William Nickols
| Snapshot Date: 2025-12-04 13:40 -0500 (Thu, 04 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: devel |
| git_last_commit: b274055 |
| git_last_commit_date: 2025-10-29 11:33:46 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-05 11:35 -0500 (Fri, 05 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4869 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4576 |
| 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 1157/2331 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maaslin3 1.3.0 (landing page) William Nickols
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | 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: 1.3.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings maaslin3_1.3.0.tar.gz |
| StartedAt: 2025-12-05 01:00:54 -0500 (Fri, 05 Dec 2025) |
| EndedAt: 2025-12-05 01:22:27 -0500 (Fri, 05 Dec 2025) |
| EllapsedTime: 1292.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maaslin3.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings maaslin3_1.3.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/maaslin3.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 ‘1.3.0’
* 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 43.095 0.373 43.470
maaslin_plot_results 42.809 0.367 43.134
maaslin3 19.032 0.566 19.602
maaslin_contrast_test 18.147 0.490 18.637
maaslin_write_results_lefse_format 14.814 0.173 14.988
maaslin_write_results 12.737 0.143 12.895
maaslin_fit 12.260 0.142 12.403
* 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-3.23-bioc/R/bin/R CMD INSTALL maaslin3 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘maaslin3’ ... ** this is package ‘maaslin3’ version ‘1.3.0’ ** 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 Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(maaslin3)
>
> test_check("maaslin3")
2025-12-05 01:07:06.646683 WARNING::Fitting problem for feature 50 returning NA
2025-12-05 01:07:06.720817 WARNING::Fitting problem for feature 62 returning NA
2025-12-05 01:07:06.809475 WARNING::Fitting problem for feature 74 returning NA
2025-12-05 01:07:06.830861 WARNING::Fitting problem for feature 78 returning NA
2025-12-05 01:07:06.864737 WARNING::Fitting problem for feature 84 returning NA
2025-12-05 01:07:06.946011 WARNING::Fitting problem for feature 96 returning NA
2025-12-05 01:07:06.951408 WARNING::Fitting problem for feature 97 returning NA
2025-12-05 01:07:06.963101 WARNING::Fitting problem for feature 99 returning NA
2025-12-05 01:07:07.072948 WARNING::Fitting problem for feature 114 returning NA
2025-12-05 01:07:07.078664 WARNING::Fitting problem for feature 115 returning NA
2025-12-05 01:07:07.12938 WARNING::Fitting problem for feature 123 returning NA
2025-12-05 01:07:07.17095 WARNING::Fitting problem for feature 130 returning NA
2025-12-05 01:07:07.182956 WARNING::Fitting problem for feature 132 returning NA
2025-12-05 01:07:07.223519 WARNING::Fitting problem for feature 139 returning NA
2025-12-05 01:07:07.303139 WARNING::Fitting problem for feature 150 returning NA
2025-12-05 01:07:23.049935 WARNING::Fitting problem for feature 50 returning NA
2025-12-05 01:07:23.123446 WARNING::Fitting problem for feature 62 returning NA
2025-12-05 01:07:23.19621 WARNING::Fitting problem for feature 74 returning NA
2025-12-05 01:07:23.21817 WARNING::Fitting problem for feature 78 returning NA
2025-12-05 01:07:23.253308 WARNING::Fitting problem for feature 84 returning NA
2025-12-05 01:07:23.339289 WARNING::Fitting problem for feature 96 returning NA
2025-12-05 01:07:23.344493 WARNING::Fitting problem for feature 97 returning NA
2025-12-05 01:07:23.355983 WARNING::Fitting problem for feature 99 returning NA
2025-12-05 01:07:23.448505 WARNING::Fitting problem for feature 114 returning NA
2025-12-05 01:07:23.45381 WARNING::Fitting problem for feature 115 returning NA
2025-12-05 01:07:23.502826 WARNING::Fitting problem for feature 123 returning NA
2025-12-05 01:07:23.543475 WARNING::Fitting problem for feature 130 returning NA
2025-12-05 01:07:23.555417 WARNING::Fitting problem for feature 132 returning NA
