William Nickols
| Snapshot Date: 2026-02-27 13:45 -0500 (Fri, 27 Feb 2026) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: RELEASE_3_22 |
| git_last_commit: 9669f95 |
| git_last_commit_date: 2025-10-29 11:33:46 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-02-28 11:57 -0500 (Sat, 28 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4891 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1170/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maaslin3 1.2.0 (landing page) William Nickols
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| See other builds for maaslin3 in R Universe. | ||||||||||||||
|
To the developers/maintainers of the maaslin3 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/maaslin3.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: maaslin3 |
| Version: 1.2.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings maaslin3_1.2.0.tar.gz |
| StartedAt: 2026-02-28 01:03:52 -0500 (Sat, 28 Feb 2026) |
| EndedAt: 2026-02-28 01:25:35 -0500 (Sat, 28 Feb 2026) |
| EllapsedTime: 1302.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maaslin3.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings maaslin3_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/maaslin3.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘1.2.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘maaslin3’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
maaslin_plot_results_from_output 44.003 0.244 44.251
maaslin_plot_results 43.896 0.271 44.141
maaslin3 20.652 0.519 21.173
maaslin_contrast_test 19.139 0.349 19.489
maaslin_write_results_lefse_format 14.972 0.208 15.182
maaslin_write_results 13.297 0.101 13.399
maaslin_fit 12.606 0.062 12.668
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
maaslin3.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL maaslin3 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘maaslin3’ ... ** this is package ‘maaslin3’ version ‘1.2.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (maaslin3)
maaslin3.Rcheck/tests/testthat.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(maaslin3)
>
> test_check("maaslin3")
2026-02-28 01:10:11.597752 WARNING::Fitting problem for feature 50 returning NA
2026-02-28 01:10:11.684542 WARNING::Fitting problem for feature 62 returning NA
2026-02-28 01:10:11.779394 WARNING::Fitting problem for feature 74 returning NA
2026-02-28 01:10:11.800875 WARNING::Fitting problem for feature 78 returning NA
2026-02-28 01:10:11.834918 WARNING::Fitting problem for feature 84 returning NA
2026-02-28 01:10:11.91018 WARNING::Fitting problem for feature 96 returning NA
2026-02-28 01:10:11.922788 WARNING::Fitting problem for feature 97 returning NA
2026-02-28 01:10:11.935263 WARNING::Fitting problem for feature 99 returning NA
2026-02-28 01:10:12.030628 WARNING::Fitting problem for feature 114 returning NA
2026-02-28 01:10:12.035877 WARNING::Fitting problem for feature 115 returning NA
2026-02-28 01:10:12.085956 WARNING::Fitting problem for feature 123 returning NA
2026-02-28 01:10:12.133554 WARNING::Fitting problem for feature 130 returning NA
2026-02-28 01:10:12.145187 WARNING::Fitting problem for feature 132 returning NA
2026-02-28 01:10:12.184259 WARNING::Fitting problem for feature 139 returning NA
2026-02-28 01:10:12.25101 WARNING::Fitting problem for feature 150 returning NA
2026-02-28 01:10:28.046179 WARNING::Fitting problem for feature 50 returning NA
2026-02-28 01:10:28.120425 WARNING::Fitting problem for feature 62 returning NA
2026-02-28 01:10:28.193706 WARNING::Fitting problem for feature 74 returning NA
2026-02-28 01:10:28.215205 WARNING::Fitting problem for feature 78 returning NA
2026-02-28 01:10:28.249202 WARNING::Fitting problem for feature 84 returning NA
2026-02-28 01:10:28.342268 WARNING::Fitting problem for feature 96 returning NA
2026-02-28 01:10:28.347565 WARNING::Fitting problem for feature 97 returning NA
2026-02-28 01:10:28.359158 WARNING::Fitting problem for feature 99 returning NA
2026-02-28 01:10:28.452212 WARNING::Fitting problem for feature 114 returning NA
2026-02-28 01:10:28.45742 WARNING::Fitting problem for feature 115 returning NA
2026-02-28 01:10:28.50669 WARNING::Fitting problem for feature 123 returning NA
