::Fitting problem for feature 124 returning NA
2026-02-17 01:52:57.227242 WARNING::Deleting existing residuals file: /tmp/RtmpN5h4M3/file1d3a0067ab0bc5/fits/residuals_linear.rds
2026-02-17 01:52:57.289053 WARNING::Deleting existing fitted file: /tmp/RtmpN5h4M3/file1d3a0067ab0bc5/fits/fitted_linear.rds
2026-02-17 01:52:57.327617 WARNING::Deleting existing residuals file: /tmp/RtmpN5h4M3/file1d3a0067ab0bc5/fits/residuals_logistic.rds
2026-02-17 01:52:57.396263 WARNING::Deleting existing fitted file: /tmp/RtmpN5h4M3/file1d3a0067ab0bc5/fits/fitted_logistic.rds
2026-02-17 01:53:15.769944 WARNING::Fitting problem for feature 50 returning NA
2026-02-17 01:53:15.848991 WARNING::Fitting problem for feature 62 returning NA
2026-02-17 01:53:15.926039 WARNING::Fitting problem for feature 74 returning NA
2026-02-17 01:53:15.94896 WARNING::Fitting problem for feature 78 returning NA
2026-02-17 01:53:15.985097 WARNING::Fitting problem for feature 84 returning NA
2026-02-17 01:53:16.064894 WARNING::Fitting problem for feature 96 returning NA
2026-02-17 01:53:16.070986 WARNING::Fitting problem for feature 97 returning NA
2026-02-17 01:53:16.083865 WARNING::Fitting problem for feature 99 returning NA
2026-02-17 01:53:16.186918 WARNING::Fitting problem for feature 114 returning NA
2026-02-17 01:53:16.192724 WARNING::Fitting problem for feature 115 returning NA
2026-02-17 01:53:16.246405 WARNING::Fitting problem for feature 123 returning NA
2026-02-17 01:53:16.291077 WARNING::Fitting problem for feature 130 returning NA
2026-02-17 01:53:16.304398 WARNING::Fitting problem for feature 132 returning NA
2026-02-17 01:53:16.348146 WARNING::Fitting problem for feature 139 returning NA
2026-02-17 01:53:16.419947 WARNING::Fitting problem for feature 150 returning NA
2026-02-17 01:53:28.805163 WARNING::Fitting problem for feature 50 returning NA
2026-02-17 01:53:28.882817 WARNING::Fitting problem for feature 62 returning NA
2026-02-17 01:53:28.959249 WARNING::Fitting problem for feature 74 returning NA
2026-02-17 01:53:28.981028 WARNING::Fitting problem for feature 78 returning NA
2026-02-17 01:53:29.016032 WARNING::Fitting problem for feature 84 returning NA
2026-02-17 01:53:29.092487 WARNING::Fitting problem for feature 96 returning NA
2026-02-17 01:53:29.097885 WARNING::Fitting problem for feature 97 returning NA
2026-02-17 01:53:29.109642 WARNING::Fitting problem for feature 99 returning NA
2026-02-17 01:53:29.209292 WARNING::Fitting problem for feature 114 returning NA
2026-02-17 01:53:29.215364 WARNING::Fitting problem for feature 115 returning NA
2026-02-17 01:53:29.268181 WARNING::Fitting problem for feature 123 returning NA
2026-02-17 01:53:29.310783 WARNING::Fitting problem for feature 130 returning NA
2026-02-17 01:53:29.323738 WARNING::Fitting problem for feature 132 returning NA
2026-02-17 01:53:29.365905 WARNING::Fitting problem for feature 139 returning NA
2026-02-17 01:53:29.479671 WARNING::Fitting problem for feature 150 returning NA
2026-02-17 01:53:29.719679 WARNING::Deleting existing residuals file: /tmp/RtmpN5h4M3/file1d3a0067ab0bc5/fits/residuals_linear.rds
2026-02-17 01:53:29.780565 WARNING::Deleting existing fitted file: /tmp/RtmpN5h4M3/file1d3a0067ab0bc5/fits/fitted_linear.rds
2026-02-17 01:53:29.843318 WARNING::Deleting existing residuals file: /tmp/RtmpN5h4M3/file1d3a0067ab0bc5/fits/residuals_logistic.rds
2026-02-17 01:53:30.142548 WARNING::Deleting existing fitted file: /tmp/RtmpN5h4M3/file1d3a0067ab0bc5/fits/fitted_logistic.rds
2026-02-17 01:53:50.555124 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2026-02-17 01:53:50.57423 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2026-02-17 01:53:50.586217 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2026-02-17 01:53:50.638067 ERROR::No fixed, group, or
ordered effects included in formula.