2025-12-05 01:07:23.595889 WARNING::Fitting problem for feature 139 returning NA
2025-12-05 01:07:23.665152 WARNING::Fitting problem for feature 150 returning NA
2025-12-05 01:07:48.676271 WARNING::Fitting problem for feature 50 returning NA
2025-12-05 01:07:48.750489 WARNING::Fitting problem for feature 62 returning NA
2025-12-05 01:07:48.824211 WARNING::Fitting problem for feature 74 returning NA
2025-12-05 01:07:48.846743 WARNING::Fitting problem for feature 78 returning NA
2025-12-05 01:07:48.881871 WARNING::Fitting problem for feature 84 returning NA
2025-12-05 01:07:48.958181 WARNING::Fitting problem for feature 96 returning NA
2025-12-05 01:07:48.963675 WARNING::Fitting problem for feature 97 returning NA
2025-12-05 01:07:48.975523 WARNING::Fitting problem for feature 99 returning NA
2025-12-05 01:07:49.070417 WARNING::Fitting problem for feature 114 returning NA
2025-12-05 01:07:49.075996 WARNING::Fitting problem for feature 115 returning NA
2025-12-05 01:07:49.128418 WARNING::Fitting problem for feature 123 returning NA
2025-12-05 01:07:49.169565 WARNING::Fitting problem for feature 130 returning NA
2025-12-05 01:07:49.181577 WARNING::Fitting problem for feature 132 returning NA
2025-12-05 01:07:49.223318 WARNING::Fitting problem for feature 139 returning NA
2025-12-05 01:07:49.32087 WARNING::Fitting problem for feature 150 returning NA
2025-12-05 01:08:01.857509 WARNING::Fitting problem for feature 50 returning NA
2025-12-05 01:08:01.932989 WARNING::Fitting problem for feature 62 returning NA
2025-12-05 01:08:02.008134 WARNING::Fitting problem for feature 74 returning NA
2025-12-05 01:08:02.029845 WARNING::Fitting problem for feature 78 returning NA
2025-12-05 01:08:02.064875 WARNING::Fitting problem for feature 84 returning NA
2025-12-05 01:08:02.141119 WARNING::Fitting problem for feature 96 returning NA
2025-12-05 01:08:02.146472 WARNING::Fitting problem for feature 97 returning NA
2025-12-05 01:08:02.158156 WARNING::Fitting problem for feature 99 returning NA
2025-12-05 01:08:02.252458 WARNING::Fitting problem for feature 114 returning NA
2025-12-05 01:08:02.257855 WARNING::Fitting problem for feature 115 returning NA
2025-12-05 01:08:02.30836 WARNING::Fitting problem for feature 123 returning NA
2025-12-05 01:08:02.348959 WARNING::Fitting problem for feature 130 returning NA
2025-12-05 01:08:02.360728 WARNING::Fitting problem for feature 132 returning NA
2025-12-05 01:08:02.413944 WARNING::Fitting problem for feature 139 returning NA
2025-12-05 01:08:02.509827 WARNING::Fitting problem for feature 150 returning NA
2025-12-05 01:08:02.713153 WARNING::Deleting existing residuals file: /tmp/RtmpcQbgi6/file3225403d6cdfd1/fits/residuals_linear.rds
2025-12-05 01:08:02.774528 WARNING::Deleting existing fitted file: /tmp/RtmpcQbgi6/file3225403d6cdfd1/fits/fitted_linear.rds
2025-12-05 01:08:02.838573 WARNING::Deleting existing residuals file: /tmp/RtmpcQbgi6/file3225403d6cdfd1/fits/residuals_logistic.rds
2025-12-05 01:08:03.139439 WARNING::Deleting existing fitted file: /tmp/RtmpcQbgi6/file3225403d6cdfd1/fits/fitted_logistic.rds
2025-12-05 01:08:25.207362 WARNING::Fitting problem for feature 50 returning NA
2025-12-05 01:08:25.29408 WARNING::Fitting problem for feature 62 returning NA
2025-12-05 01:08:25.381134 WARNING::Fitting problem for feature 74 returning NA
2025-12-05 01:08:25.406648 WARNING::Fitting problem for feature 78 returning NA
2025-12-05 01:08:25.445134 WARNING::Fitting problem for feature 84 returning NA
2025-12-05 01:08:25.531977 WARNING::Fitting problem for feature 96 returning NA
2025-12-05 01:08:25.537725 WARNING::Fitting problem for feature 97 returning NA
2025-12-05 01:08:25.550715 WARNING::Fitting problem for feature 99 returning NA
2025-12-05 01:08:25.657798 WARNING::Fitting problem for feature 114 returning NA
2025-12-05 01:08:25.664027 WARNING::Fitting problem for feature 115 returning NA
2025-12-05 01:08:25.720579 WARNING::Fitting problem for feature 123 returning NA
2025-12-05 01:08:25.765373 WARNING::Fitting problem for feature 130 returning NA
