William Nickols
| Snapshot Date: 2026-03-31 13:45 -0400 (Tue, 31 Mar 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 -0400 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-04-01 11:57 -0400 (Wed, 01 Apr 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" | 4896 |
| 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: 2026-04-01 00:54:53 -0400 (Wed, 01 Apr 2026) |
| EndedAt: 2026-04-01 01:16:26 -0400 (Wed, 01 Apr 2026) |
| EllapsedTime: 1292.5 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 24.04.4 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 42.940 0.319 43.219
maaslin_plot_results_from_output 42.849 0.333 43.185
maaslin3 19.209 0.523 19.732
maaslin_contrast_test 18.818 0.250 19.068
maaslin_write_results_lefse_format 14.950 0.093 15.043
maaslin_write_results 13.456 0.113 13.570
maaslin_fit 12.508 0.148 12.656
* 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")
2026-04-01 01:01:08.063439 WARNING::Fitting problem for feature 50 returning NA
2026-04-01 01:01:08.149068 WARNING::Fitting problem for feature 62 returning NA
2026-04-01 01:01:08.242125 WARNING::Fitting problem for feature 74 returning NA
2026-04-01 01:01:08.263734 WARNING::Fitting problem for feature 78 returning NA
2026-04-01 01:01:08.298012 WARNING::Fitting problem for feature 84 returning NA
2026-04-01 01:01:08.375434 WARNING::Fitting problem for feature 96 returning NA
2026-04-01 01:01:08.389091 WARNING::Fitting problem for feature 97 returning NA
2026-04-01 01:01:08.400726 WARNING::Fitting problem for feature 99 returning NA
2026-04-01 01:01:08.492983 WARNING::Fitting problem for feature 114 returning NA
2026-04-01 01:01:08.49819 WARNING::Fitting problem for feature 115 returning NA
2026-04-01 01:01:08.54661 WARNING::Fitting problem for feature 123 returning NA
2026-04-01 01:01:08.593189 WARNING::Fitting problem for feature 130 returning NA
2026-04-01 01:01:08.604995 WARNING::Fitting problem for feature 132 returning NA
2026-04-01 01:01:08.64492 WARNING::Fitting problem for feature 139 returning NA
2026-04-01 01:01:08.714357 WARNING::Fitting problem for feature 150 returning NA
2026-04-01 01:01:23.448622 WARNING::Fitting problem for feature 50 returning NA
2026-04-01 01:01:23.522584 WARNING::Fitting problem for feature 62 returning NA
2026-04-01 01:01:23.59602 WARNING::Fitting problem for feature 74 returning NA
2026-04-01 01:01:23.617054 WARNING::Fitting problem for feature 78 returning NA
2026-04-01 01:01:23.651783 WARNING::Fitting problem for feature 84 returning NA
2026-04-01 01:01:23.727983 WARNING::Fitting problem for feature 96 returning NA
2026-04-01 01:01:23.733533 WARNING::Fitting problem for feature 97 returning NA
2026-04-01 01:01:23.74576 WARNING::Fitting problem for feature 99 returning NA
2026-04-01 01:01:23.857322 WARNING::Fitting problem for feature 114 returning NA
2026-04-01 01:01:23.862792 WARNING::Fitting problem for feature 115 returning NA
2026-04-01 01:01:23.914573 WARNING::Fitting problem for feature 123 returning NA
2026-04-01 01:01:23.954582 WARNING::Fitting problem for feature 130 returning NA
2026-04-01 01:01:23.966187 WARNING::Fitting problem for feature 132 returning NA
2026-04-01 01:01:24.005225 WARNING::Fitting problem for feature 139 returning NA
2026-04-01 01:01:24.072444 WARNING::Fitting problem for feature 150 returning NA
2026-04-01 01:01:47.892597 WARNING::Fitting problem for feature 50 returning NA
2026-04-01 01:01:47.975736 WARNING::Fitting problem for feature 62 returning NA
2026-04-01 01:01:48.050884 WARNING::Fitting problem for feature 74 returning NA
2026-04-01 01:01:48.07245 WARNING::Fitting problem for feature 78 returning NA
2026-04-01 01:01:48.105602 WARNING::Fitting problem for feature 84 returning NA
2026-04-01 01:01:48.17924 WARNING::Fitting problem for feature 96 returning NA
2026-04-01 01:01:48.184502 WARNING::Fitting problem for feature 97 returning NA
2026-04-01 01:01:48.196119 WARNING::Fitting problem for feature 99 returning NA
