William Nickols
| Snapshot Date: 2026-01-26 13:45 -0500 (Mon, 26 Jan 2026) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: RELEASE_3_22 |
| git_last_commit: 9669f95 |
| git_last_commit_date: 2025-10-29 11:33:46 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-01-29 11:58 -0500 (Thu, 29 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4886 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1170/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maaslin3 1.2.0 (landing page) William Nickols
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the maaslin3 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/maaslin3.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: maaslin3 |
| Version: 1.2.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings maaslin3_1.2.0.tar.gz |
| StartedAt: 2026-01-27 01:09:00 -0500 (Tue, 27 Jan 2026) |
| EndedAt: 2026-01-27 01:30:48 -0500 (Tue, 27 Jan 2026) |
| EllapsedTime: 1308.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maaslin3.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings maaslin3_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/maaslin3.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘1.2.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘maaslin3’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
maaslin_plot_results_from_output 43.567 0.393 43.966
maaslin_plot_results 43.552 0.196 43.710
maaslin3 20.826 0.502 21.331
maaslin_contrast_test 19.380 0.419 19.800
maaslin_write_results_lefse_format 16.028 0.168 16.197
maaslin_write_results 13.666 0.119 13.787
maaslin_fit 13.021 0.075 13.097
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
maaslin3.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL maaslin3 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘maaslin3’ ... ** this is package ‘maaslin3’ version ‘1.2.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (maaslin3)
maaslin3.Rcheck/tests/testthat.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(maaslin3)
>
> test_check("maaslin3")
2026-01-27 01:15:20.971858 WARNING::Fitting problem for feature 50 returning NA
2026-01-27 01:15:21.058023 WARNING::Fitting problem for feature 62 returning NA
2026-01-27 01:15:21.156245 WARNING::Fitting problem for feature 74 returning NA
2026-01-27 01:15:21.184683 WARNING::Fitting problem for feature 78 returning NA
2026-01-27 01:15:21.241067 WARNING::Fitting problem for feature 84 returning NA
2026-01-27 01:15:21.320468 WARNING::Fitting problem for feature 96 returning NA
2026-01-27 01:15:21.325876 WARNING::Fitting problem for feature 97 returning NA
2026-01-27 01:15:21.337877 WARNING::Fitting problem for feature 99 returning NA
2026-01-27 01:15:21.450065 WARNING::Fitting problem for feature 114 returning NA
2026-01-27 01:15:21.455708 WARNING::Fitting problem for feature 115 returning NA
2026-01-27 01:15:21.505788 WARNING::Fitting problem for feature 123 returning NA
2026-01-27 01:15:21.545923 WARNING::Fitting problem for feature 130 returning NA
2026-01-27 01:15:21.557774 WARNING::Fitting problem for feature 132 returning NA
2026-01-27 01:15:21.598187 WARNING::Fitting problem for feature 139 returning NA
2026-01-27 01:15:21.676017 WARNING::Fitting problem for feature 150 returning NA
2026-01-27 01:15:38.083495 WARNING::Fitting problem for feature 50 returning NA
2026-01-27 01:15:38.158332 WARNING::Fitting problem for feature 62 returning NA
2026-01-27 01:15:38.232536 WARNING::Fitting problem for feature 74 returning NA
2026-01-27 01:15:38.254282 WARNING::Fitting problem for feature 78 returning NA
2026-01-27 01:15:38.289528 WARNING::Fitting problem for feature 84 returning NA
2026-01-27 01:15:38.365386 WARNING::Fitting problem for feature 96 returning NA
2026-01-27 01:15:38.37071 WARNING::Fitting problem for feature 97 returning NA
2026-01-27 01:15:38.38291 WARNING::Fitting problem for feature 99 returning NA
2026-01-27 01:15:38.493275 WARNING::Fitting problem for feature 114 returning NA
2026-01-27 01:15:38.498865 WARNING::Fitting problem for feature 115 returning NA
2026-01-27 01:15:38.54981 WARNING::Fitting problem for feature 123 returning NA
2026-01-27 01:15:38.589939 WARNING::Fitting problem for feature 130 returning NA