2026-02-28 01:10:28.545994 WARNING::Fitting problem for feature 130 returning NA
2026-02-28 01:10:28.557539 WARNING::Fitting problem for feature 132 returning NA
2026-02-28 01:10:28.597332 WARNING::Fitting problem for feature 139 returning NA
2026-02-28 01:10:28.664013 WARNING::Fitting problem for feature 150 returning NA
2026-02-28 01:10:52.963933 WARNING::Fitting problem for feature 50 returning NA
2026-02-28 01:10:53.039904 WARNING::Fitting problem for feature 62 returning NA
2026-02-28 01:10:53.115142 WARNING::Fitting problem for feature 74 returning NA
2026-02-28 01:10:53.136988 WARNING::Fitting problem for feature 78 returning NA
2026-02-28 01:10:53.171469 WARNING::Fitting problem for feature 84 returning NA
2026-02-28 01:10:53.24911 WARNING::Fitting problem for feature 96 returning NA
2026-02-28 01:10:53.254577 WARNING::Fitting problem for feature 97 returning NA
2026-02-28 01:10:53.266405 WARNING::Fitting problem for feature 99 returning NA
2026-02-28 01:10:53.362939 WARNING::Fitting problem for feature 114 returning NA
2026-02-28 01:10:53.368284 WARNING::Fitting problem for feature 115 returning NA
2026-02-28 01:10:53.417982 WARNING::Fitting problem for feature 123 returning NA
2026-02-28 01:10:53.459764 WARNING::Fitting problem for feature 130 returning NA
2026-02-28 01:10:53.472408 WARNING::Fitting problem for feature 132 returning NA
2026-02-28 01:10:53.514502 WARNING::Fitting problem for feature 139 returning NA
2026-02-28 01:10:53.58473 WARNING::Fitting problem for feature 150 returning NA
2026-02-28 01:11:06.254014 WARNING::Fitting problem for feature 50 returning NA
2026-02-28 01:11:06.353374 WARNING::Fitting problem for feature 62 returning NA
2026-02-28 01:11:06.426955 WARNING::Fitting problem for feature 74 returning NA
2026-02-28 01:11:06.448371 WARNING::Fitting problem for feature 78 returning NA
2026-02-28 01:11:06.481804 WARNING::Fitting problem for feature 84 returning NA
2026-02-28 01:11:06.554796 WARNING::Fitting problem for feature 96 returning NA
2026-02-28 01:11:06.559976 WARNING::Fitting problem for feature 97 returning NA
2026-02-28 01:11:06.571371 WARNING::Fitting problem for feature 99 returning NA
2026-02-28 01:11:06.663673 WARNING::Fitting problem for feature 114 returning NA
2026-02-28 01:11:06.669028 WARNING::Fitting problem for feature 115 returning NA
2026-02-28 01:11:06.718977 WARNING::Fitting problem for feature 123 returning NA
2026-02-28 01:11:06.760312 WARNING::Fitting problem for feature 130 returning NA
2026-02-28 01:11:06.772019 WARNING::Fitting problem for feature 132 returning NA
2026-02-28 01:11:06.812024 WARNING::Fitting problem for feature 139 returning NA
2026-02-28 01:11:06.879005 WARNING::Fitting problem for feature 150 returning NA
2026-02-28 01:11:07.075392 WARNING::Deleting existing residuals file: /tmp/RtmpEfGpsY/file7830c554256f2/fits/residuals_linear.rds
2026-02-28 01:11:07.137053 WARNING::Deleting existing fitted file: /tmp/RtmpEfGpsY/file7830c554256f2/fits/fitted_linear.rds
2026-02-28 01:11:07.200566 WARNING::Deleting existing residuals file: /tmp/RtmpEfGpsY/file7830c554256f2/fits/residuals_logistic.rds
2026-02-28 01:11:07.502278 WARNING::Deleting existing fitted file: /tmp/RtmpEfGpsY/file7830c554256f2/fits/fitted_logistic.rds
2026-02-28 01:11:29.492254 WARNING::Fitting problem for feature 50 returning NA
2026-02-28 01:11:29.570759 WARNING::Fitting problem for feature 62 returning NA
2026-02-28 01:11:29.677773 WARNING::Fitting problem for feature 74 returning NA
2026-02-28 01:11:29.700444 WARNING::Fitting problem for feature 78 returning NA
2026-02-28 01:11:29.736058 WARNING::Fitting problem for feature 84 returning NA
2026-02-28 01:11:29.813292 WARNING::Fitting problem for feature 96 returning NA
2026-02-28 01:11:29.818696 WARNING::Fitting problem for feature 97 returning NA
2026-02-28 01:11:29.830814 WARNING::Fitting problem for feature 99 returning NA
2026-02-28 01:11:29.928813 WARNING::Fitting problem for feature 114 returning NA
2026-02-28 01:11:29.934444 WARNING::Fitting problem for feature 115 returning NA
2026-02-28 01:11:29.984746 WARNING::Fitting problem for feature 123 returning NA
2026-02-28 01:11:30.024736 WARNING::Fitting problem for feature 130 returning NA