2026-04-01 01:01:48.292752 WARNING::Fitting problem for feature 114 returning NA
2026-04-01 01:01:48.298387 WARNING::Fitting problem for feature 115 returning NA
2026-04-01 01:01:48.34953 WARNING::Fitting problem for feature 123 returning NA
2026-04-01 01:01:48.391972 WARNING::Fitting problem for feature 130 returning NA
2026-04-01 01:01:48.404036 WARNING::Fitting problem for feature 132 returning NA
2026-04-01 01:01:48.444054 WARNING::Fitting problem for feature 139 returning NA
2026-04-01 01:01:48.513158 WARNING::Fitting problem for feature 150 returning NA
2026-04-01 01:02:01.025444 WARNING::Fitting problem for feature 50 returning NA
2026-04-01 01:02:01.100523 WARNING::Fitting problem for feature 62 returning NA
2026-04-01 01:02:01.204536 WARNING::Fitting problem for feature 74 returning NA
2026-04-01 01:02:01.226194 WARNING::Fitting problem for feature 78 returning NA
2026-04-01 01:02:01.260832 WARNING::Fitting problem for feature 84 returning NA
2026-04-01 01:02:01.33538 WARNING::Fitting problem for feature 96 returning NA
2026-04-01 01:02:01.340643 WARNING::Fitting problem for feature 97 returning NA
2026-04-01 01:02:01.352184 WARNING::Fitting problem for feature 99 returning NA
2026-04-01 01:02:01.446307 WARNING::Fitting problem for feature 114 returning NA
2026-04-01 01:02:01.452058 WARNING::Fitting problem for feature 115 returning NA
2026-04-01 01:02:01.504018 WARNING::Fitting problem for feature 123 returning NA
2026-04-01 01:02:01.546174 WARNING::Fitting problem for feature 130 returning NA
2026-04-01 01:02:01.558583 WARNING::Fitting problem for feature 132 returning NA
2026-04-01 01:02:01.600384 WARNING::Fitting problem for feature 139 returning NA
2026-04-01 01:02:01.670924 WARNING::Fitting problem for feature 150 returning NA
2026-04-01 01:02:01.866882 WARNING::Deleting existing residuals file: /tmp/RtmpmA8sVA/file275d0b64c0fe37/fits/residuals_linear.rds
2026-04-01 01:02:01.928244 WARNING::Deleting existing fitted file: /tmp/RtmpmA8sVA/file275d0b64c0fe37/fits/fitted_linear.rds
2026-04-01 01:02:01.991409 WARNING::Deleting existing residuals file: /tmp/RtmpmA8sVA/file275d0b64c0fe37/fits/residuals_logistic.rds
2026-04-01 01:02:02.291914 WARNING::Deleting existing fitted file: /tmp/RtmpmA8sVA/file275d0b64c0fe37/fits/fitted_logistic.rds
2026-04-01 01:02:24.86286 WARNING::Fitting problem for feature 50 returning NA
2026-04-01 01:02:24.940952 WARNING::Fitting problem for feature 62 returning NA
2026-04-01 01:02:25.016793 WARNING::Fitting problem for feature 74 returning NA
2026-04-01 01:02:25.039666 WARNING::Fitting problem for feature 78 returning NA
2026-04-01 01:02:25.074534 WARNING::Fitting problem for feature 84 returning NA
2026-04-01 01:02:25.150553 WARNING::Fitting problem for feature 96 returning NA
2026-04-01 01:02:25.155827 WARNING::Fitting problem for feature 97 returning NA
2026-04-01 01:02:25.167572 WARNING::Fitting problem for feature 99 returning NA
2026-04-01 01:02:25.266399 WARNING::Fitting problem for feature 114 returning NA
2026-04-01 01:02:25.271849 WARNING::Fitting problem for feature 115 returning NA
2026-04-01 01:02:25.320965 WARNING::Fitting problem for feature 123 returning NA
2026-04-01 01:02:25.361164 WARNING::Fitting problem for feature 130 returning NA
2026-04-01 01:02:25.37342 WARNING::Fitting problem for feature 132 returning NA
2026-04-01 01:02:25.414447 WARNING::Fitting problem for feature 139 returning NA
2026-04-01 01:02:25.483688 WARNING::Fitting problem for feature 150 returning NA
2026-04-01 01:02:37.370081 WARNING::Fitting problem for feature 50 returning NA
2026-04-01 01:02:37.447212 WARNING::Fitting problem for feature 62 returning NA
2026-04-01 01:02:37.522154 WARNING::Fitting problem for feature 74 returning NA
2026-04-01 01:02:37.545217 WARNING::Fitting problem for feature 78 returning NA
2026-04-01 01:02:37.582214 WARNING::Fitting problem for feature 84 returning NA
2026-04-01 01:02:37.659676 WARNING::Fitting problem for feature 96 returning NA
2026-04-01 01:02:37.665203 WARNING::Fitting problem for feature 97 returning NA