2026-01-27 01:15:38.602134 WARNING::Fitting problem for feature 132 returning NA
2026-01-27 01:15:38.642374 WARNING::Fitting problem for feature 139 returning NA
2026-01-27 01:15:38.712181 WARNING::Fitting problem for feature 150 returning NA
2026-01-27 01:16:03.694999 WARNING::Fitting problem for feature 50 returning NA
2026-01-27 01:16:03.777278 WARNING::Fitting problem for feature 62 returning NA
2026-01-27 01:16:03.853531 WARNING::Fitting problem for feature 74 returning NA
2026-01-27 01:16:03.875351 WARNING::Fitting problem for feature 78 returning NA
2026-01-27 01:16:03.910214 WARNING::Fitting problem for feature 84 returning NA
2026-01-27 01:16:03.986852 WARNING::Fitting problem for feature 96 returning NA
2026-01-27 01:16:03.992228 WARNING::Fitting problem for feature 97 returning NA
2026-01-27 01:16:04.003993 WARNING::Fitting problem for feature 99 returning NA
2026-01-27 01:16:04.099465 WARNING::Fitting problem for feature 114 returning NA
2026-01-27 01:16:04.10492 WARNING::Fitting problem for feature 115 returning NA
2026-01-27 01:16:04.156018 WARNING::Fitting problem for feature 123 returning NA
2026-01-27 01:16:04.197289 WARNING::Fitting problem for feature 130 returning NA
2026-01-27 01:16:04.20909 WARNING::Fitting problem for feature 132 returning NA
2026-01-27 01:16:04.249294 WARNING::Fitting problem for feature 139 returning NA
2026-01-27 01:16:04.320765 WARNING::Fitting problem for feature 150 returning NA
2026-01-27 01:16:17.453866 WARNING::Fitting problem for feature 50 returning NA
2026-01-27 01:16:17.529561 WARNING::Fitting problem for feature 62 returning NA
2026-01-27 01:16:17.603871 WARNING::Fitting problem for feature 74 returning NA
2026-01-27 01:16:17.625409 WARNING::Fitting problem for feature 78 returning NA
2026-01-27 01:16:17.659772 WARNING::Fitting problem for feature 84 returning NA
2026-01-27 01:16:17.737265 WARNING::Fitting problem for feature 96 returning NA
2026-01-27 01:16:17.742687 WARNING::Fitting problem for feature 97 returning NA
2026-01-27 01:16:17.754579 WARNING::Fitting problem for feature 99 returning NA
2026-01-27 01:16:17.85023 WARNING::Fitting problem for feature 114 returning NA
2026-01-27 01:16:17.855604 WARNING::Fitting problem for feature 115 returning NA
2026-01-27 01:16:17.905052 WARNING::Fitting problem for feature 123 returning NA
2026-01-27 01:16:17.94595 WARNING::Fitting problem for feature 130 returning NA
2026-01-27 01:16:17.95824 WARNING::Fitting problem for feature 132 returning NA
2026-01-27 01:16:18.000029 WARNING::Fitting problem for feature 139 returning NA
2026-01-27 01:16:18.075133 WARNING::Fitting problem for feature 150 returning NA
2026-01-27 01:16:18.288706 WARNING::Deleting existing residuals file: /tmp/Rtmp41Ut6W/file39e2ed3dbbae95/fits/residuals_linear.rds
2026-01-27 01:16:18.350109 WARNING::Deleting existing fitted file: /tmp/Rtmp41Ut6W/file39e2ed3dbbae95/fits/fitted_linear.rds
2026-01-27 01:16:18.413306 WARNING::Deleting existing residuals file: /tmp/Rtmp41Ut6W/file39e2ed3dbbae95/fits/residuals_logistic.rds
2026-01-27 01:16:18.714025 WARNING::Deleting existing fitted file: /tmp/Rtmp41Ut6W/file39e2ed3dbbae95/fits/fitted_logistic.rds
2026-01-27 01:16:40.662523 WARNING::Fitting problem for feature 50 returning NA
2026-01-27 01:16:40.74189 WARNING::Fitting problem for feature 62 returning NA
2026-01-27 01:16:40.823211 WARNING::Fitting problem for feature 74 returning NA
2026-01-27 01:16:40.847335 WARNING::Fitting problem for feature 78 returning NA
2026-01-27 01:16:40.884095 WARNING::Fitting problem for feature 84 returning NA
2026-01-27 01:16:40.964941 WARNING::Fitting problem for feature 96 returning NA
2026-01-27 01:16:40.970784 WARNING::Fitting problem for feature 97 returning NA
2026-01-27 01:16:40.983223 WARNING::Fitting problem for feature 99 returning NA
2026-01-27 01:16:41.086138 WARNING::Fitting problem for feature 114 returning NA
2026-01-27 01:16:41.092082 WARNING::Fitting problem for feature 115 returning NA
2026-01-27 01:16:41.143082 WARNING::Fitting problem for feature 123 returning NA
2026-01-27 01:16:41.185339 WARNING::Fitting problem for feature 130 returning NA
2026-01-27 01:16:41.198138 WARNING::Fitting problem for feature 132 returning NA