2026-02-28 01:11:30.036619 WARNING::Fitting problem for feature 132 returning NA
2026-02-28 01:11:30.077035 WARNING::Fitting problem for feature 139 returning NA
2026-02-28 01:11:30.145862 WARNING::Fitting problem for feature 150 returning NA
2026-02-28 01:11:42.270597 WARNING::Fitting problem for feature 50 returning NA
2026-02-28 01:11:42.353325 WARNING::Fitting problem for feature 62 returning NA
2026-02-28 01:11:42.432312 WARNING::Fitting problem for feature 74 returning NA
2026-02-28 01:11:42.455774 WARNING::Fitting problem for feature 78 returning NA
2026-02-28 01:11:42.492718 WARNING::Fitting problem for feature 84 returning NA
2026-02-28 01:11:42.570402 WARNING::Fitting problem for feature 96 returning NA
2026-02-28 01:11:42.575824 WARNING::Fitting problem for feature 97 returning NA
2026-02-28 01:11:42.588258 WARNING::Fitting problem for feature 99 returning NA
2026-02-28 01:11:42.685885 WARNING::Fitting problem for feature 114 returning NA
2026-02-28 01:11:42.691416 WARNING::Fitting problem for feature 115 returning NA
2026-02-28 01:11:42.741766 WARNING::Fitting problem for feature 123 returning NA
2026-02-28 01:11:42.78264 WARNING::Fitting problem for feature 130 returning NA
2026-02-28 01:11:42.79526 WARNING::Fitting problem for feature 132 returning NA
2026-02-28 01:11:42.839043 WARNING::Fitting problem for feature 139 returning NA
2026-02-28 01:11:42.915107 WARNING::Fitting problem for feature 150 returning NA
2026-02-28 01:11:43.120028 WARNING::Deleting existing residuals file: /tmp/RtmpEfGpsY/file7830c554256f2/fits/residuals_linear.rds
2026-02-28 01:11:43.181152 WARNING::Deleting existing fitted file: /tmp/RtmpEfGpsY/file7830c554256f2/fits/fitted_linear.rds
2026-02-28 01:11:43.244292 WARNING::Deleting existing residuals file: /tmp/RtmpEfGpsY/file7830c554256f2/fits/residuals_logistic.rds
2026-02-28 01:11:43.542924 WARNING::Deleting existing fitted file: /tmp/RtmpEfGpsY/file7830c554256f2/fits/fitted_logistic.rds
2026-02-28 01:12:04.801038 WARNING::Fitting problem for feature 50 returning NA
2026-02-28 01:12:04.884618 WARNING::Fitting problem for feature 62 returning NA
2026-02-28 01:12:04.966622 WARNING::Fitting problem for feature 74 returning NA
2026-02-28 01:12:04.99132 WARNING::Fitting problem for feature 78 returning NA
2026-02-28 01:12:05.030135 WARNING::Fitting problem for feature 84 returning NA
2026-02-28 01:12:05.139315 WARNING::Fitting problem for feature 96 returning NA
2026-02-28 01:12:05.145046 WARNING::Fitting problem for feature 97 returning NA
2026-02-28 01:12:05.157495 WARNING::Fitting problem for feature 99 returning NA
2026-02-28 01:12:05.259235 WARNING::Fitting problem for feature 114 returning NA
2026-02-28 01:12:05.264855 WARNING::Fitting problem for feature 115 returning NA
2026-02-28 01:12:05.315986 WARNING::Fitting problem for feature 123 returning NA
2026-02-28 01:12:05.356677 WARNING::Fitting problem for feature 130 returning NA
2026-02-28 01:12:05.368862 WARNING::Fitting problem for feature 132 returning NA
2026-02-28 01:12:05.410222 WARNING::Fitting problem for feature 139 returning NA
2026-02-28 01:12:05.481043 WARNING::Fitting problem for feature 150 returning NA
2026-02-28 01:12:18.110338 WARNING::Fitting problem for feature 50 returning NA
2026-02-28 01:12:18.197649 WARNING::Fitting problem for feature 62 returning NA
2026-02-28 01:12:18.270654 WARNING::Fitting problem for feature 74 returning NA
2026-02-28 01:12:18.292358 WARNING::Fitting problem for feature 78 returning NA
2026-02-28 01:12:18.326073 WARNING::Fitting problem for feature 84 returning NA
2026-02-28 01:12:18.400231 WARNING::Fitting problem for feature 96 returning NA
2026-02-28 01:12:18.40545 WARNING::Fitting problem for feature 97 returning NA
2026-02-28 01:12:18.417107 WARNING::Fitting problem for feature 99 returning NA
2026-02-28 01:12:18.50902 WARNING::Fitting problem for feature 114 returning NA
2026-02-28 01:12:18.514357 WARNING::Fitting problem for feature 115 returning NA
2026-02-28 01:12:18.564185 WARNING::Fitting problem for feature 123 returning NA
2026-02-28 01:12:18.609038 WARNING::Fitting problem for feature 130 returning NA
2026-02-28 01:12:18.623817 WARNING::Fitting problem for feature 132 returning NA
2026-02-28 01:12:18.669897 WARNING::Fitting problem for feature 139 returning NA