2026-04-01 01:02:37.676969 WARNING::Fitting problem for feature 99 returning NA
2026-04-01 01:02:37.773535 WARNING::Fitting problem for feature 114 returning NA
2026-04-01 01:02:37.779204 WARNING::Fitting problem for feature 115 returning NA
2026-04-01 01:02:37.832243 WARNING::Fitting problem for feature 123 returning NA
2026-04-01 01:02:37.873267 WARNING::Fitting problem for feature 130 returning NA
2026-04-01 01:02:37.885333 WARNING::Fitting problem for feature 132 returning NA
2026-04-01 01:02:37.926535 WARNING::Fitting problem for feature 139 returning NA
2026-04-01 01:02:37.999641 WARNING::Fitting problem for feature 150 returning NA
2026-04-01 01:02:38.205408 WARNING::Deleting existing residuals file: /tmp/RtmpmA8sVA/file275d0b64c0fe37/fits/residuals_linear.rds
2026-04-01 01:02:38.266557 WARNING::Deleting existing fitted file: /tmp/RtmpmA8sVA/file275d0b64c0fe37/fits/fitted_linear.rds
2026-04-01 01:02:38.329114 WARNING::Deleting existing residuals file: /tmp/RtmpmA8sVA/file275d0b64c0fe37/fits/residuals_logistic.rds
2026-04-01 01:02:38.629842 WARNING::Deleting existing fitted file: /tmp/RtmpmA8sVA/file275d0b64c0fe37/fits/fitted_logistic.rds
2026-04-01 01:03:00.056755 WARNING::Fitting problem for feature 50 returning NA
2026-04-01 01:03:00.143295 WARNING::Fitting problem for feature 62 returning NA
2026-04-01 01:03:00.229219 WARNING::Fitting problem for feature 74 returning NA
2026-04-01 01:03:00.254295 WARNING::Fitting problem for feature 78 returning NA
2026-04-01 01:03:00.305655 WARNING::Fitting problem for feature 84 returning NA
2026-04-01 01:03:00.42984 WARNING::Fitting problem for feature 96 returning NA
2026-04-01 01:03:00.43595 WARNING::Fitting problem for feature 97 returning NA
2026-04-01 01:03:00.449319 WARNING::Fitting problem for feature 99 returning NA
2026-04-01 01:03:00.556749 WARNING::Fitting problem for feature 114 returning NA
2026-04-01 01:03:00.562788 WARNING::Fitting problem for feature 115 returning NA
2026-04-01 01:03:00.61794 WARNING::Fitting problem for feature 123 returning NA
2026-04-01 01:03:00.668071 WARNING::Fitting problem for feature 130 returning NA
2026-04-01 01:03:00.681566 WARNING::Fitting problem for feature 132 returning NA
2026-04-01 01:03:00.726074 WARNING::Fitting problem for feature 139 returning NA
2026-04-01 01:03:00.801043 WARNING::Fitting problem for feature 150 returning NA
2026-04-01 01:03:13.674024 WARNING::Fitting problem for feature 50 returning NA
2026-04-01 01:03:13.772053 WARNING::Fitting problem for feature 62 returning NA
2026-04-01 01:03:13.885087 WARNING::Fitting problem for feature 74 returning NA
2026-04-01 01:03:13.910091 WARNING::Fitting problem for feature 78 returning NA
2026-04-01 01:03:13.947968 WARNING::Fitting problem for feature 84 returning NA
2026-04-01 01:03:14.028653 WARNING::Fitting problem for feature 96 returning NA
2026-04-01 01:03:14.034223 WARNING::Fitting problem for feature 97 returning NA
2026-04-01 01:03:14.046426 WARNING::Fitting problem for feature 99 returning NA
2026-04-01 01:03:14.143713 WARNING::Fitting problem for feature 114 returning NA
2026-04-01 01:03:14.149201 WARNING::Fitting problem for feature 115 returning NA
2026-04-01 01:03:14.200711 WARNING::Fitting problem for feature 123 returning NA
2026-04-01 01:03:14.243191 WARNING::Fitting problem for feature 130 returning NA
2026-04-01 01:03:14.255415 WARNING::Fitting problem for feature 132 returning NA
2026-04-01 01:03:14.296758 WARNING::Fitting problem for feature 139 returning NA
2026-04-01 01:03:14.374052 WARNING::Fitting problem for feature 150 returning NA
2026-04-01 01:03:14.59774 WARNING::Deleting existing residuals file: /tmp/RtmpmA8sVA/file275d0b64c0fe37/fits/residuals_linear.rds
2026-04-01 01:03:14.659412 WARNING::Deleting existing fitted file: /tmp/RtmpmA8sVA/file275d0b64c0fe37/fits/fitted_linear.rds
2026-04-01 01:03:14.723202 WARNING::Deleting existing residuals file: /tmp/RtmpmA8sVA/file275d0b64c0fe37/fits/residuals_logistic.rds