2025-12-05 01:08:25.778508 WARNING::Fitting problem for feature 132 returning NA
2025-12-05 01:08:25.823855 WARNING::Fitting problem for feature 139 returning NA
2025-12-05 01:08:25.919245 WARNING::Fitting problem for feature 150 returning NA
2025-12-05 01:08:38.372071 WARNING::Fitting problem for feature 50 returning NA
2025-12-05 01:08:38.451007 WARNING::Fitting problem for feature 62 returning NA
2025-12-05 01:08:38.528695 WARNING::Fitting problem for feature 74 returning NA
2025-12-05 01:08:38.551412 WARNING::Fitting problem for feature 78 returning NA
2025-12-05 01:08:38.587444 WARNING::Fitting problem for feature 84 returning NA
2025-12-05 01:08:38.670492 WARNING::Fitting problem for feature 96 returning NA
2025-12-05 01:08:38.676795 WARNING::Fitting problem for feature 97 returning NA
2025-12-05 01:08:38.689725 WARNING::Fitting problem for feature 99 returning NA
2025-12-05 01:08:38.792579 WARNING::Fitting problem for feature 114 returning NA
2025-12-05 01:08:38.798546 WARNING::Fitting problem for feature 115 returning NA
2025-12-05 01:08:38.849731 WARNING::Fitting problem for feature 123 returning NA
2025-12-05 01:08:38.889309 WARNING::Fitting problem for feature 130 returning NA
2025-12-05 01:08:38.901353 WARNING::Fitting problem for feature 132 returning NA
2025-12-05 01:08:38.940643 WARNING::Fitting problem for feature 139 returning NA
2025-12-05 01:08:39.009728 WARNING::Fitting problem for feature 150 returning NA
2025-12-05 01:08:39.218411 WARNING::Deleting existing residuals file: /tmp/RtmpcQbgi6/file3225403d6cdfd1/fits/residuals_linear.rds
2025-12-05 01:08:39.279164 WARNING::Deleting existing fitted file: /tmp/RtmpcQbgi6/file3225403d6cdfd1/fits/fitted_linear.rds
2025-12-05 01:08:39.343246 WARNING::Deleting existing residuals file: /tmp/RtmpcQbgi6/file3225403d6cdfd1/fits/residuals_logistic.rds
2025-12-05 01:08:39.642751 WARNING::Deleting existing fitted file: /tmp/RtmpcQbgi6/file3225403d6cdfd1/fits/fitted_logistic.rds
2025-12-05 01:09:01.03581 WARNING::Fitting problem for feature 50 returning NA
2025-12-05 01:09:01.111088 WARNING::Fitting problem for feature 62 returning NA
2025-12-05 01:09:01.184747 WARNING::Fitting problem for feature 74 returning NA
2025-12-05 01:09:01.205993 WARNING::Fitting problem for feature 78 returning NA
2025-12-05 01:09:01.239357 WARNING::Fitting problem for feature 84 returning NA
2025-12-05 01:09:01.312945 WARNING::Fitting problem for feature 96 returning NA
2025-12-05 01:09:01.318213 WARNING::Fitting problem for feature 97 returning NA
2025-12-05 01:09:01.329924 WARNING::Fitting problem for feature 99 returning NA
2025-12-05 01:09:01.424634 WARNING::Fitting problem for feature 114 returning NA
2025-12-05 01:09:01.430008 WARNING::Fitting problem for feature 115 returning NA
2025-12-05 01:09:01.480185 WARNING::Fitting problem for feature 123 returning NA
2025-12-05 01:09:01.521288 WARNING::Fitting problem for feature 130 returning NA
2025-12-05 01:09:01.533298 WARNING::Fitting problem for feature 132 returning NA
2025-12-05 01:09:01.574777 WARNING::Fitting problem for feature 139 returning NA
2025-12-05 01:09:01.647092 WARNING::Fitting problem for feature 150 returning NA
2025-12-05 01:09:13.270164 WARNING::Fitting problem for feature 50 returning NA
2025-12-05 01:09:13.346199 WARNING::Fitting problem for feature 62 returning NA
2025-12-05 01:09:13.479017 WARNING::Fitting problem for feature 74 returning NA
2025-12-05 01:09:13.501154 WARNING::Fitting problem for feature 78 returning NA
2025-12-05 01:09:13.535181 WARNING::Fitting problem for feature 84 returning NA
2025-12-05 01:09:13.609867 WARNING::Fitting problem for feature 96 returning NA
2025-12-05 01:09:13.615155 WARNING::Fitting problem for feature 97 returning NA
2025-12-05 01:09:13.62697 WARNING::Fitting problem for feature 99 returning NA
2025-12-05 01:09:13.721723 WARNING::Fitting problem for feature 114 returning NA
2025-12-05 01:09:13.727214 WARNING::Fitting problem for feature 115 returning NA
2025-12-05 01:09:13.777175 WARNING::Fitting problem for feature 123 returning NA