2026-01-27 01:16:41.242324 WARNING::Fitting problem for feature 139 returning NA
2026-01-27 01:16:41.413404 WARNING::Fitting problem for feature 150 returning NA
2026-01-27 01:16:54.110489 WARNING::Fitting problem for feature 50 returning NA
2026-01-27 01:16:54.185301 WARNING::Fitting problem for feature 62 returning NA
2026-01-27 01:16:54.259639 WARNING::Fitting problem for feature 74 returning NA
2026-01-27 01:16:54.281361 WARNING::Fitting problem for feature 78 returning NA
2026-01-27 01:16:54.316356 WARNING::Fitting problem for feature 84 returning NA
2026-01-27 01:16:54.393203 WARNING::Fitting problem for feature 96 returning NA
2026-01-27 01:16:54.398699 WARNING::Fitting problem for feature 97 returning NA
2026-01-27 01:16:54.440418 WARNING::Fitting problem for feature 99 returning NA
2026-01-27 01:16:54.537799 WARNING::Fitting problem for feature 114 returning NA
2026-01-27 01:16:54.543267 WARNING::Fitting problem for feature 115 returning NA
2026-01-27 01:16:54.594154 WARNING::Fitting problem for feature 123 returning NA
2026-01-27 01:16:54.635874 WARNING::Fitting problem for feature 130 returning NA
2026-01-27 01:16:54.648028 WARNING::Fitting problem for feature 132 returning NA
2026-01-27 01:16:54.688616 WARNING::Fitting problem for feature 139 returning NA
2026-01-27 01:16:54.757988 WARNING::Fitting problem for feature 150 returning NA
2026-01-27 01:16:54.951912 WARNING::Deleting existing residuals file: /tmp/Rtmp41Ut6W/file39e2ed3dbbae95/fits/residuals_linear.rds
2026-01-27 01:16:55.012957 WARNING::Deleting existing fitted file: /tmp/Rtmp41Ut6W/file39e2ed3dbbae95/fits/fitted_linear.rds
2026-01-27 01:16:55.076041 WARNING::Deleting existing residuals file: /tmp/Rtmp41Ut6W/file39e2ed3dbbae95/fits/residuals_logistic.rds
2026-01-27 01:16:55.376084 WARNING::Deleting existing fitted file: /tmp/Rtmp41Ut6W/file39e2ed3dbbae95/fits/fitted_logistic.rds
2026-01-27 01:17:16.933519 WARNING::Fitting problem for feature 50 returning NA
2026-01-27 01:17:17.018487 WARNING::Fitting problem for feature 62 returning NA
2026-01-27 01:17:17.098731 WARNING::Fitting problem for feature 74 returning NA
2026-01-27 01:17:17.155318 WARNING::Fitting problem for feature 78 returning NA
2026-01-27 01:17:17.193461 WARNING::Fitting problem for feature 84 returning NA
2026-01-27 01:17:17.27391 WARNING::Fitting problem for feature 96 returning NA
2026-01-27 01:17:17.279633 WARNING::Fitting problem for feature 97 returning NA
2026-01-27 01:17:17.291938 WARNING::Fitting problem for feature 99 returning NA
2026-01-27 01:17:17.391242 WARNING::Fitting problem for feature 114 returning NA
2026-01-27 01:17:17.397156 WARNING::Fitting problem for feature 115 returning NA
2026-01-27 01:17:17.450479 WARNING::Fitting problem for feature 123 returning NA
2026-01-27 01:17:17.495352 WARNING::Fitting problem for feature 130 returning NA
2026-01-27 01:17:17.509433 WARNING::Fitting problem for feature 132 returning NA
2026-01-27 01:17:17.556002 WARNING::Fitting problem for feature 139 returning NA
2026-01-27 01:17:17.641283 WARNING::Fitting problem for feature 150 returning NA
2026-01-27 01:17:30.306303 WARNING::Fitting problem for feature 50 returning NA
2026-01-27 01:17:30.393418 WARNING::Fitting problem for feature 62 returning NA
2026-01-27 01:17:30.476792 WARNING::Fitting problem for feature 74 returning NA
2026-01-27 01:17:30.501334 WARNING::Fitting problem for feature 78 returning NA
2026-01-27 01:17:30.5431 WARNING::Fitting problem for feature 84 returning NA
2026-01-27 01:17:30.627343 WARNING::Fitting problem for feature 96 returning NA
2026-01-27 01:17:30.633223 WARNING::Fitting problem for feature 97 returning NA
2026-01-27 01:17:30.64631 WARNING::Fitting problem for feature 99 returning NA
2026-01-27 01:17:30.747254 WARNING::Fitting problem for feature 114 returning NA
2026-01-27 01:17:30.752956 WARNING::Fitting problem for feature 115 returning NA
2026-01-27 01:17:30.804819 WARNING::Fitting problem for feature 123 returning NA
2026-01-27 01:17:30.846178 WARNING::Fitting problem for feature 130 returning NA
2026-01-27 01:17:30.858289 WARNING::Fitting problem for feature 132 returning NA
2026-01-27 01:17:30.933378 WARNING::Fitting problem for feature 139 returning NA