2026-04-01 01:03:15.025414 WARNING::Deleting existing fitted file: /tmp/RtmpmA8sVA/file275d0b64c0fe37/fits/fitted_logistic.rds
2026-04-01 01:03:37.273699 WARNING::Fitting problem for feature 50 returning NA
2026-04-01 01:03:37.361635 WARNING::Fitting problem for feature 62 returning NA
2026-04-01 01:03:37.446192 WARNING::Fitting problem for feature 74 returning NA
2026-04-01 01:03:37.471127 WARNING::Fitting problem for feature 78 returning NA
2026-04-01 01:03:37.509953 WARNING::Fitting problem for feature 84 returning NA
2026-04-01 01:03:37.595493 WARNING::Fitting problem for feature 96 returning NA
2026-04-01 01:03:37.601455 WARNING::Fitting problem for feature 97 returning NA
2026-04-01 01:03:37.614557 WARNING::Fitting problem for feature 99 returning NA
2026-04-01 01:03:37.717304 WARNING::Fitting problem for feature 114 returning NA
2026-04-01 01:03:37.72279 WARNING::Fitting problem for feature 115 returning NA
2026-04-01 01:03:37.779438 WARNING::Fitting problem for feature 123 returning NA
2026-04-01 01:03:37.823759 WARNING::Fitting problem for feature 130 returning NA
2026-04-01 01:03:37.836707 WARNING::Fitting problem for feature 132 returning NA
2026-04-01 01:03:37.880895 WARNING::Fitting problem for feature 139 returning NA
2026-04-01 01:03:37.960315 WARNING::Fitting problem for feature 150 returning NA
2026-04-01 01:03:50.433861 WARNING::Fitting problem for feature 50 returning NA
2026-04-01 01:03:50.511732 WARNING::Fitting problem for feature 62 returning NA
2026-04-01 01:03:50.587535 WARNING::Fitting problem for feature 74 returning NA
2026-04-01 01:03:50.609596 WARNING::Fitting problem for feature 78 returning NA
2026-04-01 01:03:50.644268 WARNING::Fitting problem for feature 84 returning NA
2026-04-01 01:03:50.72065 WARNING::Fitting problem for feature 96 returning NA
2026-04-01 01:03:50.72595 WARNING::Fitting problem for feature 97 returning NA
2026-04-01 01:03:50.737651 WARNING::Fitting problem for feature 99 returning NA
2026-04-01 01:03:50.83145 WARNING::Fitting problem for feature 114 returning NA
2026-04-01 01:03:50.837025 WARNING::Fitting problem for feature 115 returning NA
2026-04-01 01:03:50.890019 WARNING::Fitting problem for feature 123 returning NA
2026-04-01 01:03:50.932956 WARNING::Fitting problem for feature 130 returning NA
2026-04-01 01:03:50.945556 WARNING::Fitting problem for feature 132 returning NA
2026-04-01 01:03:50.991011 WARNING::Fitting problem for feature 139 returning NA
2026-04-01 01:03:51.067804 WARNING::Fitting problem for feature 150 returning NA
2026-04-01 01:04:16.189491 WARNING::Fitting problem for feature 124 returning NA
2026-04-01 01:04:25.037337 WARNING::Fitting problem for feature 124 returning NA
2026-04-01 01:04:50.547042 WARNING::Fitting problem for feature 124 returning NA
2026-04-01 01:05:00.696775 WARNING::Fitting problem for feature 124 returning NA
2026-04-01 01:05:01.359869 WARNING::Deleting existing residuals file: /tmp/RtmpmA8sVA/file275d0b3097db2d/fits/residuals_linear.rds
2026-04-01 01:05:01.421313 WARNING::Deleting existing fitted file: /tmp/RtmpmA8sVA/file275d0b3097db2d/fits/fitted_linear.rds
2026-04-01 01:05:01.460182 WARNING::Deleting existing residuals file: /tmp/RtmpmA8sVA/file275d0b3097db2d/fits/residuals_logistic.rds
2026-04-01 01:05:01.529907 WARNING::Deleting existing fitted file: /tmp/RtmpmA8sVA/file275d0b3097db2d/fits/fitted_logistic.rds
2026-04-01 01:05:24.377461 WARNING::Fitting problem for feature 124 returning NA
2026-04-01 01:05:29.763568 WARNING::Fitting problem for feature 124 returning NA
2026-04-01 01:05:30.065852 WARNING::Deleting existing residuals file: /tmp/RtmpmA8sVA/file275d0b3097db2d/fits/residuals_linear.rds
2026-04-01 01:05:30.130357 WARNING::Deleting existing fitted file: /tmp/RtmpmA8sVA/file275d0b3097db2d/fits/fitted_linear.rds
2026-04-01 01:05:30.1697 WARNING::Deleting existing residuals file: /tmp/RtmpmA8sVA/file275d0b3097db2d/fits/residuals_logistic.rds
2026-04-01 01:05:30.239044 WARNING::Deleting existing fitted file: /tmp/RtmpmA8sVA/file275d0b3097db2d/fits/fitted_logistic.rds