2025-12-05 01:09:13.817011 WARNING::Fitting problem for feature 130 returning NA
2025-12-05 01:09:13.828929 WARNING::Fitting problem for feature 132 returning NA
2025-12-05 01:09:13.870205 WARNING::Fitting problem for feature 139 returning NA
2025-12-05 01:09:13.940754 WARNING::Fitting problem for feature 150 returning NA
2025-12-05 01:09:14.140531 WARNING::Deleting existing residuals file: /tmp/RtmpcQbgi6/file3225403d6cdfd1/fits/residuals_linear.rds
2025-12-05 01:09:14.201187 WARNING::Deleting existing fitted file: /tmp/RtmpcQbgi6/file3225403d6cdfd1/fits/fitted_linear.rds
2025-12-05 01:09:14.264011 WARNING::Deleting existing residuals file: /tmp/RtmpcQbgi6/file3225403d6cdfd1/fits/residuals_logistic.rds
2025-12-05 01:09:14.56377 WARNING::Deleting existing fitted file: /tmp/RtmpcQbgi6/file3225403d6cdfd1/fits/fitted_logistic.rds
2025-12-05 01:09:36.761144 WARNING::Fitting problem for feature 50 returning NA
2025-12-05 01:09:36.857268 WARNING::Fitting problem for feature 62 returning NA
2025-12-05 01:09:36.932529 WARNING::Fitting problem for feature 74 returning NA
2025-12-05 01:09:36.954587 WARNING::Fitting problem for feature 78 returning NA
2025-12-05 01:09:36.98933 WARNING::Fitting problem for feature 84 returning NA
2025-12-05 01:09:37.067541 WARNING::Fitting problem for feature 96 returning NA
2025-12-05 01:09:37.072925 WARNING::Fitting problem for feature 97 returning NA
2025-12-05 01:09:37.085084 WARNING::Fitting problem for feature 99 returning NA
2025-12-05 01:09:37.180942 WARNING::Fitting problem for feature 114 returning NA
2025-12-05 01:09:37.186852 WARNING::Fitting problem for feature 115 returning NA
2025-12-05 01:09:37.236399 WARNING::Fitting problem for feature 123 returning NA
2025-12-05 01:09:37.276541 WARNING::Fitting problem for feature 130 returning NA
2025-12-05 01:09:37.288486 WARNING::Fitting problem for feature 132 returning NA
2025-12-05 01:09:37.328744 WARNING::Fitting problem for feature 139 returning NA
2025-12-05 01:09:37.398007 WARNING::Fitting problem for feature 150 returning NA
2025-12-05 01:09:48.222413 WARNING::Fitting problem for feature 50 returning NA
2025-12-05 01:09:48.299737 WARNING::Fitting problem for feature 62 returning NA
2025-12-05 01:09:48.374025 WARNING::Fitting problem for feature 74 returning NA
2025-12-05 01:09:48.395944 WARNING::Fitting problem for feature 78 returning NA
2025-12-05 01:09:48.430954 WARNING::Fitting problem for feature 84 returning NA
2025-12-05 01:09:48.506881 WARNING::Fitting problem for feature 96 returning NA
2025-12-05 01:09:48.512408 WARNING::Fitting problem for feature 97 returning NA
2025-12-05 01:09:48.524085 WARNING::Fitting problem for feature 99 returning NA
2025-12-05 01:09:48.623352 WARNING::Fitting problem for feature 114 returning NA
2025-12-05 01:09:48.628983 WARNING::Fitting problem for feature 115 returning NA
2025-12-05 01:09:48.679254 WARNING::Fitting problem for feature 123 returning NA
2025-12-05 01:09:48.719888 WARNING::Fitting problem for feature 130 returning NA
2025-12-05 01:09:48.731723 WARNING::Fitting problem for feature 132 returning NA
2025-12-05 01:09:48.773215 WARNING::Fitting problem for feature 139 returning NA
2025-12-05 01:09:48.844254 WARNING::Fitting problem for feature 150 returning NA
2025-12-05 01:10:13.283987 WARNING::Fitting problem for feature 124 returning NA
2025-12-05 01:10:21.723449 WARNING::Fitting problem for feature 124 returning NA
2025-12-05 01:10:47.257421 WARNING::Fitting problem for feature 124 returning NA
2025-12-05 01:10:55.965176 WARNING::Fitting problem for feature 124 returning NA
2025-12-05 01:10:56.626421 WARNING::Deleting existing residuals file: /tmp/RtmpcQbgi6/file322540a47725e/fits/residuals_linear.rds
2025-12-05 01:10:56.687946 WARNING::Deleting existing fitted file: /tmp/RtmpcQbgi6/file322540a47725e/fits/fitted_linear.rds
2025-12-05 01:10:56.72663 WARNING::Deleting existing residuals file: /tmp/RtmpcQbgi6/file322540a47725e/fits/residuals_logistic.rds
2025-12-05 01:10:56.7954 WARNING::Deleting existing fitted file: /tmp/RtmpcQbgi6/file322540a47725e/fits/fitted_logistic.rds