2026-01-27 01:17:31.007954 WARNING::Fitting problem for feature 150 returning NA
2026-01-27 01:17:31.203475 WARNING::Deleting existing residuals file: /tmp/Rtmp41Ut6W/file39e2ed3dbbae95/fits/residuals_linear.rds
2026-01-27 01:17:31.265461 WARNING::Deleting existing fitted file: /tmp/Rtmp41Ut6W/file39e2ed3dbbae95/fits/fitted_linear.rds
2026-01-27 01:17:31.328533 WARNING::Deleting existing residuals file: /tmp/Rtmp41Ut6W/file39e2ed3dbbae95/fits/residuals_logistic.rds
2026-01-27 01:17:31.628716 WARNING::Deleting existing fitted file: /tmp/Rtmp41Ut6W/file39e2ed3dbbae95/fits/fitted_logistic.rds
2026-01-27 01:17:53.08416 WARNING::Fitting problem for feature 50 returning NA
2026-01-27 01:17:53.162701 WARNING::Fitting problem for feature 62 returning NA
2026-01-27 01:17:53.239188 WARNING::Fitting problem for feature 74 returning NA
2026-01-27 01:17:53.261667 WARNING::Fitting problem for feature 78 returning NA
2026-01-27 01:17:53.296753 WARNING::Fitting problem for feature 84 returning NA
2026-01-27 01:17:53.376929 WARNING::Fitting problem for feature 96 returning NA
2026-01-27 01:17:53.382607 WARNING::Fitting problem for feature 97 returning NA
2026-01-27 01:17:53.39522 WARNING::Fitting problem for feature 99 returning NA
2026-01-27 01:17:53.518739 WARNING::Fitting problem for feature 114 returning NA
2026-01-27 01:17:53.524436 WARNING::Fitting problem for feature 115 returning NA
2026-01-27 01:17:53.576684 WARNING::Fitting problem for feature 123 returning NA
2026-01-27 01:17:53.630287 WARNING::Fitting problem for feature 130 returning NA
2026-01-27 01:17:53.643007 WARNING::Fitting problem for feature 132 returning NA
2026-01-27 01:17:53.686222 WARNING::Fitting problem for feature 139 returning NA
2026-01-27 01:17:53.757481 WARNING::Fitting problem for feature 150 returning NA
2026-01-27 01:18:05.67871 WARNING::Fitting problem for feature 50 returning NA
2026-01-27 01:18:05.755937 WARNING::Fitting problem for feature 62 returning NA
2026-01-27 01:18:05.831173 WARNING::Fitting problem for feature 74 returning NA
2026-01-27 01:18:05.853269 WARNING::Fitting problem for feature 78 returning NA
2026-01-27 01:18:05.888231 WARNING::Fitting problem for feature 84 returning NA
2026-01-27 01:18:05.966624 WARNING::Fitting problem for feature 96 returning NA
2026-01-27 01:18:05.972514 WARNING::Fitting problem for feature 97 returning NA
2026-01-27 01:18:05.985217 WARNING::Fitting problem for feature 99 returning NA
2026-01-27 01:18:06.084109 WARNING::Fitting problem for feature 114 returning NA
2026-01-27 01:18:06.089687 WARNING::Fitting problem for feature 115 returning NA
2026-01-27 01:18:06.140761 WARNING::Fitting problem for feature 123 returning NA
2026-01-27 01:18:06.181854 WARNING::Fitting problem for feature 130 returning NA
2026-01-27 01:18:06.194972 WARNING::Fitting problem for feature 132 returning NA
2026-01-27 01:18:06.238283 WARNING::Fitting problem for feature 139 returning NA
2026-01-27 01:18:06.308755 WARNING::Fitting problem for feature 150 returning NA
2026-01-27 01:18:30.524803 WARNING::Fitting problem for feature 124 returning NA
2026-01-27 01:18:40.592584 WARNING::Fitting problem for feature 124 returning NA
2026-01-27 01:19:05.230684 WARNING::Fitting problem for feature 124 returning NA
2026-01-27 01:19:15.598658 WARNING::Fitting problem for feature 124 returning NA
2026-01-27 01:19:16.243214 WARNING::Deleting existing residuals file: /tmp/Rtmp41Ut6W/file39e2ed57bccbec/fits/residuals_linear.rds
2026-01-27 01:19:16.305362 WARNING::Deleting existing fitted file: /tmp/Rtmp41Ut6W/file39e2ed57bccbec/fits/fitted_linear.rds
2026-01-27 01:19:16.344244 WARNING::Deleting existing residuals file: /tmp/Rtmp41Ut6W/file39e2ed57bccbec/fits/residuals_logistic.rds
2026-01-27 01:19:16.413642 WARNING::Deleting existing fitted file: /tmp/Rtmp41Ut6W/file39e2ed57bccbec/fits/fitted_logistic.rds
2026-01-27 01:19:39.33629 WARNING::Fitting problem for feature 124 returning NA
2026-01-27 01:19:45.636291 WARNING::Fitting problem for feature 124 returning NA
2026-01-27 01:19:45.930718 WARNING::Deleting existing residuals file: /tmp/Rtmp41Ut6W/file39e2ed57bccbec/fits/residuals_linear.rds
2026-01-27 01:19:45.992423 WARNING::Deleting existing fitted file: /tmp/Rtmp41Ut6W/file39e2ed57bccbec/fits/fitted_linear.rds