2026-04-01 01:05:49.330237 WARNING::Fitting problem for feature 124 returning NA
2026-04-01 01:05:55.717257 WARNING::Fitting problem for feature 124 returning NA
2026-04-01 01:05:56.014493 WARNING::Deleting existing residuals file: /tmp/RtmpmA8sVA/file275d0b3097db2d/fits/residuals_linear.rds
2026-04-01 01:05:56.076648 WARNING::Deleting existing fitted file: /tmp/RtmpmA8sVA/file275d0b3097db2d/fits/fitted_linear.rds
2026-04-01 01:05:56.115827 WARNING::Deleting existing residuals file: /tmp/RtmpmA8sVA/file275d0b3097db2d/fits/residuals_logistic.rds
2026-04-01 01:05:56.187196 WARNING::Deleting existing fitted file: /tmp/RtmpmA8sVA/file275d0b3097db2d/fits/fitted_logistic.rds
2026-04-01 01:06:14.046329 WARNING::Fitting problem for feature 50 returning NA
2026-04-01 01:06:14.122973 WARNING::Fitting problem for feature 62 returning NA
2026-04-01 01:06:14.20017 WARNING::Fitting problem for feature 74 returning NA
2026-04-01 01:06:14.225565 WARNING::Fitting problem for feature 78 returning NA
2026-04-01 01:06:14.263166 WARNING::Fitting problem for feature 84 returning NA
2026-04-01 01:06:14.345814 WARNING::Fitting problem for feature 96 returning NA
2026-04-01 01:06:14.351633 WARNING::Fitting problem for feature 97 returning NA
2026-04-01 01:06:14.364002 WARNING::Fitting problem for feature 99 returning NA
2026-04-01 01:06:14.464083 WARNING::Fitting problem for feature 114 returning NA
2026-04-01 01:06:14.470037 WARNING::Fitting problem for feature 115 returning NA
2026-04-01 01:06:14.522718 WARNING::Fitting problem for feature 123 returning NA
2026-04-01 01:06:14.591084 WARNING::Fitting problem for feature 130 returning NA
2026-04-01 01:06:14.603419 WARNING::Fitting problem for feature 132 returning NA
2026-04-01 01:06:14.644241 WARNING::Fitting problem for feature 139 returning NA
2026-04-01 01:06:14.712372 WARNING::Fitting problem for feature 150 returning NA
2026-04-01 01:06:26.609265 WARNING::Fitting problem for feature 50 returning NA
2026-04-01 01:06:26.693615 WARNING::Fitting problem for feature 62 returning NA
2026-04-01 01:06:26.773234 WARNING::Fitting problem for feature 74 returning NA
2026-04-01 01:06:26.796929 WARNING::Fitting problem for feature 78 returning NA
2026-04-01 01:06:26.83294 WARNING::Fitting problem for feature 84 returning NA
2026-04-01 01:06:26.909849 WARNING::Fitting problem for feature 96 returning NA
2026-04-01 01:06:26.915268 WARNING::Fitting problem for feature 97 returning NA
2026-04-01 01:06:26.927348 WARNING::Fitting problem for feature 99 returning NA
2026-04-01 01:06:27.027381 WARNING::Fitting problem for feature 114 returning NA
2026-04-01 01:06:27.032976 WARNING::Fitting problem for feature 115 returning NA
2026-04-01 01:06:27.083519 WARNING::Fitting problem for feature 123 returning NA
2026-04-01 01:06:27.124119 WARNING::Fitting problem for feature 130 returning NA
2026-04-01 01:06:27.136485 WARNING::Fitting problem for feature 132 returning NA
2026-04-01 01:06:27.177497 WARNING::Fitting problem for feature 139 returning NA
2026-04-01 01:06:27.247053 WARNING::Fitting problem for feature 150 returning NA
2026-04-01 01:06:27.489747 WARNING::Deleting existing residuals file: /tmp/RtmpmA8sVA/file275d0b3097db2d/fits/residuals_linear.rds
2026-04-01 01:06:27.550776 WARNING::Deleting existing fitted file: /tmp/RtmpmA8sVA/file275d0b3097db2d/fits/fitted_linear.rds
2026-04-01 01:06:27.613397 WARNING::Deleting existing residuals file: /tmp/RtmpmA8sVA/file275d0b3097db2d/fits/residuals_logistic.rds
2026-04-01 01:06:27.912732 WARNING::Deleting existing fitted file: /tmp/RtmpmA8sVA/file275d0b3097db2d/fits/fitted_logistic.rds
2026-04-01 01:06:48.419424 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2026-04-01 01:06:48.436977 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2026-04-01 01:06:48.448769 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2026-04-01 01:06:48.501639 ERROR::No fixed, group, or
ordered effects included in formula.