2026-02-17 01:53:50.654488 ERROR::Effect name not found in metadata: d
2026-02-17 01:53:50.66543 ERROR::No user formula provided
2026-02-17 01:53:50.696009 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2026-02-17 01:53:50.707651 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2026-02-17 01:53:53.506978 INFO::Writing function arguments to log file
2026-02-17 01:53:53.522432 INFO::Verifying options selected are valid
2026-02-17 01:53:55.838358 INFO::Writing function arguments to log file
2026-02-17 01:53:55.850279 INFO::Verifying options selected are valid
2026-02-17 01:53:55.851347 INFO::Determining format of input files
2026-02-17 01:53:55.852328 INFO::Input format is data samples as rows and metadata samples as rows
2026-02-17 01:53:55.854628 INFO::Running selected normalization method: TSS
2026-02-17 01:53:55.856053 INFO::Creating output feature tables folder
2026-02-17 01:53:55.856993 INFO::Writing normalized data to file /tmp/RtmpN5h4M3/file1d3a0056224fe4/features/data_norm.tsv
2026-02-17 01:53:55.858428 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2026-02-17 01:53:55.859313 INFO::Total samples in data: 16
2026-02-17 01:53:55.86016 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2026-02-17 01:53:55.861012 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2026-02-17 01:53:55.862892 INFO::Total filtered features: 0
2026-02-17 01:53:55.863822 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2026-02-17 01:53:55.864993 INFO::Total features filtered by non-zero variance filtering: 0
2026-02-17 01:53:55.865949 INFO::Filtered feature names from variance filtering:
2026-02-17 01:53:55.866802 INFO::Writing filtered data to file /tmp/RtmpN5h4M3/file1d3a0056224fe4/features/filtered_data.tsv
2026-02-17 01:53:55.868249 INFO::Running selected transform method: LOG
2026-02-17 01:53:55.869415 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpN5h4M3/file1d3a0056224fe4/features/data_transformed.tsv
2026-02-17 01:53:55.871002 INFO::Applying z-score to standardize continuous metadata
2026-02-17 01:53:55.875378 INFO::Running the linear model component
2026-02-17 01:53:55.88926 INFO::Fitting model to feature number 1, a
2026-02-17 01:53:55.893881 INFO::Fitting model to feature number 2, b
2026-02-17 01:53:55.898152 INFO::Fitting model to feature number 3, c
2026-02-17 01:53:55.905286 INFO::Counting total values for each feature
2026-02-17 01:53:55.907108 INFO::Running the logistic model component
2026-02-17 01:53:55.921118 INFO::Fitting model to feature number 1, a
2026-02-17 01:53:55.928013 INFO::Fitting model to feature number 2, b
2026-02-17 01:53:55.93445 INFO::Fitting model to feature number 3, c
2026-02-17 01:53:55.943661 INFO::Counting total values for each feature
2026-02-17 01:53:55.945918 INFO::Re-running abundances for warn_prevalence
2026-02-17 01:53:55.946897 INFO::Running selected normalization method: TSS
2026-02-17 01:53:55.948402 INFO::Running selected transform method: LOG
2026-02-17 01:53:55.962821 INFO::Fitting model to feature number 1, a
2026-02-17 01:53:55.967525 INFO::Fitting model to feature number 2, b
2026-02-17 01:53:55.971812 INFO::Fitting model to feature number 3, c
2026-02-17 01:53:56.051625 INFO::Creating fits folder
2026-02-17 01:53:56.052815 INFO::Writing residuals to file /tmp/RtmpN5h4M3/file1d3a0056224fe4/fits/residuals_linear.rds
2026-02-17 01:53:56.053995 INFO::Writing fitted values to file /tmp/RtmpN5h4M3/file1d3a0056224fe4/fits/fitted_linear.rds
2026-02-17 01:53:56.05521 INFO::Writing residuals to file /tmp/RtmpN5h4M3/file1d3a0056224fe4/fits/residuals_logistic.rds
2026-02-17 01:53:56.056387 INFO::Writing fitted values to file /tmp/RtmpN5h4M3/file1d3a0056224fe4/fits/fitted_logistic.rds
2026-02-17 01:53:56.058791 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpN5h4M3/file1d3a0056224fe4/all_results.tsv
2026-02-17 01:53:56.06042 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/RtmpN5h4M3/file1d3a0056224fe4/significant_results.tsv