2025-12-05 01:11:19.309483 WARNING::Fitting problem for feature 124 returning NA
2025-12-05 01:11:25.883952 WARNING::Fitting problem for feature 124 returning NA
2025-12-05 01:11:26.192016 WARNING::Deleting existing residuals file: /tmp/RtmpcQbgi6/file322540a47725e/fits/residuals_linear.rds
2025-12-05 01:11:26.254028 WARNING::Deleting existing fitted file: /tmp/RtmpcQbgi6/file322540a47725e/fits/fitted_linear.rds
2025-12-05 01:11:26.292562 WARNING::Deleting existing residuals file: /tmp/RtmpcQbgi6/file322540a47725e/fits/residuals_logistic.rds
2025-12-05 01:11:26.361724 WARNING::Deleting existing fitted file: /tmp/RtmpcQbgi6/file322540a47725e/fits/fitted_logistic.rds
2025-12-05 01:11:44.821131 WARNING::Fitting problem for feature 124 returning NA
2025-12-05 01:11:50.962052 WARNING::Fitting problem for feature 124 returning NA
2025-12-05 01:11:51.257226 WARNING::Deleting existing residuals file: /tmp/RtmpcQbgi6/file322540a47725e/fits/residuals_linear.rds
2025-12-05 01:11:51.318856 WARNING::Deleting existing fitted file: /tmp/RtmpcQbgi6/file322540a47725e/fits/fitted_linear.rds
2025-12-05 01:11:51.35745 WARNING::Deleting existing residuals file: /tmp/RtmpcQbgi6/file322540a47725e/fits/residuals_logistic.rds
2025-12-05 01:11:51.426496 WARNING::Deleting existing fitted file: /tmp/RtmpcQbgi6/file322540a47725e/fits/fitted_logistic.rds
2025-12-05 01:12:09.603277 WARNING::Fitting problem for feature 50 returning NA
2025-12-05 01:12:09.684752 WARNING::Fitting problem for feature 62 returning NA
2025-12-05 01:12:09.765706 WARNING::Fitting problem for feature 74 returning NA
2025-12-05 01:12:09.789665 WARNING::Fitting problem for feature 78 returning NA
2025-12-05 01:12:09.827819 WARNING::Fitting problem for feature 84 returning NA
2025-12-05 01:12:09.909552 WARNING::Fitting problem for feature 96 returning NA
2025-12-05 01:12:09.915386 WARNING::Fitting problem for feature 97 returning NA
2025-12-05 01:12:09.92795 WARNING::Fitting problem for feature 99 returning NA
2025-12-05 01:12:10.028621 WARNING::Fitting problem for feature 114 returning NA
2025-12-05 01:12:10.034727 WARNING::Fitting problem for feature 115 returning NA
2025-12-05 01:12:10.087871 WARNING::Fitting problem for feature 123 returning NA
2025-12-05 01:12:10.137937 WARNING::Fitting problem for feature 130 returning NA
2025-12-05 01:12:10.152389 WARNING::Fitting problem for feature 132 returning NA
2025-12-05 01:12:10.200851 WARNING::Fitting problem for feature 139 returning NA
2025-12-05 01:12:10.28606 WARNING::Fitting problem for feature 150 returning NA
2025-12-05 01:12:22.267005 WARNING::Fitting problem for feature 50 returning NA
2025-12-05 01:12:22.350724 WARNING::Fitting problem for feature 62 returning NA
2025-12-05 01:12:22.435001 WARNING::Fitting problem for feature 74 returning NA
2025-12-05 01:12:22.460613 WARNING::Fitting problem for feature 78 returning NA
2025-12-05 01:12:22.498606 WARNING::Fitting problem for feature 84 returning NA
2025-12-05 01:12:22.607521 WARNING::Fitting problem for feature 96 returning NA
2025-12-05 01:12:22.617018 WARNING::Fitting problem for feature 97 returning NA
2025-12-05 01:12:22.630092 WARNING::Fitting problem for feature 99 returning NA
2025-12-05 01:12:22.734206 WARNING::Fitting problem for feature 114 returning NA
2025-12-05 01:12:22.740503 WARNING::Fitting problem for feature 115 returning NA
2025-12-05 01:12:22.7955 WARNING::Fitting problem for feature 123 returning NA
2025-12-05 01:12:22.838536 WARNING::Fitting problem for feature 130 returning NA
2025-12-05 01:12:22.851087 WARNING::Fitting problem for feature 132 returning NA
2025-12-05 01:12:22.894154 WARNING::Fitting problem for feature 139 returning NA
2025-12-05 01:12:22.966193 WARNING::Fitting problem for feature 150 returning NA
2025-12-05 01:12:23.225274 WARNING::Deleting existing residuals file: /tmp/RtmpcQbgi6/file322540a47725e/fits/residuals_linear.rds
2025-12-05 01:12:23.286303 WARNING::Deleting existing fitted file: /tmp/RtmpcQbgi6/file322540a47725e/fits/fitted_linear.rds