2026-02-28 01:12:18.749227 WARNING::Fitting problem for feature 150 returning NA
2026-02-28 01:12:18.967764 WARNING::Deleting existing residuals file: /tmp/RtmpEfGpsY/file7830c554256f2/fits/residuals_linear.rds
2026-02-28 01:12:19.028796 WARNING::Deleting existing fitted file: /tmp/RtmpEfGpsY/file7830c554256f2/fits/fitted_linear.rds
2026-02-28 01:12:19.092313 WARNING::Deleting existing residuals file: /tmp/RtmpEfGpsY/file7830c554256f2/fits/residuals_logistic.rds
2026-02-28 01:12:19.392704 WARNING::Deleting existing fitted file: /tmp/RtmpEfGpsY/file7830c554256f2/fits/fitted_logistic.rds
2026-02-28 01:12:40.341501 WARNING::Fitting problem for feature 50 returning NA
2026-02-28 01:12:40.418386 WARNING::Fitting problem for feature 62 returning NA
2026-02-28 01:12:40.495907 WARNING::Fitting problem for feature 74 returning NA
2026-02-28 01:12:40.518503 WARNING::Fitting problem for feature 78 returning NA
2026-02-28 01:12:40.553072 WARNING::Fitting problem for feature 84 returning NA
2026-02-28 01:12:40.62984 WARNING::Fitting problem for feature 96 returning NA
2026-02-28 01:12:40.635376 WARNING::Fitting problem for feature 97 returning NA
2026-02-28 01:12:40.647548 WARNING::Fitting problem for feature 99 returning NA
2026-02-28 01:12:40.745848 WARNING::Fitting problem for feature 114 returning NA
2026-02-28 01:12:40.751543 WARNING::Fitting problem for feature 115 returning NA
2026-02-28 01:12:40.802627 WARNING::Fitting problem for feature 123 returning NA
2026-02-28 01:12:40.882012 WARNING::Fitting problem for feature 130 returning NA
2026-02-28 01:12:40.894381 WARNING::Fitting problem for feature 132 returning NA
2026-02-28 01:12:40.936674 WARNING::Fitting problem for feature 139 returning NA
2026-02-28 01:12:41.009283 WARNING::Fitting problem for feature 150 returning NA
2026-02-28 01:12:51.970655 WARNING::Fitting problem for feature 50 returning NA
2026-02-28 01:12:52.063182 WARNING::Fitting problem for feature 62 returning NA
2026-02-28 01:12:52.15394 WARNING::Fitting problem for feature 74 returning NA
2026-02-28 01:12:52.181852 WARNING::Fitting problem for feature 78 returning NA
2026-02-28 01:12:52.220401 WARNING::Fitting problem for feature 84 returning NA
2026-02-28 01:12:52.303877 WARNING::Fitting problem for feature 96 returning NA
2026-02-28 01:12:52.309817 WARNING::Fitting problem for feature 97 returning NA
2026-02-28 01:12:52.324168 WARNING::Fitting problem for feature 99 returning NA
2026-02-28 01:12:52.428536 WARNING::Fitting problem for feature 114 returning NA
2026-02-28 01:12:52.434247 WARNING::Fitting problem for feature 115 returning NA
2026-02-28 01:12:52.488452 WARNING::Fitting problem for feature 123 returning NA
2026-02-28 01:12:52.53011 WARNING::Fitting problem for feature 130 returning NA
2026-02-28 01:12:52.622525 WARNING::Fitting problem for feature 132 returning NA
2026-02-28 01:12:52.666692 WARNING::Fitting problem for feature 139 returning NA
2026-02-28 01:12:52.742657 WARNING::Fitting problem for feature 150 returning NA
2026-02-28 01:13:18.186136 WARNING::Fitting problem for feature 124 returning NA
2026-02-28 01:13:26.701011 WARNING::Fitting problem for feature 124 returning NA
2026-02-28 01:13:51.838813 WARNING::Fitting problem for feature 124 returning NA
2026-02-28 01:14:01.716682 WARNING::Fitting problem for feature 124 returning NA
2026-02-28 01:14:02.322424 WARNING::Deleting existing residuals file: /tmp/RtmpEfGpsY/file7830c3b4c5f12/fits/residuals_linear.rds
2026-02-28 01:14:02.384195 WARNING::Deleting existing fitted file: /tmp/RtmpEfGpsY/file7830c3b4c5f12/fits/fitted_linear.rds
2026-02-28 01:14:02.422713 WARNING::Deleting existing residuals file: /tmp/RtmpEfGpsY/file7830c3b4c5f12/fits/residuals_logistic.rds
2026-02-28 01:14:02.491699 WARNING::Deleting existing fitted file: /tmp/RtmpEfGpsY/file7830c3b4c5f12/fits/fitted_logistic.rds
2026-02-28 01:14:24.783427 WARNING::Fitting problem for feature 124 returning NA
2026-02-28 01:14:29.862476 WARNING::Fitting problem for feature 124 returning NA
2026-02-28 01:14:30.172345 WARNING::Deleting existing residuals file: /tmp/RtmpEfGpsY/file7830c3b4c5f12/fits/residuals_linear.rds
2026-02-28 01:14:30.234322 WARNING::Deleting existing fitted file: /tmp/RtmpEfGpsY/file7830c3b4c5f12/fits/fitted_linear.rds