2026-01-27 01:19:46.030946 WARNING::Deleting existing residuals file: /tmp/Rtmp41Ut6W/file39e2ed57bccbec/fits/residuals_logistic.rds
2026-01-27 01:19:46.099847 WARNING::Deleting existing fitted file: /tmp/Rtmp41Ut6W/file39e2ed57bccbec/fits/fitted_logistic.rds
2026-01-27 01:20:04.644691 WARNING::Fitting problem for feature 124 returning NA
2026-01-27 01:20:10.998568 WARNING::Fitting problem for feature 124 returning NA
2026-01-27 01:20:11.30531 WARNING::Deleting existing residuals file: /tmp/Rtmp41Ut6W/file39e2ed57bccbec/fits/residuals_linear.rds
2026-01-27 01:20:11.367143 WARNING::Deleting existing fitted file: /tmp/Rtmp41Ut6W/file39e2ed57bccbec/fits/fitted_linear.rds
2026-01-27 01:20:11.405545 WARNING::Deleting existing residuals file: /tmp/Rtmp41Ut6W/file39e2ed57bccbec/fits/residuals_logistic.rds
2026-01-27 01:20:11.476732 WARNING::Deleting existing fitted file: /tmp/Rtmp41Ut6W/file39e2ed57bccbec/fits/fitted_logistic.rds
2026-01-27 01:20:29.543046 WARNING::Fitting problem for feature 50 returning NA
2026-01-27 01:20:29.622612 WARNING::Fitting problem for feature 62 returning NA
2026-01-27 01:20:29.700658 WARNING::Fitting problem for feature 74 returning NA
2026-01-27 01:20:29.746291 WARNING::Fitting problem for feature 78 returning NA
2026-01-27 01:20:29.781335 WARNING::Fitting problem for feature 84 returning NA
2026-01-27 01:20:29.858245 WARNING::Fitting problem for feature 96 returning NA
2026-01-27 01:20:29.863647 WARNING::Fitting problem for feature 97 returning NA
2026-01-27 01:20:29.875577 WARNING::Fitting problem for feature 99 returning NA
2026-01-27 01:20:29.974774 WARNING::Fitting problem for feature 114 returning NA
2026-01-27 01:20:29.980433 WARNING::Fitting problem for feature 115 returning NA
2026-01-27 01:20:30.030788 WARNING::Fitting problem for feature 123 returning NA
2026-01-27 01:20:30.071638 WARNING::Fitting problem for feature 130 returning NA
2026-01-27 01:20:30.083564 WARNING::Fitting problem for feature 132 returning NA
2026-01-27 01:20:30.123515 WARNING::Fitting problem for feature 139 returning NA
2026-01-27 01:20:30.1924 WARNING::Fitting problem for feature 150 returning NA
2026-01-27 01:20:42.175334 WARNING::Fitting problem for feature 50 returning NA
2026-01-27 01:20:42.250848 WARNING::Fitting problem for feature 62 returning NA
2026-01-27 01:20:42.325939 WARNING::Fitting problem for feature 74 returning NA
2026-01-27 01:20:42.347877 WARNING::Fitting problem for feature 78 returning NA
2026-01-27 01:20:42.382823 WARNING::Fitting problem for feature 84 returning NA
2026-01-27 01:20:42.45898 WARNING::Fitting problem for feature 96 returning NA
2026-01-27 01:20:42.46442 WARNING::Fitting problem for feature 97 returning NA
2026-01-27 01:20:42.476223 WARNING::Fitting problem for feature 99 returning NA
2026-01-27 01:20:42.572423 WARNING::Fitting problem for feature 114 returning NA
2026-01-27 01:20:42.577929 WARNING::Fitting problem for feature 115 returning NA
2026-01-27 01:20:42.627922 WARNING::Fitting problem for feature 123 returning NA
2026-01-27 01:20:42.668664 WARNING::Fitting problem for feature 130 returning NA
2026-01-27 01:20:42.680785 WARNING::Fitting problem for feature 132 returning NA
2026-01-27 01:20:42.721573 WARNING::Fitting problem for feature 139 returning NA
2026-01-27 01:20:42.791391 WARNING::Fitting problem for feature 150 returning NA
2026-01-27 01:20:43.032165 WARNING::Deleting existing residuals file: /tmp/Rtmp41Ut6W/file39e2ed57bccbec/fits/residuals_linear.rds
2026-01-27 01:20:43.093066 WARNING::Deleting existing fitted file: /tmp/Rtmp41Ut6W/file39e2ed57bccbec/fits/fitted_linear.rds
2026-01-27 01:20:43.155802 WARNING::Deleting existing residuals file: /tmp/Rtmp41Ut6W/file39e2ed57bccbec/fits/residuals_logistic.rds
2026-01-27 01:20:43.454273 WARNING::Deleting existing fitted file: /tmp/Rtmp41Ut6W/file39e2ed57bccbec/fits/fitted_logistic.rds
2026-01-27 01:21:04.023206 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2026-01-27 01:21:04.040555 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2026-01-27 01:21:04.052601 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2026-01-27 01:21:04.105596 ERROR::No fixed, group, or
ordered effects included in formula.