2026-02-17 01:53:56.061749 INFO::Creating output figures folder
2026-02-17 01:53:56.063093 INFO::Writing summary plot of significant
results to file: /tmp/RtmpN5h4M3/file1d3a0056224fe4/figures/summary_plot.pdf
2026-02-17 01:53:57.667066 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpN5h4M3/file1d3a0056224fe4/figures
2026-02-17 01:53:57.669027 INFO::Plotting associations from most to least significant, grouped by metadata
2026-02-17 01:53:57.674139 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-02-17 01:53:58.197276 INFO::Writing summary plot of
significant results to file: /tmp/RtmpN5h4M3/file1d3a0056224fe4/figures/summary_plot.pdf
2026-02-17 01:53:59.801957 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpN5h4M3/file1d3a0056224fe4/figures
2026-02-17 01:53:59.803618 INFO::Plotting associations from most to least significant, grouped by metadata
2026-02-17 01:53:59.808842 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-02-17 01:54:00.334093 INFO::Running the linear model component
2026-02-17 01:54:00.342678 INFO::Fitting model to feature number 1, a
2026-02-17 01:54:00.34681 INFO::Fitting model to feature number 2, b
2026-02-17 01:54:00.350621 INFO::Fitting model to feature number 3, c
2026-02-17 01:54:00.357125 INFO::Counting total values for each feature
2026-02-17 01:54:00.358657 INFO::Running the logistic model component
2026-02-17 01:54:00.366655 INFO::Fitting model to feature number 1, a
2026-02-17 01:54:00.372411 INFO::Fitting model to feature number 2, b
2026-02-17 01:54:00.377925 INFO::Fitting model to feature number 3, c
2026-02-17 01:54:00.386097 INFO::Counting total values for each feature
2026-02-17 01:54:00.387948 INFO::Re-running abundances for warn_prevalence
2026-02-17 01:54:00.388662 INFO::Running selected normalization method: TSS
2026-02-17 01:54:00.389921 INFO::Running selected transform method: LOG
2026-02-17 01:54:00.398167 INFO::Fitting model to feature number 1, a
2026-02-17 01:54:00.40216 INFO::Fitting model to feature number 2, b
2026-02-17 01:54:00.405931 INFO::Fitting model to feature number 3, c
2026-02-17 01:54:00.478362 INFO::Creating output folder
2026-02-17 01:54:00.479267 INFO::Creating output figures folder
2026-02-17 01:54:00.480445 INFO::Writing summary plot of significant
results to file: /tmp/RtmpN5h4M3/file1d3a00341e8e4a/figures/summary_plot.pdf
2026-02-17 01:54:02.078653 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpN5h4M3/file1d3a00341e8e4a/figures
2026-02-17 01:54:02.080656 INFO::Plotting associations from most to least significant, grouped by metadata
2026-02-17 01:54:02.086452 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-02-17 01:54:03.057166 INFO::Applying z-score to standardize continuous metadata
2026-02-17 01:54:03.064141 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2026-02-17 01:54:03.065 INFO::Bypass z-score application to metadata
2026-02-17 01:54:03.067557 INFO::Bypass z-score application to metadata
2026-02-17 01:54:03.086275 INFO::Determining format of input files
2026-02-17 01:54:03.087241 INFO::Input format is data samples as rows and metadata samples as rows
2026-02-17 01:54:03.088063 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2026-02-17 01:54:03.095433 INFO::Determining format of input files
2026-02-17 01:54:03.096394 INFO::Input format is data samples as columns and metadata samples as rows
2026-02-17 01:54:03.097664 INFO::Input format is feature_specific_covariate samples as columns
2026-02-17 01:54:03.105498 INFO::Determining format of input files
2026-02-17 01:54:03.106375 INFO::Input format is data samples as rows and metadata samples as rows
2026-02-17 01:54:03.107349 INFO::Input format is feature_specific_covariate samples as columns
2026-02-17 01:54:03.108954 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2026-02-17 01:54:03.109702 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2026-02-17 01:54:03.120861 INFO::Running selected transform method: LOG