2026-02-28 01:14:30.272864 WARNING::Deleting existing residuals file: /tmp/RtmpEfGpsY/file7830c3b4c5f12/fits/residuals_logistic.rds
2026-02-28 01:14:30.341585 WARNING::Deleting existing fitted file: /tmp/RtmpEfGpsY/file7830c3b4c5f12/fits/fitted_logistic.rds
2026-02-28 01:14:49.141537 WARNING::Fitting problem for feature 124 returning NA
2026-02-28 01:14:55.478881 WARNING::Fitting problem for feature 124 returning NA
2026-02-28 01:14:55.775889 WARNING::Deleting existing residuals file: /tmp/RtmpEfGpsY/file7830c3b4c5f12/fits/residuals_linear.rds
2026-02-28 01:14:55.837614 WARNING::Deleting existing fitted file: /tmp/RtmpEfGpsY/file7830c3b4c5f12/fits/fitted_linear.rds
2026-02-28 01:14:55.876309 WARNING::Deleting existing residuals file: /tmp/RtmpEfGpsY/file7830c3b4c5f12/fits/residuals_logistic.rds
2026-02-28 01:14:55.945796 WARNING::Deleting existing fitted file: /tmp/RtmpEfGpsY/file7830c3b4c5f12/fits/fitted_logistic.rds
2026-02-28 01:15:15.101686 WARNING::Fitting problem for feature 50 returning NA
2026-02-28 01:15:15.178277 WARNING::Fitting problem for feature 62 returning NA
2026-02-28 01:15:15.254219 WARNING::Fitting problem for feature 74 returning NA
2026-02-28 01:15:15.277048 WARNING::Fitting problem for feature 78 returning NA
2026-02-28 01:15:15.313091 WARNING::Fitting problem for feature 84 returning NA
2026-02-28 01:15:15.39166 WARNING::Fitting problem for feature 96 returning NA
2026-02-28 01:15:15.397141 WARNING::Fitting problem for feature 97 returning NA
2026-02-28 01:15:15.409103 WARNING::Fitting problem for feature 99 returning NA
2026-02-28 01:15:15.506357 WARNING::Fitting problem for feature 114 returning NA
2026-02-28 01:15:15.531106 WARNING::Fitting problem for feature 115 returning NA
2026-02-28 01:15:15.589575 WARNING::Fitting problem for feature 123 returning NA
2026-02-28 01:15:15.638557 WARNING::Fitting problem for feature 130 returning NA
2026-02-28 01:15:15.650735 WARNING::Fitting problem for feature 132 returning NA
2026-02-28 01:15:15.692499 WARNING::Fitting problem for feature 139 returning NA
2026-02-28 01:15:15.762771 WARNING::Fitting problem for feature 150 returning NA
2026-02-28 01:15:26.408343 WARNING::Fitting problem for feature 50 returning NA
2026-02-28 01:15:26.485618 WARNING::Fitting problem for feature 62 returning NA
2026-02-28 01:15:26.55981 WARNING::Fitting problem for feature 74 returning NA
2026-02-28 01:15:26.581306 WARNING::Fitting problem for feature 78 returning NA
2026-02-28 01:15:26.616321 WARNING::Fitting problem for feature 84 returning NA
2026-02-28 01:15:26.691718 WARNING::Fitting problem for feature 96 returning NA
2026-02-28 01:15:26.69702 WARNING::Fitting problem for feature 97 returning NA
2026-02-28 01:15:26.708754 WARNING::Fitting problem for feature 99 returning NA
2026-02-28 01:15:26.802209 WARNING::Fitting problem for feature 114 returning NA
2026-02-28 01:15:26.807612 WARNING::Fitting problem for feature 115 returning NA
2026-02-28 01:15:26.857609 WARNING::Fitting problem for feature 123 returning NA
2026-02-28 01:15:26.897499 WARNING::Fitting problem for feature 130 returning NA
2026-02-28 01:15:26.909226 WARNING::Fitting problem for feature 132 returning NA
2026-02-28 01:15:26.949034 WARNING::Fitting problem for feature 139 returning NA
2026-02-28 01:15:27.019026 WARNING::Fitting problem for feature 150 returning NA
2026-02-28 01:15:27.30455 WARNING::Deleting existing residuals file: /tmp/RtmpEfGpsY/file7830c3b4c5f12/fits/residuals_linear.rds
2026-02-28 01:15:27.366206 WARNING::Deleting existing fitted file: /tmp/RtmpEfGpsY/file7830c3b4c5f12/fits/fitted_linear.rds
2026-02-28 01:15:27.429824 WARNING::Deleting existing residuals file: /tmp/RtmpEfGpsY/file7830c3b4c5f12/fits/residuals_logistic.rds
2026-02-28 01:15:27.728991 WARNING::Deleting existing fitted file: /tmp/RtmpEfGpsY/file7830c3b4c5f12/fits/fitted_logistic.rds
2026-02-28 01:15:48.382695 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2026-02-28 01:15:48.399497 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2026-02-28 01:15:48.411043 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2026-02-28 01:15:48.46435 ERROR::No fixed, group, or
ordered effects included in formula.