2026-01-27 01:21:04.122623 ERROR::Effect name not found in metadata: d
2026-01-27 01:21:04.134181 ERROR::No user formula provided
2026-01-27 01:21:04.165352 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2026-01-27 01:21:04.176718 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2026-01-27 01:21:07.027264 INFO::Writing function arguments to log file
2026-01-27 01:21:07.041717 INFO::Verifying options selected are valid
2026-01-27 01:21:09.383355 INFO::Writing function arguments to log file
2026-01-27 01:21:09.396424 INFO::Verifying options selected are valid
2026-01-27 01:21:09.397563 INFO::Determining format of input files
2026-01-27 01:21:09.398606 INFO::Input format is data samples as rows and metadata samples as rows
2026-01-27 01:21:09.401003 INFO::Running selected normalization method: TSS
2026-01-27 01:21:09.402534 INFO::Creating output feature tables folder
2026-01-27 01:21:09.403575 INFO::Writing normalized data to file /tmp/Rtmp41Ut6W/file39e2ed3c634dfc/features/data_norm.tsv
2026-01-27 01:21:09.405135 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2026-01-27 01:21:09.406059 INFO::Total samples in data: 16
2026-01-27 01:21:09.406954 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2026-01-27 01:21:09.40785 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2026-01-27 01:21:09.409828 INFO::Total filtered features: 0
2026-01-27 01:21:09.41081 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2026-01-27 01:21:09.411996 INFO::Total features filtered by non-zero variance filtering: 0
2026-01-27 01:21:09.412986 INFO::Filtered feature names from variance filtering:
2026-01-27 01:21:09.413899 INFO::Writing filtered data to file /tmp/Rtmp41Ut6W/file39e2ed3c634dfc/features/filtered_data.tsv
2026-01-27 01:21:09.415441 INFO::Running selected transform method: LOG
2026-01-27 01:21:09.416682 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp41Ut6W/file39e2ed3c634dfc/features/data_transformed.tsv
2026-01-27 01:21:09.418361 INFO::Applying z-score to standardize continuous metadata
2026-01-27 01:21:09.423038 INFO::Running the linear model component
2026-01-27 01:21:09.437471 INFO::Fitting model to feature number 1, a
2026-01-27 01:21:09.442062 INFO::Fitting model to feature number 2, b
2026-01-27 01:21:09.446419 INFO::Fitting model to feature number 3, c
2026-01-27 01:21:09.453754 INFO::Counting total values for each feature
2026-01-27 01:21:09.455582 INFO::Running the logistic model component
2026-01-27 01:21:09.469562 INFO::Fitting model to feature number 1, a
2026-01-27 01:21:09.476216 INFO::Fitting model to feature number 2, b
2026-01-27 01:21:09.482489 INFO::Fitting model to feature number 3, c
2026-01-27 01:21:09.491642 INFO::Counting total values for each feature
2026-01-27 01:21:09.49385 INFO::Re-running abundances for warn_prevalence
2026-01-27 01:21:09.494836 INFO::Running selected normalization method: TSS
2026-01-27 01:21:09.496338 INFO::Running selected transform method: LOG
2026-01-27 01:21:09.510751 INFO::Fitting model to feature number 1, a
2026-01-27 01:21:09.515456 INFO::Fitting model to feature number 2, b
2026-01-27 01:21:09.519866 INFO::Fitting model to feature number 3, c
2026-01-27 01:21:09.613804 INFO::Creating fits folder
2026-01-27 01:21:09.615092 INFO::Writing residuals to file /tmp/Rtmp41Ut6W/file39e2ed3c634dfc/fits/residuals_linear.rds
2026-01-27 01:21:09.616302 INFO::Writing fitted values to file /tmp/Rtmp41Ut6W/file39e2ed3c634dfc/fits/fitted_linear.rds
2026-01-27 01:21:09.617519 INFO::Writing residuals to file /tmp/Rtmp41Ut6W/file39e2ed3c634dfc/fits/residuals_logistic.rds
2026-01-27 01:21:09.618711 INFO::Writing fitted values to file /tmp/Rtmp41Ut6W/file39e2ed3c634dfc/fits/fitted_logistic.rds
2026-01-27 01:21:09.621428 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/Rtmp41Ut6W/file39e2ed3c634dfc/all_results.tsv
2026-01-27 01:21:09.623097 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/Rtmp41Ut6W/file39e2ed3c634dfc/significant_results.tsv