2026-04-01 01:06:48.518425 ERROR::Effect name not found in metadata: d
2026-04-01 01:06:48.529793 ERROR::No user formula provided
2026-04-01 01:06:48.561924 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2026-04-01 01:06:48.573655 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2026-04-01 01:06:51.408907 INFO::Writing function arguments to log file
2026-04-01 01:06:51.423113 INFO::Verifying options selected are valid
2026-04-01 01:06:53.674672 INFO::Writing function arguments to log file
2026-04-01 01:06:53.686766 INFO::Verifying options selected are valid
2026-04-01 01:06:53.687818 INFO::Determining format of input files
2026-04-01 01:06:53.688782 INFO::Input format is data samples as rows and metadata samples as rows
2026-04-01 01:06:53.691064 INFO::Running selected normalization method: TSS
2026-04-01 01:06:53.69249 INFO::Creating output feature tables folder
2026-04-01 01:06:53.693436 INFO::Writing normalized data to file /tmp/RtmpmA8sVA/file275d0b575fd68/features/data_norm.tsv
2026-04-01 01:06:53.694879 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2026-04-01 01:06:53.695765 INFO::Total samples in data: 16
2026-04-01 01:06:53.696611 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2026-04-01 01:06:53.697447 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2026-04-01 01:06:53.699319 INFO::Total filtered features: 0
2026-04-01 01:06:53.700245 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2026-04-01 01:06:53.701388 INFO::Total features filtered by non-zero variance filtering: 0
2026-04-01 01:06:53.702309 INFO::Filtered feature names from variance filtering:
2026-04-01 01:06:53.703163 INFO::Writing filtered data to file /tmp/RtmpmA8sVA/file275d0b575fd68/features/filtered_data.tsv
2026-04-01 01:06:53.704608 INFO::Running selected transform method: LOG
2026-04-01 01:06:53.705767 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpmA8sVA/file275d0b575fd68/features/data_transformed.tsv
2026-04-01 01:06:53.707362 INFO::Applying z-score to standardize continuous metadata
2026-04-01 01:06:53.711778 INFO::Running the linear model component
2026-04-01 01:06:53.725576 INFO::Fitting model to feature number 1, a
2026-04-01 01:06:53.729987 INFO::Fitting model to feature number 2, b
2026-04-01 01:06:53.734168 INFO::Fitting model to feature number 3, c
2026-04-01 01:06:53.741143 INFO::Counting total values for each feature
2026-04-01 01:06:53.742903 INFO::Running the logistic model component
2026-04-01 01:06:53.756573 INFO::Fitting model to feature number 1, a
2026-04-01 01:06:53.762922 INFO::Fitting model to feature number 2, b
2026-04-01 01:06:53.768935 INFO::Fitting model to feature number 3, c
2026-04-01 01:06:53.77779 INFO::Counting total values for each feature
2026-04-01 01:06:53.779938 INFO::Re-running abundances for warn_prevalence
2026-04-01 01:06:53.780884 INFO::Running selected normalization method: TSS
2026-04-01 01:06:53.782375 INFO::Running selected transform method: LOG
2026-04-01 01:06:53.796318 INFO::Fitting model to feature number 1, a
2026-04-01 01:06:53.800747 INFO::Fitting model to feature number 2, b
2026-04-01 01:06:53.805001 INFO::Fitting model to feature number 3, c
2026-04-01 01:06:53.879339 INFO::Creating fits folder
2026-04-01 01:06:53.880456 INFO::Writing residuals to file /tmp/RtmpmA8sVA/file275d0b575fd68/fits/residuals_linear.rds
2026-04-01 01:06:53.88158 INFO::Writing fitted values to file /tmp/RtmpmA8sVA/file275d0b575fd68/fits/fitted_linear.rds
2026-04-01 01:06:53.882771 INFO::Writing residuals to file /tmp/RtmpmA8sVA/file275d0b575fd68/fits/residuals_logistic.rds
2026-04-01 01:06:53.883936 INFO::Writing fitted values to file /tmp/RtmpmA8sVA/file275d0b575fd68/fits/fitted_logistic.rds
2026-04-01 01:06:53.886188 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpmA8sVA/file275d0b575fd68/all_results.tsv
2026-04-01 01:06:53.887825 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/RtmpmA8sVA/file275d0b575fd68/significant_results.tsv