2026-02-17 01:54:03.12194 INFO::Creating output feature tables folder
2026-02-17 01:54:03.122757 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpN5h4M3/file1d3a00c264ecd/features/data_transformed.tsv
2026-02-17 01:54:03.126516 INFO::Running selected transform method: LOG
2026-02-17 01:54:03.127524 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpN5h4M3/file1d3a00c264ecd/features/data_transformed.tsv
2026-02-17 01:54:03.135348 INFO::Running selected transform method: PLOG
2026-02-17 01:54:03.136941 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpN5h4M3/file1d3a00c264ecd/features/data_transformed.tsv
2026-02-17 01:54:03.139767 INFO::Running selected transform method: NONE
2026-02-17 01:54:03.140539 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpN5h4M3/file1d3a00c264ecd/features/data_transformed.tsv
2026-02-17 01:54:03.147786 INFO::Running the linear model component
2026-02-17 01:54:03.15666 INFO::Fitting model to feature number 1, a
2026-02-17 01:54:03.161016 INFO::Fitting model to feature number 2, b
2026-02-17 01:54:03.16518 INFO::Fitting model to feature number 3, c
2026-02-17 01:54:03.17232 INFO::Counting total values for each feature
2026-02-17 01:54:03.173993 INFO::Running the logistic model component
2026-02-17 01:54:03.182353 INFO::Fitting model to feature number 1, a
2026-02-17 01:54:03.188482 INFO::Fitting model to feature number 2, b
2026-02-17 01:54:03.19429 INFO::Fitting model to feature number 3, c
2026-02-17 01:54:03.203022 INFO::Counting total values for each feature
2026-02-17 01:54:03.20506 INFO::Re-running abundances for warn_prevalence
2026-02-17 01:54:03.205863 INFO::Running selected normalization method: TSS
2026-02-17 01:54:03.207197 INFO::Running selected transform method: LOG
2026-02-17 01:54:03.215644 INFO::Fitting model to feature number 1, a
2026-02-17 01:54:03.219752 INFO::Fitting model to feature number 2, b
2026-02-17 01:54:03.223669 INFO::Fitting model to feature number 3, c
2026-02-17 01:54:03.313703 INFO::Creating output folder
2026-02-17 01:54:03.314651 INFO::Creating fits folder
2026-02-17 01:54:03.315516 INFO::Writing residuals to file /tmp/RtmpN5h4M3/file1d3a0022703acc/fits/residuals_linear.rds
2026-02-17 01:54:03.316473 INFO::Writing fitted values to file /tmp/RtmpN5h4M3/file1d3a0022703acc/fits/fitted_linear.rds
2026-02-17 01:54:03.317487 INFO::Writing residuals to file /tmp/RtmpN5h4M3/file1d3a0022703acc/fits/residuals_logistic.rds
2026-02-17 01:54:03.318461 INFO::Writing fitted values to file /tmp/RtmpN5h4M3/file1d3a0022703acc/fits/fitted_logistic.rds
2026-02-17 01:54:03.320638 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpN5h4M3/file1d3a0022703acc/all_results.tsv
2026-02-17 01:54:03.322081 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/RtmpN5h4M3/file1d3a0022703acc/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
362.002 5.287 367.281
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 20.472 | 0.533 | 21.008 | |
| maaslin_check_arguments | 0.141 | 0.002 | 0.143 | |
| maaslin_check_formula | 0.154 | 0.002 | 0.156 | |
| maaslin_compute_formula | 0.144 | 0.001 | 0.146 | |
| maaslin_contrast_test | 19.174 | 0.324 | 19.498 | |
| maaslin_filter | 0.459 | 0.010 | 0.468 | |
| maaslin_fit | 12.886 | 0.059 | 12.946 | |
| maaslin_log_arguments | 0.138 | 0.001 | 0.140 | |
| maaslin_normalize | 0.286 | 0.006 | 0.292 | |
| maaslin_plot_results | 44.357 | 0.262 | 44.577 | |
| maaslin_plot_results_from_output | 43.696 | 0.293 | 43.993 | |
| maaslin_process_metadata | 0.487 | 0.019 | 0.507 | |
| maaslin_read_data | 0.134 | 0.000 | 0.134 | |
| maaslin_reorder_data | 0.135 | 0.000 | 0.135 | |
| maaslin_transform | 0.575 | 0.018 | 0.593 | |
| maaslin_write_results | 14.361 | 0.163 | 14.525 | |
| maaslin_write_results_lefse_format | 14.946 | 0.101 | 15.049 | |
| preprocess_dna_mtx | 0.003 | 0.001 | 0.003 | |
| preprocess_taxa_mtx | 0.004 | 0.000 | 0.004 | |