2026-01-27 01:21:09.624437 INFO::Creating output figures folder
2026-01-27 01:21:09.625821 INFO::Writing summary plot of significant
results to file: /tmp/Rtmp41Ut6W/file39e2ed3c634dfc/figures/summary_plot.pdf
2026-01-27 01:21:11.294492 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmp41Ut6W/file39e2ed3c634dfc/figures
2026-01-27 01:21:11.296618 INFO::Plotting associations from most to least significant, grouped by metadata
2026-01-27 01:21:11.301847 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-01-27 01:21:11.822966 INFO::Writing summary plot of
significant results to file: /tmp/Rtmp41Ut6W/file39e2ed3c634dfc/figures/summary_plot.pdf
2026-01-27 01:21:13.490897 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmp41Ut6W/file39e2ed3c634dfc/figures
2026-01-27 01:21:13.492428 INFO::Plotting associations from most to least significant, grouped by metadata
2026-01-27 01:21:13.497163 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-01-27 01:21:14.023239 INFO::Running the linear model component
2026-01-27 01:21:14.044209 INFO::Fitting model to feature number 1, a
2026-01-27 01:21:14.049494 INFO::Fitting model to feature number 2, b
2026-01-27 01:21:14.054122 INFO::Fitting model to feature number 3, c
2026-01-27 01:21:14.061738 INFO::Counting total values for each feature
2026-01-27 01:21:14.063504 INFO::Running the logistic model component
2026-01-27 01:21:14.072349 INFO::Fitting model to feature number 1, a
2026-01-27 01:21:14.079241 INFO::Fitting model to feature number 2, b
2026-01-27 01:21:14.085257 INFO::Fitting model to feature number 3, c
2026-01-27 01:21:14.094252 INFO::Counting total values for each feature
2026-01-27 01:21:14.09635 INFO::Re-running abundances for warn_prevalence
2026-01-27 01:21:14.097183 INFO::Running selected normalization method: TSS
2026-01-27 01:21:14.098591 INFO::Running selected transform method: LOG
2026-01-27 01:21:14.107441 INFO::Fitting model to feature number 1, a
2026-01-27 01:21:14.111978 INFO::Fitting model to feature number 2, b
2026-01-27 01:21:14.116135 INFO::Fitting model to feature number 3, c
2026-01-27 01:21:14.197376 INFO::Creating output folder
2026-01-27 01:21:14.198453 INFO::Creating output figures folder
2026-01-27 01:21:14.19977 INFO::Writing summary plot of significant
results to file: /tmp/Rtmp41Ut6W/file39e2ed71d37207/figures/summary_plot.pdf
2026-01-27 01:21:15.842796 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmp41Ut6W/file39e2ed71d37207/figures
2026-01-27 01:21:15.84471 INFO::Plotting associations from most to least significant, grouped by metadata
2026-01-27 01:21:15.849815 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-01-27 01:21:16.836479 INFO::Applying z-score to standardize continuous metadata
2026-01-27 01:21:16.843684 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2026-01-27 01:21:16.844599 INFO::Bypass z-score application to metadata
2026-01-27 01:21:16.847206 INFO::Bypass z-score application to metadata
2026-01-27 01:21:16.867911 INFO::Determining format of input files
2026-01-27 01:21:16.86897 INFO::Input format is data samples as rows and metadata samples as rows
2026-01-27 01:21:16.869855 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2026-01-27 01:21:16.877552 INFO::Determining format of input files
2026-01-27 01:21:16.878699 INFO::Input format is data samples as columns and metadata samples as rows
2026-01-27 01:21:16.880101 INFO::Input format is feature_specific_covariate samples as columns
2026-01-27 01:21:16.888951 INFO::Determining format of input files
2026-01-27 01:21:16.889966 INFO::Input format is data samples as rows and metadata samples as rows
2026-01-27 01:21:16.891117 INFO::Input format is feature_specific_covariate samples as columns
2026-01-27 01:21:16.893012 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2026-01-27 01:21:16.893875 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2026-01-27 01:21:16.906647 INFO::Running selected transform method: LOG