2025-12-05 01:12:23.349617 WARNING::Deleting existing residuals file: /tmp/RtmpcQbgi6/file322540a47725e/fits/residuals_logistic.rds
2025-12-05 01:12:23.650264 WARNING::Deleting existing fitted file: /tmp/RtmpcQbgi6/file322540a47725e/fits/fitted_logistic.rds
2025-12-05 01:12:44.051076 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-12-05 01:12:44.069157 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-12-05 01:12:44.081653 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-12-05 01:12:44.135719 ERROR::No fixed, group, or
ordered effects included in formula.
2025-12-05 01:12:44.152755 ERROR::Effect name not found in metadata: d
2025-12-05 01:12:44.16442 ERROR::No user formula provided
2025-12-05 01:12:44.207343 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-12-05 01:12:44.219389 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-12-05 01:12:47.109421 INFO::Writing function arguments to log file
2025-12-05 01:12:47.123327 INFO::Verifying options selected are valid
2025-12-05 01:12:49.582541 INFO::Writing function arguments to log file
2025-12-05 01:12:49.594863 INFO::Verifying options selected are valid
2025-12-05 01:12:49.595999 INFO::Determining format of input files
2025-12-05 01:12:49.597005 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-05 01:12:49.599328 INFO::Running selected normalization method: TSS
2025-12-05 01:12:49.600872 INFO::Creating output feature tables folder
2025-12-05 01:12:49.6019 INFO::Writing normalized data to file /tmp/RtmpcQbgi6/file322540ebafcfd/features/data_norm.tsv
2025-12-05 01:12:49.603552 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-12-05 01:12:49.60452 INFO::Total samples in data: 16
2025-12-05 01:12:49.605446 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-12-05 01:12:49.606369 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-12-05 01:12:49.608413 INFO::Total filtered features: 0
2025-12-05 01:12:49.609422 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-12-05 01:12:49.610649 INFO::Total features filtered by non-zero variance filtering: 0
2025-12-05 01:12:49.61165 INFO::Filtered feature names from variance filtering:
2025-12-05 01:12:49.612594 INFO::Writing filtered data to file /tmp/RtmpcQbgi6/file322540ebafcfd/features/filtered_data.tsv
2025-12-05 01:12:49.614233 INFO::Running selected transform method: LOG
2025-12-05 01:12:49.615474 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpcQbgi6/file322540ebafcfd/features/data_transformed.tsv
2025-12-05 01:12:49.617171 INFO::Applying z-score to standardize continuous metadata
2025-12-05 01:12:49.622752 INFO::Running the linear model component
2025-12-05 01:12:49.636725 INFO::Fitting model to feature number 1, a
2025-12-05 01:12:49.641755 INFO::Fitting model to feature number 2, b
2025-12-05 01:12:49.64636 INFO::Fitting model to feature number 3, c
2025-12-05 01:12:49.654267 INFO::Counting total values for each feature
2025-12-05 01:12:49.656341 INFO::Running the logistic model component
2025-12-05 01:12:49.670328 INFO::Fitting model to feature number 1, a
2025-12-05 01:12:49.676963 INFO::Fitting model to feature number 2, b
2025-12-05 01:12:49.683332 INFO::Fitting model to feature number 3, c
2025-12-05 01:12:49.692734 INFO::Counting total values for each feature
2025-12-05 01:12:49.695076 INFO::Re-running abundances for warn_prevalence
2025-12-05 01:12:49.696071 INFO::Running selected normalization method: TSS
2025-12-05 01:12:49.69762 INFO::Running selected transform method: LOG
2025-12-05 01:12:49.711485 INFO::Fitting model to feature number 1, a
2025-12-05 01:12:49.716155 INFO::Fitting model to feature number 2, b
2025-12-05 01:12:49.72057 INFO::Fitting model to feature number 3, c
2025-12-05 01:12:49.809041 INFO::Creating fits folder
2025-12-05 01:12:49.810377 INFO::Writing residuals to file /tmp/RtmpcQbgi6/file322540ebafcfd/fits/residuals_linear.rds
2025-12-05 01:12:49.811594 INFO::Writing fitted values to file /tmp/RtmpcQbgi6/file322540ebafcfd/fits/fitted_linear.rds
2025-12-05 01:12:49.812912 INFO::Writing residuals to file /tmp/RtmpcQbgi6/file322540ebafcfd/fits/residuals_logistic.rds