2026-02-28 01:15:48.482613 ERROR::Effect name not found in metadata: d
2026-02-28 01:15:48.494977 ERROR::No user formula provided
2026-02-28 01:15:48.527422 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2026-02-28 01:15:48.539563 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2026-02-28 01:15:51.408676 INFO::Writing function arguments to log file
2026-02-28 01:15:51.423628 INFO::Verifying options selected are valid
2026-02-28 01:15:53.746468 INFO::Writing function arguments to log file
2026-02-28 01:15:53.759359 INFO::Verifying options selected are valid
2026-02-28 01:15:53.760461 INFO::Determining format of input files
2026-02-28 01:15:53.761465 INFO::Input format is data samples as rows and metadata samples as rows
2026-02-28 01:15:53.763817 INFO::Running selected normalization method: TSS
2026-02-28 01:15:53.765266 INFO::Creating output feature tables folder
2026-02-28 01:15:53.766226 INFO::Writing normalized data to file /tmp/RtmpEfGpsY/file7830c2c23c626/features/data_norm.tsv
2026-02-28 01:15:53.7677 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2026-02-28 01:15:53.768588 INFO::Total samples in data: 16
2026-02-28 01:15:53.769448 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2026-02-28 01:15:53.770309 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2026-02-28 01:15:53.772249 INFO::Total filtered features: 0
2026-02-28 01:15:53.773208 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2026-02-28 01:15:53.774356 INFO::Total features filtered by non-zero variance filtering: 0
2026-02-28 01:15:53.775319 INFO::Filtered feature names from variance filtering:
2026-02-28 01:15:53.776222 INFO::Writing filtered data to file /tmp/RtmpEfGpsY/file7830c2c23c626/features/filtered_data.tsv
2026-02-28 01:15:53.777759 INFO::Running selected transform method: LOG
2026-02-28 01:15:53.778965 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpEfGpsY/file7830c2c23c626/features/data_transformed.tsv
2026-02-28 01:15:53.780613 INFO::Applying z-score to standardize continuous metadata
2026-02-28 01:15:53.785165 INFO::Running the linear model component
2026-02-28 01:15:53.799467 INFO::Fitting model to feature number 1, a
2026-02-28 01:15:53.8042 INFO::Fitting model to feature number 2, b
2026-02-28 01:15:53.808636 INFO::Fitting model to feature number 3, c
2026-02-28 01:15:53.816078 INFO::Counting total values for each feature
2026-02-28 01:15:53.81794 INFO::Running the logistic model component
2026-02-28 01:15:53.832041 INFO::Fitting model to feature number 1, a
2026-02-28 01:15:53.838807 INFO::Fitting model to feature number 2, b
2026-02-28 01:15:53.845153 INFO::Fitting model to feature number 3, c
2026-02-28 01:15:53.85465 INFO::Counting total values for each feature
2026-02-28 01:15:53.856871 INFO::Re-running abundances for warn_prevalence
2026-02-28 01:15:53.857831 INFO::Running selected normalization method: TSS
2026-02-28 01:15:53.859344 INFO::Running selected transform method: LOG
2026-02-28 01:15:53.873747 INFO::Fitting model to feature number 1, a
2026-02-28 01:15:53.878299 INFO::Fitting model to feature number 2, b
2026-02-28 01:15:53.882651 INFO::Fitting model to feature number 3, c
2026-02-28 01:15:53.96016 INFO::Creating fits folder
2026-02-28 01:15:53.961344 INFO::Writing residuals to file /tmp/RtmpEfGpsY/file7830c2c23c626/fits/residuals_linear.rds
2026-02-28 01:15:53.962503 INFO::Writing fitted values to file /tmp/RtmpEfGpsY/file7830c2c23c626/fits/fitted_linear.rds
2026-02-28 01:15:53.963699 INFO::Writing residuals to file /tmp/RtmpEfGpsY/file7830c2c23c626/fits/residuals_logistic.rds
2026-02-28 01:15:53.964867 INFO::Writing fitted values to file /tmp/RtmpEfGpsY/file7830c2c23c626/fits/fitted_logistic.rds
2026-02-28 01:15:53.967245 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpEfGpsY/file7830c2c23c626/all_results.tsv
2026-02-28 01:15:53.968924 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/RtmpEfGpsY/file7830c2c23c626/significant_results.tsv