2026-01-27 01:21:16.907856 INFO::Creating output feature tables folder
2026-01-27 01:21:16.908767 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp41Ut6W/file39e2ed10c710c2/features/data_transformed.tsv
2026-01-27 01:21:16.912925 INFO::Running selected transform method: LOG
2026-01-27 01:21:16.913997 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp41Ut6W/file39e2ed10c710c2/features/data_transformed.tsv
2026-01-27 01:21:16.918147 INFO::Running selected transform method: PLOG
2026-01-27 01:21:16.919747 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp41Ut6W/file39e2ed10c710c2/features/data_transformed.tsv
2026-01-27 01:21:16.922698 INFO::Running selected transform method: NONE
2026-01-27 01:21:16.923485 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp41Ut6W/file39e2ed10c710c2/features/data_transformed.tsv
2026-01-27 01:21:16.931436 INFO::Running the linear model component
2026-01-27 01:21:16.940617 INFO::Fitting model to feature number 1, a
2026-01-27 01:21:16.945067 INFO::Fitting model to feature number 2, b
2026-01-27 01:21:16.949246 INFO::Fitting model to feature number 3, c
2026-01-27 01:21:16.95647 INFO::Counting total values for each feature
2026-01-27 01:21:16.958156 INFO::Running the logistic model component
2026-01-27 01:21:16.966985 INFO::Fitting model to feature number 1, a
2026-01-27 01:21:16.973236 INFO::Fitting model to feature number 2, b
2026-01-27 01:21:16.979208 INFO::Fitting model to feature number 3, c
2026-01-27 01:21:16.988123 INFO::Counting total values for each feature
2026-01-27 01:21:16.990132 INFO::Re-running abundances for warn_prevalence
2026-01-27 01:21:16.990911 INFO::Running selected normalization method: TSS
2026-01-27 01:21:16.992279 INFO::Running selected transform method: LOG
2026-01-27 01:21:17.00106 INFO::Fitting model to feature number 1, a
2026-01-27 01:21:17.005239 INFO::Fitting model to feature number 2, b
2026-01-27 01:21:17.009294 INFO::Fitting model to feature number 3, c
2026-01-27 01:21:17.090238 INFO::Creating output folder
2026-01-27 01:21:17.091276 INFO::Creating fits folder
2026-01-27 01:21:17.092162 INFO::Writing residuals to file /tmp/Rtmp41Ut6W/file39e2ed74b8e128/fits/residuals_linear.rds
2026-01-27 01:21:17.093174 INFO::Writing fitted values to file /tmp/Rtmp41Ut6W/file39e2ed74b8e128/fits/fitted_linear.rds
2026-01-27 01:21:17.094267 INFO::Writing residuals to file /tmp/Rtmp41Ut6W/file39e2ed74b8e128/fits/residuals_logistic.rds
2026-01-27 01:21:17.095338 INFO::Writing fitted values to file /tmp/Rtmp41Ut6W/file39e2ed74b8e128/fits/fitted_logistic.rds
2026-01-27 01:21:17.097943 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/Rtmp41Ut6W/file39e2ed74b8e128/all_results.tsv
2026-01-27 01:21:17.099455 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/Rtmp41Ut6W/file39e2ed74b8e128/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
361.978 5.631 367.578
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 20.826 | 0.502 | 21.331 | |
| maaslin_check_arguments | 0.144 | 0.001 | 0.144 | |
| maaslin_check_formula | 0.159 | 0.001 | 0.160 | |
| maaslin_compute_formula | 0.149 | 0.001 | 0.149 | |
| maaslin_contrast_test | 19.380 | 0.419 | 19.800 | |
| maaslin_filter | 0.442 | 0.037 | 0.479 | |
| maaslin_fit | 13.021 | 0.075 | 13.097 | |
| maaslin_log_arguments | 0.132 | 0.000 | 0.132 | |
| maaslin_normalize | 0.263 | 0.004 | 0.267 | |
| maaslin_plot_results | 43.552 | 0.196 | 43.710 | |
| maaslin_plot_results_from_output | 43.567 | 0.393 | 43.966 | |
| maaslin_process_metadata | 0.467 | 0.010 | 0.478 | |
| maaslin_read_data | 0.134 | 0.000 | 0.134 | |
| maaslin_reorder_data | 0.142 | 0.002 | 0.144 | |
| maaslin_transform | 0.540 | 0.010 | 0.551 | |
| maaslin_write_results | 13.666 | 0.119 | 13.787 | |
| maaslin_write_results_lefse_format | 16.028 | 0.168 | 16.197 | |
| preprocess_dna_mtx | 0.003 | 0.000 | 0.004 | |
| preprocess_taxa_mtx | 0.004 | 0.000 | 0.004 | |