2025-12-05 01:12:49.814103 INFO::Writing fitted values to file /tmp/RtmpcQbgi6/file322540ebafcfd/fits/fitted_logistic.rds
2025-12-05 01:12:49.81688 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpcQbgi6/file322540ebafcfd/all_results.tsv
2025-12-05 01:12:49.818559 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/RtmpcQbgi6/file322540ebafcfd/significant_results.tsv
2025-12-05 01:12:49.820012 INFO::Creating output figures folder
2025-12-05 01:12:49.821493 INFO::Writing summary plot of significant
results to file: /tmp/RtmpcQbgi6/file322540ebafcfd/figures/summary_plot.pdf
2025-12-05 01:12:51.441456 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpcQbgi6/file322540ebafcfd/figures
2025-12-05 01:12:51.443386 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-05 01:12:51.448338 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-05 01:12:51.973524 INFO::Writing summary plot of
significant results to file: /tmp/RtmpcQbgi6/file322540ebafcfd/figures/summary_plot.pdf
2025-12-05 01:12:53.630608 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpcQbgi6/file322540ebafcfd/figures
2025-12-05 01:12:53.632305 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-05 01:12:53.63801 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-05 01:12:54.184761 INFO::Running the linear model component
2025-12-05 01:12:54.194278 INFO::Fitting model to feature number 1, a
2025-12-05 01:12:54.198748 INFO::Fitting model to feature number 2, b
2025-12-05 01:12:54.203017 INFO::Fitting model to feature number 3, c
2025-12-05 01:12:54.210171 INFO::Counting total values for each feature
2025-12-05 01:12:54.211997 INFO::Running the logistic model component
2025-12-05 01:12:54.220621 INFO::Fitting model to feature number 1, a
2025-12-05 01:12:54.226854 INFO::Fitting model to feature number 2, b
2025-12-05 01:12:54.232661 INFO::Fitting model to feature number 3, c
2025-12-05 01:12:54.241545 INFO::Counting total values for each feature
2025-12-05 01:12:54.243643 INFO::Re-running abundances for warn_prevalence
2025-12-05 01:12:54.244463 INFO::Running selected normalization method: TSS
2025-12-05 01:12:54.245844 INFO::Running selected transform method: LOG
2025-12-05 01:12:54.254441 INFO::Fitting model to feature number 1, a
2025-12-05 01:12:54.258798 INFO::Fitting model to feature number 2, b
2025-12-05 01:12:54.262776 INFO::Fitting model to feature number 3, c
2025-12-05 01:12:54.352315 INFO::Creating output folder
2025-12-05 01:12:54.353512 INFO::Creating output figures folder
2025-12-05 01:12:54.35493 INFO::Writing summary plot of significant
results to file: /tmp/RtmpcQbgi6/file3225405c62ce8d/figures/summary_plot.pdf
2025-12-05 01:12:56.031595 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpcQbgi6/file3225405c62ce8d/figures
2025-12-05 01:12:56.033385 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-05 01:12:56.038419 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-05 01:12:57.036017 INFO::Applying z-score to standardize continuous metadata
2025-12-05 01:12:57.04437 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-12-05 01:12:57.045351 INFO::Bypass z-score application to metadata
2025-12-05 01:12:57.048029 INFO::Bypass z-score application to metadata
2025-12-05 01:12:57.067829 INFO::Determining format of input files
2025-12-05 01:12:57.068905 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-05 01:12:57.069896 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-12-05 01:12:57.07813 INFO::Determining format of input files
2025-12-05 01:12:57.079223 INFO::Input format is data samples as columns and metadata samples as rows
2025-12-05 01:12:57.08058 INFO::Input format is feature_specific_covariate samples as columns
2025-12-05 01:12:57.089041 INFO::Determining format of input files
2025-12-05 01:12:57.090006 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-05 01:12:57.091095 INFO::Input format is feature_specific_covariate samples as columns