2026-04-01 01:06:53.889114 INFO::Creating output figures folder
2026-04-01 01:06:53.890441 INFO::Writing summary plot of significant
results to file: /tmp/RtmpmA8sVA/file275d0b575fd68/figures/summary_plot.pdf
2026-04-01 01:06:55.509885 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpmA8sVA/file275d0b575fd68/figures
2026-04-01 01:06:55.511769 INFO::Plotting associations from most to least significant, grouped by metadata
2026-04-01 01:06:55.516692 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-04-01 01:06:56.046242 INFO::Writing summary plot of
significant results to file: /tmp/RtmpmA8sVA/file275d0b575fd68/figures/summary_plot.pdf
2026-04-01 01:06:57.625323 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpmA8sVA/file275d0b575fd68/figures
2026-04-01 01:06:57.626941 INFO::Plotting associations from most to least significant, grouped by metadata
2026-04-01 01:06:57.631812 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-04-01 01:06:58.151699 INFO::Running the linear model component
2026-04-01 01:06:58.160711 INFO::Fitting model to feature number 1, a
2026-04-01 01:06:58.1651 INFO::Fitting model to feature number 2, b
2026-04-01 01:06:58.169204 INFO::Fitting model to feature number 3, c
2026-04-01 01:06:58.176419 INFO::Counting total values for each feature
2026-04-01 01:06:58.178127 INFO::Running the logistic model component
2026-04-01 01:06:58.186721 INFO::Fitting model to feature number 1, a
2026-04-01 01:06:58.192948 INFO::Fitting model to feature number 2, b
2026-04-01 01:06:58.19883 INFO::Fitting model to feature number 3, c
2026-04-01 01:06:58.207623 INFO::Counting total values for each feature
2026-04-01 01:06:58.209638 INFO::Re-running abundances for warn_prevalence
2026-04-01 01:06:58.21041 INFO::Running selected normalization method: TSS
2026-04-01 01:06:58.211747 INFO::Running selected transform method: LOG
2026-04-01 01:06:58.220499 INFO::Fitting model to feature number 1, a
2026-04-01 01:06:58.224657 INFO::Fitting model to feature number 2, b
2026-04-01 01:06:58.228758 INFO::Fitting model to feature number 3, c
2026-04-01 01:06:58.416247 INFO::Creating output folder
2026-04-01 01:06:58.417366 INFO::Creating output figures folder
2026-04-01 01:06:58.418875 INFO::Writing summary plot of significant
results to file: /tmp/RtmpmA8sVA/file275d0b7f6088a2/figures/summary_plot.pdf
2026-04-01 01:07:00.062333 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpmA8sVA/file275d0b7f6088a2/figures
2026-04-01 01:07:00.064252 INFO::Plotting associations from most to least significant, grouped by metadata
2026-04-01 01:07:00.069482 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-04-01 01:07:01.077265 INFO::Applying z-score to standardize continuous metadata
2026-04-01 01:07:01.084911 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2026-04-01 01:07:01.085864 INFO::Bypass z-score application to metadata
2026-04-01 01:07:01.088594 INFO::Bypass z-score application to metadata
2026-04-01 01:07:01.108814 INFO::Determining format of input files
2026-04-01 01:07:01.109831 INFO::Input format is data samples as rows and metadata samples as rows
2026-04-01 01:07:01.110721 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2026-04-01 01:07:01.118693 INFO::Determining format of input files
2026-04-01 01:07:01.119807 INFO::Input format is data samples as columns and metadata samples as rows
2026-04-01 01:07:01.121113 INFO::Input format is feature_specific_covariate samples as columns
2026-04-01 01:07:01.129761 INFO::Determining format of input files
2026-04-01 01:07:01.130808 INFO::Input format is data samples as rows and metadata samples as rows
2026-04-01 01:07:01.131873 INFO::Input format is feature_specific_covariate samples as columns
2026-04-01 01:07:01.133642 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2026-04-01 01:07:01.134449 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2026-04-01 01:07:01.146665 INFO::Running selected transform method: LOG