2026-02-28 01:15:53.970258 INFO::Creating output figures folder
2026-02-28 01:15:53.971641 INFO::Writing summary plot of significant
results to file: /tmp/RtmpEfGpsY/file7830c2c23c626/figures/summary_plot.pdf
2026-02-28 01:15:55.585225 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpEfGpsY/file7830c2c23c626/figures
2026-02-28 01:15:55.595906 INFO::Plotting associations from most to least significant, grouped by metadata
2026-02-28 01:15:55.602374 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-02-28 01:15:56.119669 INFO::Writing summary plot of
significant results to file: /tmp/RtmpEfGpsY/file7830c2c23c626/figures/summary_plot.pdf
2026-02-28 01:15:57.75212 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpEfGpsY/file7830c2c23c626/figures
2026-02-28 01:15:57.753711 INFO::Plotting associations from most to least significant, grouped by metadata
2026-02-28 01:15:57.758633 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-02-28 01:15:58.272868 INFO::Running the linear model component
2026-02-28 01:15:58.281707 INFO::Fitting model to feature number 1, a
2026-02-28 01:15:58.286068 INFO::Fitting model to feature number 2, b
2026-02-28 01:15:58.290027 INFO::Fitting model to feature number 3, c
2026-02-28 01:15:58.296899 INFO::Counting total values for each feature
2026-02-28 01:15:58.29853 INFO::Running the logistic model component
2026-02-28 01:15:58.306773 INFO::Fitting model to feature number 1, a
2026-02-28 01:15:58.312944 INFO::Fitting model to feature number 2, b
2026-02-28 01:15:58.318802 INFO::Fitting model to feature number 3, c
2026-02-28 01:15:58.327461 INFO::Counting total values for each feature
2026-02-28 01:15:58.329469 INFO::Re-running abundances for warn_prevalence
2026-02-28 01:15:58.330248 INFO::Running selected normalization method: TSS
2026-02-28 01:15:58.331584 INFO::Running selected transform method: LOG
2026-02-28 01:15:58.340056 INFO::Fitting model to feature number 1, a
2026-02-28 01:15:58.34422 INFO::Fitting model to feature number 2, b
2026-02-28 01:15:58.348161 INFO::Fitting model to feature number 3, c
2026-02-28 01:15:58.42334 INFO::Creating output folder
2026-02-28 01:15:58.424298 INFO::Creating output figures folder
2026-02-28 01:15:58.425534 INFO::Writing summary plot of significant
results to file: /tmp/RtmpEfGpsY/file7830cab9bf43/figures/summary_plot.pdf
2026-02-28 01:16:00.020607 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpEfGpsY/file7830cab9bf43/figures
2026-02-28 01:16:00.022387 INFO::Plotting associations from most to least significant, grouped by metadata
2026-02-28 01:16:00.027421 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-02-28 01:16:01.014839 INFO::Applying z-score to standardize continuous metadata
2026-02-28 01:16:01.022622 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2026-02-28 01:16:01.023557 INFO::Bypass z-score application to metadata
2026-02-28 01:16:01.026318 INFO::Bypass z-score application to metadata
2026-02-28 01:16:01.046099 INFO::Determining format of input files
2026-02-28 01:16:01.047167 INFO::Input format is data samples as rows and metadata samples as rows
2026-02-28 01:16:01.048066 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2026-02-28 01:16:01.055981 INFO::Determining format of input files
2026-02-28 01:16:01.057073 INFO::Input format is data samples as columns and metadata samples as rows
2026-02-28 01:16:01.058407 INFO::Input format is feature_specific_covariate samples as columns
2026-02-28 01:16:01.085153 INFO::Determining format of input files
2026-02-28 01:16:01.086609 INFO::Input format is data samples as rows and metadata samples as rows
2026-02-28 01:16:01.08811 INFO::Input format is feature_specific_covariate samples as columns
2026-02-28 01:16:01.090386 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2026-02-28 01:16:01.091221 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2026-02-28 01:16:01.104141 INFO::Running selected transform method: LOG