2025-12-05 01:12:57.092778 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-12-05 01:12:57.093597 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-12-05 01:12:57.10575 INFO::Running selected transform method: LOG
2025-12-05 01:12:57.10688 INFO::Creating output feature tables folder
2025-12-05 01:12:57.107779 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpcQbgi6/file32254053c03486/features/data_transformed.tsv
2025-12-05 01:12:57.111722 INFO::Running selected transform method: LOG
2025-12-05 01:12:57.1128 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpcQbgi6/file32254053c03486/features/data_transformed.tsv
2025-12-05 01:12:57.116496 INFO::Running selected transform method: PLOG
2025-12-05 01:12:57.118116 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpcQbgi6/file32254053c03486/features/data_transformed.tsv
2025-12-05 01:12:57.120919 INFO::Running selected transform method: NONE
2025-12-05 01:12:57.121682 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpcQbgi6/file32254053c03486/features/data_transformed.tsv
2025-12-05 01:12:57.129494 INFO::Running the linear model component
2025-12-05 01:12:57.138495 INFO::Fitting model to feature number 1, a
2025-12-05 01:12:57.142761 INFO::Fitting model to feature number 2, b
2025-12-05 01:12:57.146753 INFO::Fitting model to feature number 3, c
2025-12-05 01:12:57.153896 INFO::Counting total values for each feature
2025-12-05 01:12:57.155562 INFO::Running the logistic model component
2025-12-05 01:12:57.163873 INFO::Fitting model to feature number 1, a
2025-12-05 01:12:57.169702 INFO::Fitting model to feature number 2, b
2025-12-05 01:12:57.175257 INFO::Fitting model to feature number 3, c
2025-12-05 01:12:57.183854 INFO::Counting total values for each feature
2025-12-05 01:12:57.185931 INFO::Re-running abundances for warn_prevalence
2025-12-05 01:12:57.186708 INFO::Running selected normalization method: TSS
2025-12-05 01:12:57.188078 INFO::Running selected transform method: LOG
2025-12-05 01:12:57.196319 INFO::Fitting model to feature number 1, a
2025-12-05 01:12:57.200451 INFO::Fitting model to feature number 2, b
2025-12-05 01:12:57.204488 INFO::Fitting model to feature number 3, c
2025-12-05 01:12:57.292456 INFO::Creating output folder
2025-12-05 01:12:57.293461 INFO::Creating fits folder
2025-12-05 01:12:57.294324 INFO::Writing residuals to file /tmp/RtmpcQbgi6/file3225404adca972/fits/residuals_linear.rds
2025-12-05 01:12:57.295294 INFO::Writing fitted values to file /tmp/RtmpcQbgi6/file3225404adca972/fits/fitted_linear.rds
2025-12-05 01:12:57.296358 INFO::Writing residuals to file /tmp/RtmpcQbgi6/file3225404adca972/fits/residuals_logistic.rds
2025-12-05 01:12:57.297388 INFO::Writing fitted values to file /tmp/RtmpcQbgi6/file3225404adca972/fits/fitted_logistic.rds
2025-12-05 01:12:57.299937 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpcQbgi6/file3225404adca972/all_results.tsv
2025-12-05 01:12:57.301403 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/RtmpcQbgi6/file3225404adca972/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
357.165 4.827 361.975
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 19.032 | 0.566 | 19.602 | |
| maaslin_check_arguments | 0.139 | 0.003 | 0.142 | |
| maaslin_check_formula | 0.163 | 0.002 | 0.166 | |
| maaslin_compute_formula | 0.146 | 0.012 | 0.158 | |
| maaslin_contrast_test | 18.147 | 0.490 | 18.637 | |
| maaslin_filter | 0.421 | 0.026 | 0.447 | |
| maaslin_fit | 12.260 | 0.142 | 12.403 | |
| maaslin_log_arguments | 0.129 | 0.001 | 0.131 | |
| maaslin_normalize | 0.948 | 0.070 | 1.019 | |
| maaslin_plot_results | 42.809 | 0.367 | 43.134 | |
| maaslin_plot_results_from_output | 43.095 | 0.373 | 43.470 | |
| maaslin_process_metadata | 0.444 | 0.010 | 0.454 | |
| maaslin_read_data | 0.120 | 0.004 | 0.125 | |
| maaslin_reorder_data | 0.128 | 0.002 | 0.129 | |
| maaslin_transform | 0.543 | 0.008 | 0.552 | |
| maaslin_write_results | 12.737 | 0.143 | 12.895 | |
| maaslin_write_results_lefse_format | 14.814 | 0.173 | 14.988 | |
| preprocess_dna_mtx | 0.003 | 0.001 | 0.004 | |
| preprocess_taxa_mtx | 0.004 | 0.000 | 0.004 | |