2026-04-01 01:07:01.147885 INFO::Creating output feature tables folder
2026-04-01 01:07:01.148783 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpmA8sVA/file275d0b3a000023/features/data_transformed.tsv
2026-04-01 01:07:01.152979 INFO::Running selected transform method: LOG
2026-04-01 01:07:01.154025 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpmA8sVA/file275d0b3a000023/features/data_transformed.tsv
2026-04-01 01:07:01.158143 INFO::Running selected transform method: PLOG
2026-04-01 01:07:01.161331 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpmA8sVA/file275d0b3a000023/features/data_transformed.tsv
2026-04-01 01:07:01.165225 INFO::Running selected transform method: NONE
2026-04-01 01:07:01.166054 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpmA8sVA/file275d0b3a000023/features/data_transformed.tsv
2026-04-01 01:07:01.174029 INFO::Running the linear model component
2026-04-01 01:07:01.182755 INFO::Fitting model to feature number 1, a
2026-04-01 01:07:01.187046 INFO::Fitting model to feature number 2, b
2026-04-01 01:07:01.191086 INFO::Fitting model to feature number 3, c
2026-04-01 01:07:01.198108 INFO::Counting total values for each feature
2026-04-01 01:07:01.199778 INFO::Running the logistic model component
2026-04-01 01:07:01.208232 INFO::Fitting model to feature number 1, a
2026-04-01 01:07:01.214745 INFO::Fitting model to feature number 2, b
2026-04-01 01:07:01.220879 INFO::Fitting model to feature number 3, c
2026-04-01 01:07:01.230073 INFO::Counting total values for each feature
2026-04-01 01:07:01.23226 INFO::Re-running abundances for warn_prevalence
2026-04-01 01:07:01.233106 INFO::Running selected normalization method: TSS
2026-04-01 01:07:01.234467 INFO::Running selected transform method: LOG
2026-04-01 01:07:01.243593 INFO::Fitting model to feature number 1, a
2026-04-01 01:07:01.248019 INFO::Fitting model to feature number 2, b
2026-04-01 01:07:01.252134 INFO::Fitting model to feature number 3, c
2026-04-01 01:07:01.33382 INFO::Creating output folder
2026-04-01 01:07:01.334883 INFO::Creating fits folder
2026-04-01 01:07:01.335746 INFO::Writing residuals to file /tmp/RtmpmA8sVA/file275d0b74b1471a/fits/residuals_linear.rds
2026-04-01 01:07:01.336755 INFO::Writing fitted values to file /tmp/RtmpmA8sVA/file275d0b74b1471a/fits/fitted_linear.rds
2026-04-01 01:07:01.337858 INFO::Writing residuals to file /tmp/RtmpmA8sVA/file275d0b74b1471a/fits/residuals_logistic.rds
2026-04-01 01:07:01.338931 INFO::Writing fitted values to file /tmp/RtmpmA8sVA/file275d0b74b1471a/fits/fitted_logistic.rds
2026-04-01 01:07:01.341304 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpmA8sVA/file275d0b74b1471a/all_results.tsv
2026-04-01 01:07:01.342973 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/RtmpmA8sVA/file275d0b74b1471a/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
356.369 7.656 364.014
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 19.209 | 0.523 | 19.732 | |
| maaslin_check_arguments | 0.162 | 0.001 | 0.164 | |
| maaslin_check_formula | 0.143 | 0.002 | 0.145 | |
| maaslin_compute_formula | 0.181 | 0.011 | 0.192 | |
| maaslin_contrast_test | 18.818 | 0.250 | 19.068 | |
| maaslin_filter | 0.456 | 0.034 | 0.490 | |
| maaslin_fit | 12.508 | 0.148 | 12.656 | |
| maaslin_log_arguments | 0.133 | 0.002 | 0.135 | |
| maaslin_normalize | 0.261 | 0.003 | 0.264 | |
| maaslin_plot_results | 42.940 | 0.319 | 43.219 | |
| maaslin_plot_results_from_output | 42.849 | 0.333 | 43.185 | |
| maaslin_process_metadata | 0.445 | 0.012 | 0.457 | |
| maaslin_read_data | 0.120 | 0.001 | 0.122 | |
| maaslin_reorder_data | 0.128 | 0.001 | 0.128 | |
| maaslin_transform | 0.524 | 0.042 | 0.565 | |
| maaslin_write_results | 13.456 | 0.113 | 13.570 | |
| maaslin_write_results_lefse_format | 14.950 | 0.093 | 15.043 | |
| preprocess_dna_mtx | 0.004 | 0.000 | 0.003 | |
| preprocess_taxa_mtx | 0.004 | 0.000 | 0.004 | |