2026-02-28 01:16:01.105425 INFO::Creating output feature tables folder
2026-02-28 01:16:01.106407 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpEfGpsY/file7830c656a1775/features/data_transformed.tsv
2026-02-28 01:16:01.110754 INFO::Running selected transform method: LOG
2026-02-28 01:16:01.111881 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpEfGpsY/file7830c656a1775/features/data_transformed.tsv
2026-02-28 01:16:01.116288 INFO::Running selected transform method: PLOG
2026-02-28 01:16:01.117979 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpEfGpsY/file7830c656a1775/features/data_transformed.tsv
2026-02-28 01:16:01.121205 INFO::Running selected transform method: NONE
2026-02-28 01:16:01.121986 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpEfGpsY/file7830c656a1775/features/data_transformed.tsv
2026-02-28 01:16:01.130128 INFO::Running the linear model component
2026-02-28 01:16:01.13907 INFO::Fitting model to feature number 1, a
2026-02-28 01:16:01.143776 INFO::Fitting model to feature number 2, b
2026-02-28 01:16:01.148081 INFO::Fitting model to feature number 3, c
2026-02-28 01:16:01.155621 INFO::Counting total values for each feature
2026-02-28 01:16:01.157352 INFO::Running the logistic model component
2026-02-28 01:16:01.1661 INFO::Fitting model to feature number 1, a
2026-02-28 01:16:01.172994 INFO::Fitting model to feature number 2, b
2026-02-28 01:16:01.179496 INFO::Fitting model to feature number 3, c
2026-02-28 01:16:01.188865 INFO::Counting total values for each feature
2026-02-28 01:16:01.190955 INFO::Re-running abundances for warn_prevalence
2026-02-28 01:16:01.191792 INFO::Running selected normalization method: TSS
2026-02-28 01:16:01.193187 INFO::Running selected transform method: LOG
2026-02-28 01:16:01.201939 INFO::Fitting model to feature number 1, a
2026-02-28 01:16:01.206371 INFO::Fitting model to feature number 2, b
2026-02-28 01:16:01.210457 INFO::Fitting model to feature number 3, c
2026-02-28 01:16:01.29239 INFO::Creating output folder
2026-02-28 01:16:01.293462 INFO::Creating fits folder
2026-02-28 01:16:01.294364 INFO::Writing residuals to file /tmp/RtmpEfGpsY/file7830c92e4f32/fits/residuals_linear.rds
2026-02-28 01:16:01.295404 INFO::Writing fitted values to file /tmp/RtmpEfGpsY/file7830c92e4f32/fits/fitted_linear.rds
2026-02-28 01:16:01.296518 INFO::Writing residuals to file /tmp/RtmpEfGpsY/file7830c92e4f32/fits/residuals_logistic.rds
2026-02-28 01:16:01.297561 INFO::Writing fitted values to file /tmp/RtmpEfGpsY/file7830c92e4f32/fits/fitted_logistic.rds
2026-02-28 01:16:01.299911 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpEfGpsY/file7830c92e4f32/all_results.tsv
2026-02-28 01:16:01.301433 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/RtmpEfGpsY/file7830c92e4f32/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
356.803 4.070 360.864
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 20.652 | 0.519 | 21.173 | |
| maaslin_check_arguments | 0.163 | 0.000 | 0.162 | |
| maaslin_check_formula | 0.186 | 0.002 | 0.189 | |
| maaslin_compute_formula | 0.155 | 0.002 | 0.158 | |
| maaslin_contrast_test | 19.139 | 0.349 | 19.489 | |
| maaslin_filter | 0.440 | 0.009 | 0.449 | |
| maaslin_fit | 12.606 | 0.062 | 12.668 | |
| maaslin_log_arguments | 0.145 | 0.000 | 0.145 | |
| maaslin_normalize | 0.257 | 0.002 | 0.259 | |
| maaslin_plot_results | 43.896 | 0.271 | 44.141 | |
| maaslin_plot_results_from_output | 44.003 | 0.244 | 44.251 | |
| maaslin_process_metadata | 0.442 | 0.006 | 0.448 | |
| maaslin_read_data | 0.127 | 0.001 | 0.128 | |
| maaslin_reorder_data | 0.142 | 0.001 | 0.143 | |
| maaslin_transform | 0.562 | 0.007 | 0.569 | |
| maaslin_write_results | 13.297 | 0.101 | 13.399 | |
| maaslin_write_results_lefse_format | 14.972 | 0.208 | 15.182 | |
| preprocess_dna_mtx | 0.003 | 0.000 | 0.003 | |
| preprocess_taxa_mtx | 0.003 | 0.000 | 0.004 | |